Mercurial > repos > ecology > pampa_plotglm

annotate FunctPAMPAGalaxy.r @ 2:c448e026f122 draft default tip

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
author ecology
date Sat, 26 Jun 2021 07:20:47 +0000
parents 5ddca052c314
children
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3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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1 #Rscript
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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4 ##################################################################################################################################
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5 ####################### PAMPA Galaxy tools functions : Calculate metrics, compute GLM and plot #################################
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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6 ##################################################################################################################################
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8 #### Based on Yves Reecht R script
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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9 #### Modified by Coline ROYAUX for integrating within Galaxy-E
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11 ######################################### start of the function fact.def.f called by FunctExeCalcCommIndexesGalaxy.r and FunctExeCalcPresAbsGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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12 ####### Define the finest aggregation with the observation table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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14 fact_det_f <- function(obs,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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15 size_class = "size.class",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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16 code_species = "species.code",
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17 unitobs = "observation.unit") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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18 if (any(is.element(c(size_class), colnames(obs))) && all(! is.na(obs[, size_class]))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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19 factors <- c(unitobs, code_species, size_class)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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20 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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21 factors <- c(unitobs, code_species)
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22 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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23 return(factors)
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24 }
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26 ######################################### end of the function fact.def.f
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28 ######################################### start of the function def_typeobs_f called by FunctExeCalcCommIndexesGalaxy.r and FunctExeCalcPresAbsGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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29 ####### Define observation type from colnames
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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31 def_typeobs_f <- function(obs) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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32 if (any(is.element(c("rotation", "rot", "rotate"), colnames(obs)))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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33 obs_type <- "SVR"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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34 }else{
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35 obs_type <- "other"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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36 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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37 return(obs_type)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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38 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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39 ######################################### end of the function fact.def.f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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41 ######################################### start of the function create_unitobs called by FunctExeCalcCommIndexesGalaxy.r and FunctExeCalcPresAbsGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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42 ####### Create unitobs column when inexistant
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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43 create_unitobs <- function(data, year = "year", location = "location", unitobs = "observation.unit") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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44 if (is.element(paste(unitobs), colnames(data))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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45 unitab <- data
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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46 }else{
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48 unitab <- tidyr::unite(data, col = "observation.unit", c(year, location))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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49 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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50 return(unitab)
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51 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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52 ######################################### start of the function create_unitobs
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53
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54 ######################################### start of the function create_year_location called by FunctExeCalcCommIndexesGalaxy.r and FunctExeCalcPresAbsGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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55 ####### separate unitobs column when existant
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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56 create_year_location <- function(data, year = "year", location = "location", unitobs = "observation.unit") {
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57 if (all(grepl("[1-2][0|8|9][0-9]{2}_.*", data[, unitobs])) == TRUE) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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58 tab <- tidyr::separate(data, col = unitobs, into = c(year, location), sep = "_")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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59 }else{
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60 if (all(grepl("[A-Z]{2}[0-9]{2}.*", data[, unitobs]) == TRUE)) {
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61 tab <- tidyr::separate(data, col = unitobs, into = c("site1", year, "obs"), sep = c(2, 4))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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62 tab <- tidyr::unite(tab, col = location, c("site1", "obs"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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63 }else{
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64 tab <- data
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65 }
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66 }
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67
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68 tab <- cbind(tab, observation.unit = data[, unitobs])
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69
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70 return(tab)
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71 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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72 ######################################### start of the function create_year_location
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73
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74 ######################################### start of the function check_file called by every Galaxy Rscripts
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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76 check_file <- function(dataset, err_msg, vars, nb_vars) {
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77
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78 ## Purpose: General function to check integrity of input file. Will
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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79 ## check numbers and contents of variables(colnames).
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80 ## return an error message and exit if mismatch detected
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81 ## ----------------------------------------------------------------------
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82 ## Arguments: dataset : dataset name
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83 ## err_msg : output error
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84 ## vars : expected name of variables
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85 ## nb_vars : expected number of variables
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86 ## ----------------------------------------------------------------------
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87 ## Author: Alan Amosse, Benjamin Yguel
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88
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89 if (ncol(dataset) < nb_vars) { #checking for right number of columns in the file if not = error message
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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90 cat("\nerr nb var\n")
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91 stop(err_msg, call. = FALSE)
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92 }
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93
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94 for (i in vars) {
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95 if (!(i %in% names(dataset))) { #checking colnames
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96 stop(err_msg, call. = FALSE)
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97 }
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98 }
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99 }
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100
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101 ######################################### end of the function check_file
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102
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103
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104 ######################################### start of the function stat_rotations_nb_f called by calc_numbers_f
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105
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106 stat_rotations_nb_f <- function(factors, obs) {
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107 ## Purpose: Computing abundance statistics by rotation (max, sd)
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108 ## on SVR data
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109 ## ----------------------------------------------------------------------
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110 ## Arguments: factors : Names of aggregation factors
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111 ## obs : observation data
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112 ## ----------------------------------------------------------------------
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113 ## Author: Yves Reecht, Date: 29 oct. 2012, 16:01 modified by Coline ROYAUX 04 june 2020
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114
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115 ## Identification of valid rotations :
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116 if (is.element("observation.unit", factors)) {
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117 ## valid rotations (empty must be there as well) :
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118 rotations <- tapply(obs$rotation,
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119 as.list(obs[, c("observation.unit", "rotation"), drop = FALSE]),
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120 function(x)length(x) > 0)
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121
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122 ## Changing NA rotations in FALSE :
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123 rotations[is.na(rotations)] <- FALSE
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124 }
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125
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126 ## ###########################################################
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127 ## Abundance per rotation at chosen aggregation factors :
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128 nombres_rot <- tapply(obs$number,
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129 as.list(obs[, c(factors, "rotation"), drop = FALSE]),
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130 function(x, ...) {
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131 ifelse(all(is.na(x)), NA, sum(x, ...))
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132 },
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133 na.rm = TRUE)
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134
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135 ## If valid rotation NA are considered 0 :
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136 nombres_rot <- sweep(nombres_rot,
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137 match(names(dimnames(rotations)), names(dimnames(nombres_rot)), nomatch = NULL),
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138 rotations, # Tableau des secteurs valides (booléens).
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139 function(x, y) {
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140 x[is.na(x) & y] <- 0 # Lorsque NA et secteur valide => 0.
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141 return(x)
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142 })
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143
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144 ## ##################################################
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145 ## Statistics :
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146
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147 ## Means :
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148 nb_mean <- apply(nombres_rot, which(is.element(names(dimnames(nombres_rot)), factors)),
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149 function(x, ...) {
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150 ifelse(all(is.na(x)), NA, mean(x, ...))
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151 }, na.rm = TRUE)
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152
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153 ## Maxima :
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154 nb_max <- apply(nombres_rot, which(is.element(names(dimnames(nombres_rot)), factors)),
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155 function(x, ...) {
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156 ifelse(all(is.na(x)), NA, max(x, ...))
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157 }, na.rm = TRUE)
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158
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159 ## SD :
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160 nb_sd <- apply(nombres_rot, which(is.element(names(dimnames(nombres_rot)), factors)),
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161 function(x, ...) {
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162 ifelse(all(is.na(x)), NA, sd(x, ...))
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163 }, na.rm = TRUE)
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164
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165 ## Valid rotations count :
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166 nombres_rotations <- apply(rotations, 1, sum, na.rm = TRUE)
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167
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168 ## Results returned as list :
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169 return(list(nb_mean = nb_mean, nb_max = nb_max, nb_sd = nb_sd,
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170 nombres_rotations = nombres_rotations, nombresTot = nombres_rot))
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171 }
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172
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173 ######################################### end of the function stat_rotations_nb_f
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174
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175 ######################################### start of the function calc_nb_default_f called by calc_numbers_f
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176
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177 calc_nb_default_f <- function(obs,
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178 factors = c("observation.unit", "species.code", "size.class"),
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179 nb_name = "number") {
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180 ## Purpose : Compute abundances at finest aggregation
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181 ## ---------------------------------------------------------------------
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182 ## Arguments: obs : observation table
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183 ## factors : aggregation factors
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184 ## nb_name : name of abundance column.
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185 ##
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186 ## Output: array with ndimensions = nfactors.
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187 ## ----------------------------------------------------------------------
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188 ## Author: Yves Reecht, Date: 19 déc. 2011, 13:38 modified by Coline ROYAUX 04 june 2020
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189
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190 ## Sum individuals number :
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191 nbr <- tapply(obs[, nb_name],
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192 as.list(obs[, factors]),
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193 sum, na.rm = TRUE)
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194
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195 ## Absences as "true zero" :
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196 nbr[is.na(nbr)] <- 0
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197
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198 return(nbr)
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199 }
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200
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201 ######################################### end of the function calc_nb_default_f
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202
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203 ######################################### start of the function calc_numbers_f
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204
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205 calc_numbers_f <- function(obs, obs_type = "", factors = c("observation.unit", "species.code", "size.class"), nb_name = "number") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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206 ## Purpose: Produce data.frame used as table from output of calc_nb_default_f().
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207 ## ----------------------------------------------------------------------
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208 ## Arguments: obs : observation table
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209 ## obs_type : Type of observation (SVR, LIT, ...)
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210 ## factors : aggregation factors
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211 ## nb_name : name of abundance column
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212 ##
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213 ## Output: data.frame with (N aggregation factors + 1) columns
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214 ## ----------------------------------------------------------------------
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215 ## Author: Yves Reecht, Date: 19 déc. 2011, 13:46 modified by Coline ROYAUX 04 june 2020
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216
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217 if (obs_type == "SVR") {
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218 ## Compute SVR abundances statistics :
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219 stat_rotations <- stat_rotations_nb_f(factors = factors,
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220 obs = obs)
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221
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222 ## Mean for rotating videos (3 rotations at most times) :
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223 nbr <- stat_rotations[["nb_mean"]]
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224
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225 }else{
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226
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227 nbr <- calc_nb_default_f(obs, factors, nb_name)
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228 }
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229
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230 res <- as.data.frame(as.table(nbr), responseName = nb_name)
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231
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232 if (is.element("size.class", colnames(res))) {
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233 res$size.class[res$size.class == ""] <- NA
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234 }
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235
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236 ## If integer abundances :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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237 if (isTRUE(all.equal(res[, nb_name], as.integer(res[, nb_name])))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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238 res[, nb_name] <- as.integer(res[, nb_name])
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239 }
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240
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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241 if (obs_type == "SVR") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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242 ## statistics on abundances :
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243 res[, "number.max"] <- as.vector(stat_rotations[["nb_max"]])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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244 res[, "number.sd"] <- as.vector(stat_rotations[["nb_sd"]])
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245
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246 }
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247
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248 return(res)
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249 }
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250
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251 ######################################### end of the function calc_numbers_f
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252
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
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253 ######################################### start of the function pres_abs_f called by calc_biodiv_f
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254
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255 pres_abs_f <- function(nombres, logical = FALSE) {
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256 ## Purpose: Compute presence absence from abundances
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257 ## ----------------------------------------------------------------------
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258 ## Arguments: nombres : vector of individuals count.
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259 ## logical : (boolean) results as boolean or 0/1 ?
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260 ## ----------------------------------------------------------------------
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261 ## Author: Yves Reecht, Date: 29 oct. 2010, 10:20 modified by Coline ROYAUX 04 june 2020
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262
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263 if (any(nombres < 0, na.rm = TRUE)) {
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264 stop("Negative abundances!")
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265 }
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266
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267 if (logical) {
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268 return(nombres > 0)
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269 }else{
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270 nombres[nombres > 0] <- 1
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271 return(nombres)
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272 }
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273 }
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274
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275 ######################################### end of the function pres_abs_f
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276
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277 ######################################### start of the function bettercbind called by agregations_generic_f
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278
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279 bettercbind <- function(..., df_list = NULL, deparse.level = 1) {
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280 ## Purpose: Apply cbind to data frame with mathcing columns but without
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281 ## redundancies.
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282 ## ----------------------------------------------------------------------
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283 ## Arguments: same as cbind...
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284 ## df_list : data.frames list
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285 ## ----------------------------------------------------------------------
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286 ## Author: Yves Reecht, Date: 17 janv. 2012, 21:10 modified by Coline ROYAUX 04 june 2020
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287
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288 if (is.null(df_list)) {
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289 df_list <- list(...)
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290 }
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291
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292 return(do.call(cbind,
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293 c(list(df_list[[1]][, c(tail(colnames(df_list[[1]]), -1),
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294 head(colnames(df_list[[1]]), 1))]),
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295 lapply(df_list[- 1],
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296 function(x, coldel) {
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297 return(x[, !is.element(colnames(x),
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298 coldel),
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299 drop = FALSE])
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300 },
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301 coldel = colnames(df_list[[1]])),
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diff changeset
302 deparse.level = deparse.level)))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
303 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
304
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
305 ######################################### end of the function bettercbind
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
306
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
307 ######################################### start of the function agregation_f called by agregations_generic_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
308
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
309 agregation_f <- function(metric, d_ata, factors, cas_metric,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
310 nb_name = "number") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
311 ## Purpose: metric aggregation
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
312 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
313 ## Arguments: metric: colnames of chosen metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
314 ## d_ata: Unaggregated data table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
315 ## factors: aggregation factors vector
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
316 ## cas_metric: named vector of observation types depending
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
317 ## on chosen metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
318 ## nb_name : abundance column name
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
319 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
320 ## Author: Yves Reecht, Date: 20 déc. 2011, 14:29 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
321
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
322 switch(cas_metric[metric],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
323 "sum" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
324 res <- tapply(d_ata[, metric],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
325 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
326 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
327 ifelse(all(is.na(x)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
328 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
329 sum(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
330 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
331 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
332 "w.mean" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
333 res <- tapply(seq_len(nrow(d_ata)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
334 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
335 function(ii) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
336 ifelse(all(is.na(d_ata[ii, metric])),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
337 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
338 weighted.mean(d_ata[ii, metric],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
339 d_ata[ii, nb_name],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
340 na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
341 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
342 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
343 "w.mean.colonies" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
344 res <- tapply(seq_len(nrow(d_ata)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
345 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
346 function(ii) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
347 ifelse(all(is.na(d_ata[ii, metric])),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
348 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
349 weighted.mean(d_ata[ii, metric],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
350 d_ata[ii, "colonies"],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
351 na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
352 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
353 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
354 "w.mean.prop" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
355 res <- tapply(seq_len(nrow(d_ata)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
356 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
357 function(ii) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
358 ifelse(all(is.na(d_ata[ii, metric])) || sum(d_ata[ii, "nombre.tot"], na.rm = TRUE) == 0,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
359 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
360 ifelse(all(na.omit(d_ata[ii, metric]) == 0),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
361 0,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
362 (sum(d_ata[ii, nb_name][!is.na(d_ata[ii, metric])], na.rm = TRUE) /
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
363 sum(d_ata[ii, "nombre.tot"], na.rm = TRUE)) *
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
364 ## Correction if size class isn't an aggregation factor
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
365 ## (otherwise value divided by number of present classes) :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
366 ifelse(is.element("size.class", factors),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
367 100,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
368 100 * length(unique(d_ata$size.class)))))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
369 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
370
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
371 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
372 "w.mean.prop.bio" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
373 res <- tapply(seq_len(nrow(d_ata)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
374 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
375 function(ii) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
376 ifelse(all(is.na(d_ata[ii, metric])) || sum(d_ata[ii, "tot.biomass"], na.rm = TRUE) == 0,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
377 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
378 ifelse(all(na.omit(d_ata[ii, metric]) == 0),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
379 0,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
380 (sum(d_ata[ii, "biomass"][!is.na(d_ata[ii, metric])], na.rm = TRUE) /
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
381 sum(d_ata[ii, "tot.biomass"], na.rm = TRUE)) *
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
382 ## Correction if size class isn't an aggregation factor
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
383 ## (otherwise value divided by number of present classes) :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
384 ifelse(is.element("size.class", factors),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
385 100,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
386 100 * length(unique(d_ata$size.class)))))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
387 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
388
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
389 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
390 "pres" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
391 res <- tapply(d_ata[, metric],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
392 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
393 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
394 ifelse(all(is.na(x)), # When only NAs.
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
395 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
396 ifelse(any(x > 0, na.rm = TRUE), # Otherwise...
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
397 1, # ... presence if at least one observation in the group.
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
398 0))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
399 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
400 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
401 "nbMax" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
402
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
403 ## Sum by factor cross / rotation :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
404 nb_tmp2 <- apply(nb_tmp,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
405 which(is.element(names(dimnames(nb_tmp)), c(factors, "rotation"))),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
406 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
407 ifelse(all(is.na(x)), NA, sum(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
408 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
409
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
410 ## Sum by factor cross :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
411 res <- as.array(apply(nb_tmp2,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
412 which(is.element(names(dimnames(nb_tmp)), factors)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
413 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
414 ifelse(all(is.na(x)), NA, max(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
415 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
416 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
417 "nbSD" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
418
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
419 ## Sum by factor cross / rotation :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
420 nb_tmp2 <- apply(nb_tmp,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
421 which(is.element(names(dimnames(nb_tmp)), c(factors, "rotation"))),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
422 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
423 ifelse(all(is.na(x)), NA, sum(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
424 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
425
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
426 ## Sum by factor cross :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
427 res <- as.array(apply(nb_tmp2,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
428 which(is.element(names(dimnames(nb_tmp)), factors)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
429 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
430 ifelse(all(is.na(x)), NA, sd(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
431 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
432 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
433 "densMax" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
434
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
435 ## Sum by factor cross / rotation :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
436 dens_tmp2 <- apply(dens_tmp,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
437 which(is.element(names(dimnames(dens_tmp)), c(factors, "rotation"))),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
438 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
439 ifelse(all(is.na(x)), NA, sum(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
440 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
441
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
442 ## Sum by factor cross :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
443 res <- as.array(apply(dens_tmp2,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
444 which(is.element(names(dimnames(dens_tmp)), factors)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
445 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
446 ifelse(all(is.na(x)), NA, max(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
447 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
448 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
449 "densSD" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
450
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
451 ## Sum by factor cross / rotation :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
452 dens_tmp2 <- apply(dens_tmp,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
453 which(is.element(names(dimnames(dens_tmp)), c(factors, "rotation"))),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
454 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
455 ifelse(all(is.na(x)), NA, sum(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
456 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
457
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
458 ## Sum by factor cross :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
459 res <- as.array(apply(dens_tmp2,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
460 which(is.element(names(dimnames(dens_tmp)), factors)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
461 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
462 ifelse(all(is.na(x)), NA, sd(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
463 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
464 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
465 "%.nesting" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
466 res <- tapply(seq_len(nrow(d_ata)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
467 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
468 function(ii) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
469 ifelse(all(is.na(d_ata[ii, metric])),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
470 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
471 weighted.mean(d_ata[ii, metric],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
472 d_ata[ii, "readable.tracks"],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
473 na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
474 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
475 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
476 stop("Not implemented!")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
477 )
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
478
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
479 ## dimension names
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
480 names(dimnames(res)) <- c(factors)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
481
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
482 ## Transformation to long format :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
483 reslong <- as.data.frame(as.table(res), responseName = metric)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
484 reslong <- reslong[, c(tail(colnames(reslong), 1), head(colnames(reslong), -1))] # metric first
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
485
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
486 return(reslong)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
487 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
488
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
489 ######################################### end of the function agregation_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
490
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
491 ######################################### start of the function agregations_generic_f called y calc_biodiv_f in FucntExeCalcCommIndexesGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
492
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
493 agregations_generic_f <- function(d_ata, metrics, factors, list_fact = NULL, unit_sp_sz = NULL, unit_sp = NULL,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
494 nb_name = "number") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
495 ## Purpose: Aggregate data
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
496 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
497 ## Arguments: d_ata : data set
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
498 ## metrics : aggregated metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
499 ## factors : aggregation factors
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
500 ## list_fact : other factors to aggregate and add to output
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
501 ## unit_sp_sz : Metrics table by unitobs/species/Size Class
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
502 ## unit_sp : Metrics table by unitobs/species
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
503 ## nb_name : abundance colname
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
504 ##
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
505 ## Output : aggregated data frame
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
506 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
507 ## Author: Yves Reecht, Date: 18 oct. 2010, 15:47 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
508
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
509 ## trt depending on metric type :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
510 cas_metric <- c("number" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
511 "mean.length" = "w.mean",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
512 "taille_moy" = "w.mean",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
513 "biomass" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
514 "Biomass" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
515 "weight" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
516 "mean.weight" = "w.mean",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
517 "density" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
518 "Density" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
519 "CPUE" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
520 "CPUE.biomass" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
521 "presence_absence" = "pres",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
522 "abundance.prop.SC" = "w.mean.prop", # Not OK [!!!] ?
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
523 "biomass.prop.SC" = "w.mean.prop.bio", # Not OK [!!!] ?
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
524 ## Benthos :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
525 "colonies" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
526 "coverage" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
527 "mean.size.colonies" = "w.mean.colonies",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
528 ## SVR (expérimental) :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
529 "number.max" = "nbMax",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
530 "number.sd" = "nbSD",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
531 "density.max" = "densMax",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
532 "density.sd" = "densSD",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
533 "biomass.max" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
534 "spawning.success" = "%.nesting",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
535 "spawnings" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
536 "readable.tracks" = "sum",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
537 "tracks.number" = "sum")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
538
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
539 ## add "readable.tracks" for egg laying percentage :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
540 if (any(cas_metric[metrics] == "%.nesting")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
541 if (is.element("size.class", colnames(d_ata))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
542 if (is.null(unit_sp_sz)) stop("unit_sp_sz doit être défini")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
543
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
544 d_ata <- merge(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
545 unit_sp_sz[, c("species.code", "observation.unit", "size.class", "readable.tracks")],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
546 by = c("species.code", "observation.unit", "size.class"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
547 suffixes = c("", ".y"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
548 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
549 if (is.null(unit_sp)) stop("unit_sp must be defined")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
550
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
551 d_ata <- merge(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
552 unit_sp[, c("species.code", "observation.unit", "readable.tracks")],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
553 by = c("species.code", "observation.unit"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
554 suffixes = c("", ".y"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
555 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
556 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
557
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
558 ## Add "number" field for computing ponderate means if absent :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
559 if (any(cas_metric[metrics] == "w.mean" | cas_metric[metrics] == "w.mean.prop")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
560 if (is.element("size.class", colnames(d_ata))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
561 if (is.null(unit_sp_sz)) stop("unit_sp_sz must be defined")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
562
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
563 d_ata <- merge(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
564 unit_sp_sz[, c("species.code", "observation.unit", "size.class", nb_name)],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
565 by = c("species.code", "observation.unit", "size.class"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
566 suffixes = c("", ".y"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
567
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
568 ## add tot abundance / species / observation unit :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
569 nb_tot <- tapply(unit_sp_sz[, nb_name],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
570 as.list(unit_sp_sz[, c("species.code", "observation.unit")]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
571 sum, na.rm = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
572
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
573 d_ata <- merge(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
574 as.data.frame(as.table(nb_tot), responseName = "nombre.tot"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
575 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
576 if (is.null(unit_sp)) stop("unit_sp must be defined")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
577
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
578 d_ata <- merge(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
579 unit_sp[, c("species.code", "observation.unit", nb_name)], # [!!!] unit_sp_sz ?
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
580 by = c("species.code", "observation.unit"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
581 suffixes = c("", ".y"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
582 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
583 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
584
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
585 ## Add biomass field of biomass proportion by size class :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
586 if (any(cas_metric[metrics] == "w.mean.prop.bio")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
587 if (is.null(unit_sp_sz)) stop("unit_sp_sz doit être défini")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
588
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
589 d_ata <- merge(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
590 unit_sp_sz[, c("species.code", "observation.unit", "size.class", "biomass")],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
591 by = c("species.code", "observation.unit", "size.class"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
592 suffixes = c("", ".y"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
593
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
594 ## add tot biomass / species / observation unit :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
595 biom_tot <- tapply(unit_sp_sz$biomass,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
596 as.list(unit_sp_sz[, c("species.code", "observation.unit")]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
597 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
598 ifelse(all(is.na(x)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
599 NA,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
600 sum(x, na.rm = TRUE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
601 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
602
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
603 d_ata <- merge(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
604 as.data.frame(as.table(biom_tot), responseName = "tot.biomass"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
605 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
606
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
607 ## add colony field for ponderate means pondérées if absent :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
608 if (any(cas_metric[metrics] == "w.mean.colonies" & ! is.element("colonies", colnames(d_ata)))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
609 d_ata$colonies <- unit_sp[match(apply(d_ata[, c("species.code", "observation.unit")],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
610 1, paste, collapse = "*"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
611 apply(unit_sp[, c("species.code", "observation.unit")],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
612 1, paste, collapse = "*")), "colonies"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
613 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
614
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
615
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
616 ## Aggregation of metric depending on factors :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
617 reslong <- bettercbind(df_list = lapply(metrics, # sapply used to have names
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
618 agregation_f,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
619 d_ata = d_ata, factors = factors, cas_metric = cas_metric,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
620 nb_name = nb_name))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
621
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
622 ## Aggregation and add other factors :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
623 if (! (is.null(list_fact) || length(list_fact) == 0)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
624 reslong <- cbind(reslong,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
625 sapply(d_ata[, list_fact, drop = FALSE],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
626 function(fact) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
627 tapply(fact,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
628 as.list(d_ata[, factors, drop = FALSE]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
629 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
630 if (length(x) > 1 && length(unique(x)) > 1) { # must be one modality
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
631 return(NULL) # otherwise it is NULL
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
632 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
633 unique(as.character(x))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
634 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
635 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
636 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
637 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
638
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
639 ## If some factors aren't at the right class :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
640 if (any(tmp <- sapply(reslong[, list_fact, drop = FALSE], class) != sapply(d_ata[, list_fact, drop = FALSE], class))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
641 for (i in which(tmp)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
642 switch(sapply(d_ata[, list_fact, drop = FALSE], class)[i],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
643 "integer" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
644 reslong[, list_fact[i]] <- as.integer(as.character(reslong[, list_fact[i]]))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
645 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
646 "numeric" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
647 reslong[, list_fact[i]] <- as.numeric(as.character(reslong[, list_fact[i]]))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
648 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
649 reslong[, list_fact[i]] <- eval(call(paste("as", sapply(d_ata[, list_fact, drop = FALSE], class)[i], sep = "."),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
650 reslong[, list_fact[i]]))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
651 )
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
652 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
653 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
654
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
655 ## Initial order of factors levels :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
656 reslong <- as.data.frame(sapply(colnames(reslong),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
657 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
658 if (is.factor(reslong[, x])) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
659 return(factor(reslong[, x], levels = levels(d_ata[, x])))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
660 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
661 return(reslong[, x])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
662 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
663 }, simplify = FALSE))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
664
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
665
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
666 ## Check of other aggregated factors supplémentaires. There must be no NULL elements :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
667 if (any(sapply(reslong[, list_fact], function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
668 any(is.null(unlist(x)))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
669 }))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
670 warning(paste("One of the suppl. factors is probably a subset",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
671 " of the observations grouping factor(s).", sep = ""))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
672 return(NULL)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
673 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
674 return(reslong)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
675 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
676 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
677
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
678 ######################################### end of the function agregations_generic_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
679
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
680 ######################################### start of the function drop_levels_f called y calc_biodiv_f in FucntExeCalcCommIndexesGalaxy.r and glm_community in FunctExeCalcGLMGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
681 drop_levels_f <- function(df, which = NULL) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
682 ## Purpose: Suppress unused levels of factors
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
683 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
684 ## Arguments: df : a data.frame
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
685 ## which : included columns index (all by default)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
686 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
687 ## Author: Yves Reecht, Date: 10 août 2010, 13:29 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
688
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
689 if (class(df) != "data.frame") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
690 stop("'df' must be a data.frame")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
691 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
692 if (is.null(which)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
693 x <- as.data.frame(sapply(df, function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
694 return(x[, drop = TRUE])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
695 }, simplify = FALSE),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
696 stringsAsFactors = FALSE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
697 }else{ # Only some columns used
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
698 x <- df
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
699
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
700 x[, which] <- as.data.frame(sapply(df[, which, drop = FALSE],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
701 function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
702 return(x[, drop = TRUE])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
703 }, simplify = FALSE),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
704 stringsAsFactors = FALSE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
705 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
706
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
707 return(x)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
708 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
709 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
710 ######################################### end of the function drop_levels_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
711
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
712 ######################################### start of the function subset_all_tables_f called by glm_community in FunctExeCalcGLMGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
713
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
714 subset_all_tables_f <- function(metrique, tab_metrics, facteurs, selections,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
715 tab_unitobs, refesp, tab_metrique = "", nb_name = "number", obs_type = "",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
716 exclude = NULL, add = c("species.code", "observation.unit")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
717 ## Purpose: Extract useful data only from chosen metrics and factors
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
718 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
719 ## Arguments: metrique : chosen metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
720 ## facteurs : all chosen factors
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
721 ## selections : corresponding modality selected
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
722 ## tab_metrique : metrics table name
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
723 ## exclude : factors levels to exclude
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
724 ## add : field to add to data table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
725 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
726 ## Author: Yves Reecht, Date: 6 août 2010, 16:46 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
727
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
728 ## If no metrics table available :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
729 if (is.element(tab_metrique, c("", "TableOccurrences", "TablePresAbs"))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
730 tab_metrique <- "unit_sp"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
731 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
732
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
733 cas_tables <- c("unit_sp" = "unit_sp",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
734 "TablePresAbs" = "unit_sp",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
735 "unit_sp_sz" = "unit_sp_sz")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
736
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
737 ## Recuperation of metrics table :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
738 data_metric <- tab_metrics
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
739 unitobs <- tab_unitobs
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
740 refesp <- refesp
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
741
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
742 ## If no metrics available or already computed :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
743 if (is.element(metrique, c("", "occurrence.frequency"))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
744 metrique <- "tmp"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
745 data_metric$tmp <- 0
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
746 data_metric$tmp[data_metric[, nb_name] > 0] <- 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
747 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
748
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
749 if (!is.null(add)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
750 metriques <- c(metrique, add[is.element(add, colnames(data_metric))])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
751 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
752 metriques <- metrique
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
753 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
754
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
755 ## Subset depending on metrics table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
756 switch(cas_tables[tab_metrique],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
757 ## Observation table by unitobs and species :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
758 unit_sp = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
759 restmp <- cbind(data_metric[!is.na(data_metric[, metrique]), metriques, drop = FALSE],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
760 unitobs[match(data_metric$observation.unit[!is.na(data_metric[, metrique])],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
761 unitobs$observation.unit), # ajout des colonnes sélectionnées d'unitobs
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
762 facteurs[is.element(facteurs, colnames(unitobs))], drop = FALSE],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
763 refesp[match(data_metric$species.code[!is.na(data_metric[, metrique])],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
764 refesp$species.code), # ajout des colonnes sélectionnées d'especes
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
765 facteurs[is.element(facteurs, colnames(refesp))], drop = FALSE])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
766 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
767 ## Observation table by unitobs, species and size class :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
768 unit_sp_sz = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
769 restmp <- cbind(data_metric[!is.na(data_metric[, metrique]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
770 c(metriques, "size.class"), drop = FALSE],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
771 unitobs[match(data_metric$observation.unit[!is.na(data_metric[, metrique])],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
772 unitobs$observation.unit), # ajout des colonnes sélectionnées d'unitobs
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
773 facteurs[is.element(facteurs, colnames(unitobs))], drop = FALSE],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
774 refesp[match(data_metric$species.code[!is.na(data_metric[, metrique])],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
775 refesp$species.code), # ajout des colonnes sélectionnées d'especes
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
776 facteurs[is.element(facteurs, colnames(refesp))], drop = FALSE])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
777 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
778 ## Other cases :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
779 restmp <- cbind(data_metric[!is.na(data_metric[, metrique]), metriques, drop = FALSE],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
780 unitobs[match(data_metric$observation.unit[!is.na(data_metric[, metrique])],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
781 unitobs$observation.unit), # ajout des colonnes sélectionnées d'unitobs.
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
782 facteurs[is.element(facteurs, colnames(unitobs))], drop = FALSE])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
783 )
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
784
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
785 sel_col <- which(!is.na(selections))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
786 if (!is.null(exclude)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
787 sel_col <- sel_col[sel_col != exclude]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
788 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
789
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
790 ## Particular case of size classes :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
791 if (is.element("size.class", colnames(restmp))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
792 if (length(grep("^[[:digit:]]*[-_][[:digit:]]*$", unique(as.character(restmp$size.class)), perl = TRUE)) ==
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
793 length(unique(as.character(restmp$size.class)))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
794 restmp[, "size.class"] <-
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
795 factor(as.character(restmp$size.class),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
796 levels = unique(as.character(restmp$size.class))[
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
797 order(as.numeric(sub("^([[:digit:]]*)[-_][[:digit:]]*$",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
798 "\\1",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
799 unique(as.character(restmp$size.class)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
800 perl = TRUE)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
801 na.last = FALSE)])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
802 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
803 restmp[, "size.class"] <- factor(restmp$size.class)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
804 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
805 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
806
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
807 ## Biomass and density conversion -> /100m² :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
808 if (any(is.element(colnames(restmp), c("biomass", "density",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
809 "biomass.max", "density.max",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
810 "biomass.sd", "density.sd"))) && obs_type != "fishing") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
811 restmp[, is.element(colnames(restmp),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
812 c("biomass", "density",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
813 "biomass.max", "density.max",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
814 "biomass.sd", "density.sd"))] <- 100 *
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
815 restmp[, is.element(colnames(restmp),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
816 c("biomass", "density",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
817 "biomass.max", "density.max",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
818 "biomass.sd", "density.sd"))]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
819 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
820
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
821 return(restmp)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
822 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
823
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
824 ######################################### end of the function subset_all_tables_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
825
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
826 ######################################### start of the function organise_fact called by modeleLineaireWP2.xxx.f in FunctExeCalcGLMxxGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
827
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
828 organise_fact <- function(list_rand, list_fact) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
829 ## Purpose: organise response factors
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
830 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
831 ## Arguments: list_rand : Analysis random factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
832 ## list_fact : Analysis factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
833 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
834 ## Author: Coline ROYAUX 14 november 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
835
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
836 if (list_rand[1] != "None") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
837 if (all(is.element(list_fact, list_rand)) || list_fact[1] == "None") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
838 resp_fact <- paste("(1|", paste(list_rand, collapse = ") + (1|"), ")")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
839 list_f <- NULL
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
840 list_fact <- list_rand
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
841 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
842 list_f <- list_fact[!is.element(list_fact, list_rand)]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
843 resp_fact <- paste(paste(list_f, collapse = " + "), " + (1|", paste(list_rand, collapse = ") + (1|"), ")")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
844 list_fact <- c(list_f, list_rand)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
845 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
846 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
847 list_f <- list_fact
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
848 resp_fact <- paste(list_fact, collapse = " + ")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
849 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
850 return(list(resp_fact, list_f, list_fact))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
851 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
852
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
853 ######################################### end of the function organise_fact
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
854
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
855 ######################################### start of the function organise_fact called by modeleLineaireWP2.xxx.f in FunctExeCalcGLMxxGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
856 distrib_choice <- function(distrib = distrib, metrique = metrique, data = tmpd_ata) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
857 ## Purpose: choose the right distribution
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
858 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
859 ## Arguments: data : data used for analysis
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
860 ## metrique : Chosen metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
861 ## distrib : distribution law selected by user
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
862 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
863 ## Author: Coline ROYAUX 14 november 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
864
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
865 if (distrib == "None") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
866 if (metrique == "presence_absence") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
867 chose_distrib <- "binomial"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
868 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
869 switch(class(data[, metrique]),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
870 "integer" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
871 chose_distrib <- "poisson"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
872 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
873 "numeric" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
874 chose_distrib <- "gaussian"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
875 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
876 stop("Selected metric class doesn't fit, you should select an integer or a numeric variable"))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
877 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
878 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
879 chose_distrib <- distrib
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
880 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
881 return(chose_distrib)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
882 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
883
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
884 ######################################### end of the function organise_fact
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
885
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
886 ######################################### start of the function create_res_table called by modeleLineaireWP2.xxx.f in FunctExeCalcGLMxxGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
887 create_res_table <- function(list_rand, list_fact, row, lev, distrib) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
888 ## Purpose: create results table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
889 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
890 ## Arguments: list_rand : Analysis random factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
891 ## list_fact : Analysis factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
892 ## row : rows of results table = species or separation factor
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
893 ## lev : Levels of analysis factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
894 ## distrib : distribution law
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
895 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
896 ## Author: Coline ROYAUX 04 october 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
897
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
898 if (list_rand[1] != "None") { ## if random effects
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
899 tab_sum <- data.frame(analysis = row, Interest.var = NA, distribution = NA, AIC = NA, BIC = NA, logLik = NA, deviance = NA, df.resid = NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
900 colrand <- unlist(lapply(list_rand,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
901 FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
902 lapply(c("Std.Dev", "NbObservation", "NbLevels"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
903 FUN = function(y) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
904 paste(x, y, collapse = ":")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
905 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
906 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
907 tab_sum[, colrand] <- NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
908
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
909 if (! is.null(lev)) { ## if fixed effects + random effects
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
910 colcoef <- unlist(lapply(c("(Intercept)", lev),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
911 FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
912 lapply(c("Estimate", "Std.Err", "Zvalue", "Pvalue", "IC_up", "IC_inf", "signif"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
913 FUN = function(y) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
914 paste(x, y, collapse = ":")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
915 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
916 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
917
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
918 }else{ ## if no fixed effects
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
919 colcoef <- NULL
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
920 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
921
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
922 }else{ ## if no random effects
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
923 tab_sum <- data.frame(analysis = row, Interest.var = NA, distribution = NA, AIC = NA, Resid.deviance = NA, df.resid = NA, Null.deviance = NA, df.null = NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
924
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
925 switch(distrib,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
926 "gaussian" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
927 colcoef <- unlist(lapply(c("(Intercept)", lev),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
928 FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
929 lapply(c("Estimate", "Std.Err", "Tvalue", "Pvalue", "IC_up", "IC_inf", "signif"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
930 FUN = function(y) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
931 paste(x, y, collapse = ":")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
932 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
933 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
934
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
935 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
936 "quasipoisson" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
937 colcoef <- unlist(lapply(c("(Intercept)", lev),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
938 FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
939 lapply(c("Estimate", "Std.Err", "Tvalue", "Pvalue", "IC_up", "IC_inf", "signif"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
940 FUN = function(y) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
941 paste(x, y, collapse = ":")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
942 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
943 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
944
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
945 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
946 , {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
947 colcoef <- unlist(lapply(c("(Intercept)", lev),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
948 FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
949 lapply(c("Estimate", "Std.Err", "Zvalue", "Pvalue", "IC_up", "IC_inf", "signif"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
950 FUN = function(y) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
951 paste(x, y, collapse = ":")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
952 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
953 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
954 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
955
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
956 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
957
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
958 tab_sum[, colcoef] <- NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
959
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
960
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
961 return(tab_sum)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
962 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
963 ######################################### end of the function create_res_table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
964
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
965 ######################################### start of the function sorties_lm_f called by glm_community in FunctExeCalcGLMGalaxy.r
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
966 sorties_lm_f <- function(obj_lm, obj_lmy, tab_sum, #formule,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
967 metrique, fact_ana, cut, col_ana, list_fact, list_rand, lev = NULL, d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
968 log = FALSE, sufixe = NULL) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
969 ## Purpose: Form GLM and LM results
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
970 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
971 ## Arguments: obj_lm : lm object
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
972 ## obj_lmy : lm object with year as continuous
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
973 ## tab_sum : output summary table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
974 ## formule : LM formula
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
975 ## metrique : Chosen metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
976 ## fact_ana : separation factor
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
977 ## cut : level of separation factor
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
978 ## col_ana : colname for separation factor in output summary table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
979 ## list_fact : Analysis factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
980 ## list_rand : Analysis random factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
981 ## levels : Levels of analysis factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
982 ## d_ata : d_ata used for analysis
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
983 ## log : put log on metric ? (boolean)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
984 ## sufixe : sufix for file name
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
985 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
986 ## Author: Yves Reecht, Date: 25 août 2010, 16:19 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
987
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
988 tab_sum[, "Interest.var"] <- as.character(metrique)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
989 sum_lm <- summary(obj_lm)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
990 tab_sum[, "distribution"] <- as.character(sum_lm$family[1])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
991
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
992 if (length(grep("^glmmTMB", obj_lm$call)) > 0) { #if random effects
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
993 tab_sum[tab_sum[, col_ana] == cut, "AIC"] <- sum_lm$AICtab[1]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
994 tab_sum[tab_sum[, col_ana] == cut, "BIC"] <- sum_lm$AICtab[2]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
995 tab_sum[tab_sum[, col_ana] == cut, "logLik"] <- sum_lm$AICtab[3]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
996 tab_sum[tab_sum[, col_ana] == cut, "deviance"] <- sum_lm$AICtab[4]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
997 tab_sum[tab_sum[, col_ana] == cut, "df.resid"] <- sum_lm$AICtab[5]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
998
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
999 if (! is.null(lev)) { ## if fixed effects + random effects
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1000 tab_coef <- as.data.frame(sum_lm$coefficients$cond)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1001 tab_coef$signif <- lapply(tab_coef[, "Pr(>|z|)"], FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1002 if (!is.na(x) && x < 0.05) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1003 "yes"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1004 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1005 "no"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1006 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1007 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1008
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1009 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Zvalue", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "z value"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1010 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Pvalue", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "Pr(>|z|)"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1011
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1012 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Zvalue", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1013 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1014 tab_coef[grepl(x, rownames(tab_coef)), "z value"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1015 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1016 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1017 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1018 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1019 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Pvalue", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1020 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1021 tab_coef[grepl(x, rownames(tab_coef)), "Pr(>|z|)"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1022 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1023 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1024 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1025 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1026
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1027 if (any(obj_lmy != "")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1028 sum_lmy <- summary(obj_lmy)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1029 tab_coefy <- as.data.frame(sum_lmy$coefficients$cond)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1030 tab_coefy$signif <- lapply(tab_coefy[, "Pr(>|z|)"], FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1031 if (!is.na(x) && x < 0.05) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1032 "yes"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1033 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1034 "no"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1035 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1036 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1037 tab_sum[tab_sum[, col_ana] == cut, "year Zvalue"] <- ifelse(length(tab_coefy["year", "z value"]) > 0, tab_coefy["year", "z value"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1038 tab_sum[tab_sum[, col_ana] == cut, "year Pvalue"] <- ifelse(length(tab_coefy["year", "Pr(>|z|)"]) > 0, tab_coefy["year", "Pr(>|z|)"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1039 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1040
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1041 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1042
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1043 switch(as.character(length(sum_lm$varcor$cond)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1044 "1" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1045 std_d <- c(sum_lm$varcor$cond[[1]])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1046 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1047 "2" = {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1048 std_d <- c(sum_lm$varcor$cond[[1]], sum_lm$varcor$cond[[2]])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1049 },
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1050 std_d <- NULL)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1051
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1052 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(list_rand, "Std.Dev", collapse = "|"), colnames(tab_sum))] <- std_d
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1053 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(list_rand, "NbObservation", collapse = "|"), colnames(tab_sum))] <- sum_lm$nobs
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1054 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(list_rand, "NbLevels", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(list_rand, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1055 nlevels(d_ata[, x])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1056 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1057
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1058 }else{ ## if fixed effects only
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1059
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1060 tab_sum[tab_sum[, col_ana] == cut, "AIC"] <- sum_lm$aic
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1061 tab_sum[tab_sum[, col_ana] == cut, "Resid.deviance"] <- sum_lm$deviance
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1062 tab_sum[tab_sum[, col_ana] == cut, "df.resid"] <- sum_lm$df.residual
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1063 tab_sum[tab_sum[, col_ana] == cut, "Null.deviance"] <- sum_lm$null.deviance
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1064 tab_sum[tab_sum[, col_ana] == cut, "df.null"] <- sum_lm$df.null
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1065 tab_coef <- as.data.frame(sum_lm$coefficients)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1066
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1067 if (any(obj_lmy != "")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1068 sum_lmy <- summary(obj_lmy)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1069 tab_coefy <- as.data.frame(sum_lmy$coefficients)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1070 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1071
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1072 if (sum_lm$family[1] == "gaussian" || sum_lm$family[1] == "quasipoisson") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1073
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1074 tab_coef$signif <- lapply(tab_coef[, "Pr(>|t|)"], FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1075 if (!is.na(x) && x < 0.05) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1076 "yes"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1077 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1078 "no"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1079 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1080 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1081 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Tvalue", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "t value"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1082 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Pvalue", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "Pr(>|t|)"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1083
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1084 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Tvalue", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1085 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1086 tab_coef[grepl(x, rownames(tab_coef)), "t value"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1087 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1088 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1089 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1090 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1091
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1092 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Pvalue", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1093 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1094 tab_coef[grepl(x, rownames(tab_coef)), "Pr(>|t|)"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1095 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1096 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1097 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1098 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1099
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1100 if (any(obj_lmy != "")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1101 tab_coefy$signif <- lapply(tab_coefy[, "Pr(>|t|)"], FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1102 if (!is.na(x) && x < 0.05) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1103 "yes"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1104 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1105 "no"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1106 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1107 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1108 tab_sum[tab_sum[, col_ana] == cut, "year Tvalue"] <- ifelse(length(tab_coefy["year", "t value"]) > 0, tab_coefy["year", "t value"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1109 tab_sum[tab_sum[, col_ana] == cut, "year Pvalue"] <- ifelse(length(tab_coefy["year", "Pr(>|z|)"]) > 0, tab_coefy["year", "Pr(>|t|)"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1110 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1111
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1112 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1113 tab_coef$signif <- lapply(tab_coef[, "Pr(>|z|)"], FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1114 if (!is.na(x) && x < 0.05) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1115 "yes"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1116 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1117 "no"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1118 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1119 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1120
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1121 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Zvalue", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "z value"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1122 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Pvalue", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "Pr(>|z|)"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1123
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1124 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Zvalue", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1125 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1126 tab_coef[grepl(x, rownames(tab_coef)), "z value"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1127 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1128 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1129 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1130 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1131 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Pvalue", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1132 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1133 tab_coef[grepl(x, rownames(tab_coef)), "Pr(>|z|)"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1134 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1135 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1136 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1137 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1138
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1139 if (any(obj_lmy != "")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1140 tab_coefy$signif <- lapply(tab_coefy[, "Pr(>|z|)"], FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1141 if (!is.na(x) && x < 0.05) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1142 "yes"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1143 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1144 "no"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1145 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1146 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1147
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1148 tab_sum[tab_sum[, col_ana] == cut, "year Zvalue"] <- ifelse(length(tab_coefy["year", "z value"]) > 0, tab_coefy["year", "z value"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1149 tab_sum[tab_sum[, col_ana] == cut, "year Pvalue"] <- ifelse(length(tab_coefy["year", "Pr(>|z|)"]) > 0, tab_coefy["year", "Pr(>|z|)"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1150 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1151 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1152 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1153
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1154 if (! is.null(lev)) { ## if fixed effects
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1155 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Estimate", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "Estimate"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1156 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*Std.Err", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "Std. Error"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1157 tab_sum[tab_sum[, col_ana] == cut, grepl("Intercept.*signif", colnames(tab_sum))] <- tab_coef[grepl("Intercept", rownames(tab_coef)), "signif"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1158
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1159 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Estimate", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1160 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1161 tab_coef[grepl(x, rownames(tab_coef)), "Estimate"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1162 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1163 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1164 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1165 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1166 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "Std.Err", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1167 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1168 tab_coef[grepl(x, rownames(tab_coef)), "Std. Error"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1169 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1170 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1171 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1172 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1173 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "signif", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1174 if (length(grep(x, rownames(tab_coef))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1175 tab_coef[grepl(x, rownames(tab_coef)), "signif"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1176 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1177 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1178 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1179 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1180
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1181 if (any(obj_lmy != "")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1182 tab_sum[tab_sum[, col_ana] == cut, "year Estimate"] <- ifelse(length(tab_coefy["year", "Estimate"]) > 0, tab_coefy["year", "Estimate"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1183 tab_sum[tab_sum[, col_ana] == cut, "year Std.Err"] <- ifelse(length(tab_coefy["year", "Std. Error"]) > 0, tab_coefy["year", "Std. Error"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1184 tab_sum[tab_sum[, col_ana] == cut, "year signif"] <- ifelse(length(tab_coefy["year", "signif"]) > 0, tab_coefy["year", "signif"], NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1185 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1186
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1187 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1188
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1189 ic <- tryCatch(as.data.frame(confint(obj_lm)), error = function(e) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1190 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1191
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1192 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "IC_up", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1193 if (length(grep(x, rownames(ic))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1194 ic[grepl(x, rownames(ic)), "97.5 %"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1195 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1196 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1197 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1198 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1199 tab_sum[tab_sum[, col_ana] == cut, grepl(paste(lev, "IC_inf", collapse = "|"), colnames(tab_sum))] <- unlist(lapply(lev, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1200 if (length(grep(x, rownames(ic))) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1201 ic[grepl(x, rownames(ic)), "2.5 %"]
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1202 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1203 NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1204 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1205 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1206
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1207 return(tab_sum)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1208
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1209 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1210
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1211
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1212 ######################################### end of the function sorties_lm_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1213
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1214
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1215 ######################################### start of the function note_glm_f called by glm_species and glm_community
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1216
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1217 note_glm_f <- function(data, obj_lm, metric, list_fact, details = FALSE) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1218 ## Purpose: Note your GLM analysis
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1219 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1220 ## Arguments: data : d_ataframe used for analysis
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1221 ## obj_lm : GLM assessed
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1222 ## metric : selected metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1223 ## list_fact : Analysis factors list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1224 ## details : detailed output ?
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1225 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1226 ## Author: Coline ROYAUX, 26 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1227
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1228 rate <- 0
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1229 detres <- list(complete_plan = NA, balanced_plan = NA, NA_proportion_OK = NA, no_residual_dispersion = NA, uniform_residuals = NA, outliers_proportion_OK = NA, no_zero_inflation = NA, observation_factor_ratio_OK = NA, enough_levels_random_effect = NA, rate = NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1230
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1231 #### d_ata criterions ####
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1232
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1233 ## Plan
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1234
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1235 plan <- as.data.frame(table(data[, list_fact]))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1236
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1237 if (nrow(plan[plan$Freq == 0, ]) < nrow(plan) * 0.1) { # +0.5 if less than 10% of possible factor's level combinations aren't represented in the sampling scheme
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1238 rate <- rate + 0.5
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1239 detres$complete_plan <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1240
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1241 if (summary(as.factor(plan$Freq))[1] > nrow(plan) * 0.9) { # +0.5 if the frequency of the most represented frequency of possible factor's levels combinations is superior to 90% of the total number of possible factor's levels combinations
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1242 rate <- rate + 0.5
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1243 detres$balanced_plan <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1244 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1245
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1246 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1247 detres$complete_plan <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1248 detres$balanced_plan <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1249 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1250
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1251 if (nrow(data) - nrow(na.omit(data)) < nrow(data) * 0.1) { # +1 if less than 10% of the lines in the dataframe bares a NA
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1252 rate <- rate + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1253 detres["NA_proportion_OK"] <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1254 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1255 detres["NA_proportion_OK"] <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1256 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1257
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1258 #### Model criterions ####
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1259
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1260 if (length(grep("quasi", obj_lm$family)) == 0) { #DHARMa doesn't work with quasi distributions
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1261
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1262 residuals <- DHARMa::simulateResiduals(obj_lm)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1263
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1264 capture.output(test_res <- DHARMa::testResiduals(residuals))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1265 test_zero <- DHARMa::testZeroInflation(residuals)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1266
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1267 ## dispersion of residuals
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1268
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1269 if (test_res$dispersion$p.value > 0.05) { # +1.5 if dispersion tests not significative
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1270 rate <- rate + 1.5
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1271 detres$no_residual_dispersion <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1272 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1273 detres$no_residual_dispersion <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1274 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1275
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1276 ## uniformity of residuals
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1277
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1278 if (test_res$uniformity$p.value > 0.05) { # +1 if uniformity tests not significative
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1279 rate <- rate + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1280 detres$uniform_residuals <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1281 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1282 detres$uniform_residuals <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1283 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1284
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1285 ## residuals outliers
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1286
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1287 if (test_res$outliers$p.value > 0.05) { # +0.5 if outliers tests not significative
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1288 rate <- rate + 0.5
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1289 detres["outliers_proportion_OK"] <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1290 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1291 detres["outliers_proportion_OK"] <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1292 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1293
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1294 ## Zero inflation test
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1295
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1296 if (test_zero$p.value > 0.05) { # +1 if zero inflation tests not significative
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1297 rate <- rate + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1298 detres$no_zero_inflation <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1299 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1300 detres$no_zero_inflation <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1301 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1302
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1303 ## Factors/observations ratio
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1304
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1305 if (length(list_fact) / nrow(na.omit(data)) < 0.1) { # +1 if quantity of factors is less than 10% of the quantity of observations
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1306 rate <- rate + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1307 detres["observation_factor_ratio_OK"] <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1308 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1309 detres["observation_factor_ratio_OK"] <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1310 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1311
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1312 ## less than 10 factors' level on random effect
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1313
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1314 if (length(grep("^glmmTMB", obj_lm$call)) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1315 nlev_rand <- c()
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1316 for (fact in names(summary(obj_lm)$varcor$cond)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1317 nlev_rand <- c(nlev_rand, length(unlist(unique(data[, fact]))))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1318 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1319
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1320 if (all(nlev_rand > 10)) { # +1 if more than 10 levels in one random effect
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1321 rate <- rate + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1322 detres$enough_levels_random_effect <- TRUE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1323 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1324 detres$enough_levels_random_effect <- FALSE
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1325 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1326 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1327
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1328 detres$rate <- rate
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1329
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1330 if (details) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1331 return(detres)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1332 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1333 return(rate)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1334 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1335
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1336 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1337 return(NA)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1338 cat("Models with quasi distributions can't be rated for now")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1339 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1340 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1341
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1342 ######################################### end of the function note_glm_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1343
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1344 ######################################### start of the function note_glms_f called by glm_species and glm_community
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1345
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1346 note_glms_f <- function(tab_rate, expr_lm, obj_lm, file_out = FALSE) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1347 ## Purpose: Note your GLM analysis
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1348 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1349 ## Arguments: tab_rate : rates table from note_glm_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1350 ## expr_lm : GLM expression assessed
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1351 ## obj_lm : GLM object
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1352 ## file_out : Output as file ? else global rate only
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1353 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1354 ## Author: Coline ROYAUX, 26 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1355 namefile <- "RatingGLM.txt"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1356
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1357 if (length(grep("quasi", obj_lm$family)) == 0) { #DHARMa doesn't work with quasi distributions
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1358
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1359 rate_m <- median(na.omit(tab_rate[, "rate"]))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1360 sum <- summary(obj_lm)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1361
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1362 if (length(grep("^glmmTMB", obj_lm$call)) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1363 if (median(na.omit(tab_rate[, "rate"])) >= 6) { # if 50% has a rate superior or equal to 6 +1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1364 rate_m <- rate_m + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1365 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1366
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1367 if (quantile(na.omit(tab_rate[, "rate"]), probs = 0.9) >= 6) { # if 90% has a rate superior or equal to 6 +1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1368 rate_m <- rate_m + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1369 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1370 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1371 if (median(na.omit(tab_rate[, "rate"])) >= 5) { # if 50% has a rate superior or equal to 5 +1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1372 rate_m <- rate_m + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1373 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1374
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1375 if (quantile(na.omit(tab_rate[, "rate"]), probs = 0.9) >= 5) { # if 90% has a rate superior or equal to 5 +1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1376 rate_m <- rate_m + 1
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1377 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1378 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1379
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1380 if (file_out) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1381
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1382 cat("###########################################################################",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1383 "\n########################### Analysis evaluation ###########################",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1384 "\n###########################################################################", file = namefile, fill = 1, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1385
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1386 ## Informations on model :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1387 cat("\n\n######################################### \nFitted model:", file = namefile, fill = 1, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1388 cat("\t", deparse(expr_lm), "\n\n", file = namefile, sep = "", append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1389 cat("Family: ", sum$family[[1]],
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1390 file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1391 cat("\n\nNumber of analysis: ", nrow(tab_rate), file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1392
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1393 ## Global rate :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1394 cat("\n\n######################################### \nGlobal rate for all analysis:",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1395 "\n\n", rate_m, "out of 10", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1396
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1397 ## details on every GLM :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1398
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1399 cat("\n\n######################################### \nDetails on every analysis:\n\n", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1400 cat("Analysis\tC1\tC2\tC3\tC4\tC5\tC6\tC7\tC8\tC9\tFinal rate", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1401 apply(tab_rate, 1, FUN = function(x) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1402
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1403 if (!is.na(x["complete_plan"]) && x["complete_plan"] == TRUE) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1404 cat("\n", x[1], "\tyes", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1405 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1406 cat("\n", x[1], "\tno", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1407 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1408
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1409 for (i in c("balanced_plan", "NA_proportion_OK", "no_residual_dispersion", "uniform_residuals", "outliers_proportion_OK", "no_zero_inflation", "observation_factor_ratio_OK", "enough_levels_random_effect")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1410 if (!is.na(x[i]) && x[i] == TRUE) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1411 cat("\tyes", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1412 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1413 cat("\tno", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1414 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1415 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1416
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1417 cat("\t", x["rate"], "/ 8", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1418
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1419
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1420 })
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1421 cat("\n\nC1: Complete plan?\nC2: Balanced plan?\nC3: Few NA?\nC4: Regular dispersion?\nC5: Uniform residuals?\nC6: Regular outliers proportion?\nC7: No zero-inflation?\nC8: Good observation/factor ratio?\nC9: Enough levels on random effect?", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1422
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1423 ## Red flags - advice :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1424 cat("\n\n######################################### \nRed flags - advice:\n\n", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1425 if (all(na.omit(tab_rate["NA_proportion_OK"]) == FALSE)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1426 cat("\n", "\t- More than 10% of lines of your dataset contains NAs", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1427 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1428
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1429 if (length(grep("FALSE", tab_rate["no_residual_dispersion"])) / length(na.omit(tab_rate["no_residual_dispersion"])) > 0.5) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1430 cat("\n", "\t- More than 50% of your analyses are over- or under- dispersed : Try with another distribution family", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1431 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1432
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1433 if (length(grep("FALSE", tab_rate["uniform_residuals"])) / length(na.omit(tab_rate["uniform_residuals"])) > 0.5) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1434 cat("\n", "\t- More than 50% of your analyses haven't an uniform distribution of residuals : Try with another distribution family", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1435 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1436
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1437 if (length(grep("FALSE", tab_rate["outliers_proportion_OK"])) / length(na.omit(tab_rate["outliers_proportion_OK"])) > 0.5) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1438 cat("\n", "\t- More than 50% of your analyses have too much outliers : Try with another distribution family or try to select or filter your data", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1439 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1440
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1441 if (length(grep("FALSE", tab_rate["no_zero_inflation"])) / length(na.omit(tab_rate["no_zero_inflation"])) > 0.5) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1442 cat("\n", "\t- More than 50% of your analyses have zero inflation : Try to select or filter your data", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1443 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1444
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1445 if (length(grep("FALSE", tab_rate["observation_factor_ratio_OK"])) / length(na.omit(tab_rate["observation_factor_ratio_OK"])) > 0.5) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1446 cat("\n", "\t- More than 50% of your analyses have not enough observations for the amount of factors : Try to use less factors in your analysis or try to use another separation factor", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1447 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1448
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1449 if (any(tab_rate["enough_levels_random_effect"] == FALSE, na.rm = TRUE) && length(grep("^glmmTMB", obj_lm$call)) > 0) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1450 cat("\n", "\t- Random effect hasn't enough levels to be robust : If it has less than ten levels remove the random effect", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1451 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1452 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1453
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1454 return(rate_m)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1455
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1456 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1457 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1458 cat("Models with quasi distributions can't be rated for now", file = namefile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1459 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1460 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1461
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1462 ######################################### end of the function note_glm_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1463
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1464 ######################################### start of the function info_stats_f called by glm_species and glm_community
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1465
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1466 info_stats_f <- function(filename, d_ata, agreg_level = c("species", "unitobs"), type = c("graph", "stat"),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1467 metrique, fact_graph, fact_graph_sel, list_fact, list_fact_sel) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1468 ## Purpose: informations and simple statistics
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1469 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1470 ## Arguments: filename : name of file
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1471 ## d_ata : input data
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1472 ## agreg_level : aggregation level
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1473 ## type : type of function calling
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1474 ## metrique : selected metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1475 ## fact_graph : selection factor
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1476 ## fact_graph_sel : list of factors levels selected for this factor
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1477 ## list_fact : list of grouping factors
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1478 ## list_fact_sel : list of factors levels selected for these factors
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1479 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1480 ## Author: Yves Reecht, Date: 10 sept. 2012, 15:26 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1481
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1482 ## Open file :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1483 f_ile <- file(description = filename,
1
5ddca052c314 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
ecology
parents: 0
diff changeset
1484 open = "w", encoding = "UTF-8")
0
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1485
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1486 ## if error :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1487 on.exit(if (exists("filename") &&
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1488 tryCatch(isOpen(f_ile),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1489 error = function(e)return(FALSE))) close(f_ile))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1490
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1491 ## Metrics and factors infos :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1492 print_selection_info_f(metrique = metrique, #fact_graph = fact_graph, fact_graph_sel = fact_graph_sel,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1493 list_fact = list_fact, #list_fact_sel = list_fact_sel,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1494 f_ile = f_ile,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1495 agreg_level = agreg_level, type = type)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1496
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1497 ## statistics :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1498 if (class(d_ata) == "list") {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1499 cat("\n###################################################",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1500 "\nStatistics per level of splitting factor:\n",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1501 sep = "", file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1502
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1503 invisible(sapply(seq_len(length(d_ata)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1504 function(i) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1505 print_stats_f(d_ata = d_ata[[i]], metrique = metrique, list_fact = list_fact, f_ile = f_ile,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1506 headline = fact_graph_sel[i])
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1507 }))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1508 }else{
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1509 print_stats_f(d_ata = d_ata, metrique = metrique, list_fact = list_fact, f_ile = f_ile,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1510 headline = NULL)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1511 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1512
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1513 ## Close file :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1514 close(f_ile)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1515
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1516 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1517
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1518 ######################################### end of the function info_stats_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1519
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1520
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1521 ######################################### start of the function print_selection_info_f called by info_stats_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1522
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1523 print_selection_info_f <- function(metrique, list_fact,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1524 f_ile,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1525 agreg_level = c("species", "unitobs"), type = c("graph", "stat")) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1526 ## Purpose: Write data informations
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1527 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1528 ## Arguments: metrique : chosen metric
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1529 ## list_fact : factor's list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1530 ## f_ile : Results file name
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1531 ## agreg_level : aggregation level
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1532 ## type : function type
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1533 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1534 ## Author: Yves Reecht, Date: 11 sept. 2012, 10:41 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1535
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1536 cat("\n##################################################\n",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1537 "Metrics and factors (and possible units/selections):\n",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1538 sep = "", file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1539
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1540 ## metric info :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1541 cat("\n Metrics:", metrique,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1542 "\n", file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1543
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1544 ## Clustering factors :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1545 if (is.element(agreg_level, c("spCL_unitobs", "spCL_espece", "spSpecies", "spEspece",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1546 "spUnitobs", "spUnitobs(CL)"))) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1547 type <- "spatialGraph"
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1548 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1549
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1550 cat(switch(type,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1551 "graph" = "\nGrouping factor(s): \n * ",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1552 "stat" = "\nAnalyses factor(s): \n * ",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1553 "spatialGraph" = "\nSpatial aggregation factor(s): \n * "),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1554 paste(list_fact, collaspe = "\n * "), "\n", file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1555
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1556 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1557
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1558 ######################################### end of the function print_selection_info_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1559
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1560
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1561 ######################################### start of the function print_stats_f called by info_stats_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1562
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1563 print_stats_f <- function(d_ata, metrique, list_fact, f_ile, headline = NULL) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1564 ## Purpose: Write general statistics table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1565 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1566 ## Arguments: d_ata : Analysis data
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1567 ## metrique : metric's name
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1568 ## list_fact : Factor's list
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1569 ## f_ile : Simple statistics file name
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1570 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1571 ## Author: Yves Reecht, Date: 11 sept. 2012, 10:09 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1572
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1573 ## Header :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1574 if (! is.null(headline)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1575 cat("\n", rep("#", nchar(headline) + 3), "\n",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1576 "## ", headline, "\n",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1577 sep = "", file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1578 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1579
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1580 cat("\n########################\nBase statistics:\n\n", file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1581
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1582 capture.output(print(summary_fr(d_ata[, metrique])), file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1583
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1584 if (! is.null(list_fact)) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1585 cat("\n#########################################",
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1586 "\nStatistics per combination of factor levels:\n\n", file = f_ile, sep = "", append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1587
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1588 ## Compute summary for each existing factor's cross :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1589 res <- with(d_ata,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1590 tapply(eval(parse(text = metrique)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1591 INDEX = do.call(paste,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1592 c(lapply(list_fact,
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1593 function(y)eval(parse(text = y))),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1594 sep = ".")),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1595 FUN = summary_fr))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1596
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1597 ## results in table
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1598 capture.output(print(do.call(rbind, res)),
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1599 file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1600 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1601
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1602 ## empty line :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1603 cat("\n", file = f_ile, append = TRUE)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1604 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1605
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1606 ######################################### end of the function print_stats_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1607
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1608
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1609 ######################################### start of the function summary_fr called by print_stats_f
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1610 summary_fr <- function(object, digits = max(3, getOption("digits") - 3), ...) {
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1611 ## Purpose: Adding SD and N to summary
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1612 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1613 ## Arguments: object : Object to summarise
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1614 ## ----------------------------------------------------------------------
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1615 ## Author: Yves Reecht, Date: 13 sept. 2012, 15:47 modified by Coline ROYAUX 04 june 2020
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1616
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1617 if (! is.numeric(object)) stop("Programming error")
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1618
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1619 ## Compute summary :
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1620 res <- c(summary(object = object, digits, ...), "sd" = signif(sd(x = object), digits = digits), "N" = length(object))
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1621
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1622 return(res)
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1623 }
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1624
3ab852a7ff53 "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"
ecology
parents:
diff changeset
1625 ######################################### start of the function summary_fr