Mercurial > repos > ecology > ecology_presence_abs_abund

annotate functions.r @ 1:4ed07d2d442b draft default tip

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:16:26 +0000
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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1 #Rscript
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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3 #########################################################################################
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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4 ####################### Exploration data tools function #################################
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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5 #########################################################################################
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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6 #### Based on Romain Lorrillière R script
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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7 #### Modified by Alan Amosse, Benjamin Yguel and Marie Jossé for integrating within Galaxy-E
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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9 ######################################### start of the function makeTableAnalyse
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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10 ##Species are placed in separated columns and addition of zero on plots where at least one selected species is present
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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11 make_table_analyse <- function(data, var, spe, var2, var3) {
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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12 tab <- reshape(data
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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13 , v.names = var
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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14 , idvar = c(var2, var3)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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15 , timevar = spe
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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16 , direction = "wide")
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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17 tab[is.na(tab)] <- 0 ###### remplace les na par des 0 / replace NAs by 0
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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19 colnames(tab) <- sub(paste0(var, "."), "", colnames(tab))### remplace le premier pattern "abond." par le second "" / replace the column names "abond." by ""
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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20 return(tab)
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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21 }
4ed07d2d442b "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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22 ######################################### end of the function makeTableAnalyse