Mercurial > repos > ecology > ecology_stat_presence_abs

annotate graph_lcbd.r @ 1:9a2e0195bb43 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:18:21 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
1 #Rscript
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
2
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
3 #########################
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
4 ## Beta diversity ##
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
5 #########################
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
6
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
7 #####Packages : ggplot2
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
8 # vegan
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
9 # adespatial
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
10 # dplyr
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
11 # tibble
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
12 # tdyr
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
13
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
14 #####Load arguments
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
15
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
16 args <- commandArgs(trailingOnly = TRUE)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
17
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
18 if (length(args) < 2) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
19 stop("This tool needs at least 2 arguments")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
20 }else{
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
21 table <- args[1]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
22 hr <- args[2]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
23 abund <- as.numeric(args[3])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
24 loc <- as.numeric(args[4])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
25 spe <- as.numeric(args[5])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
26 date <- as.numeric(args[6])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
27 map <- as.logical(args[7])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
28 sepa <- as.logical(args[8])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
29 not <- as.logical(args[9])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
30 lat <- as.numeric(args[10])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
31 long <- as.numeric(args[11])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
32 var <- as.numeric(args[12])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
33 source(args[13])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
34 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
35
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
36 if (hr == "false") {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
37 hr <- FALSE
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
38 }else{
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
39 hr <- TRUE
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
40 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
41
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
42 #####Import data
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
43 data <- read.table(table, sep = "\t", dec = ".", header = hr, fill = TRUE, encoding = "UTF-8")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
44 colabund <- colnames(data)[abund]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
45 colloc <- colnames(data)[loc]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
46 if (map) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
47 collat <- colnames(data)[lat]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
48 collong <- colnames(data)[long]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
49 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
50 colspe <- colnames(data)[spe]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
51 coldate <- colnames(data)[date]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
52 data[, coldate] <- as.factor(data[, coldate])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
53
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
54 data <- data[grep("^$", data[, spe], invert = TRUE), ]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
55
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
56 if (sepa) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
57 colvar <- colnames(data)[var]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
58 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
59
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
60 # Data for species
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
61 data_num <- make_table_analyse(data, colabund, colspe, colloc, coldate)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
62 nb_spe <- length(unique(data[, spe]))
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
63 nb_col <- ncol(data_num) - nb_spe + 1
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
64
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
65 #Data with coordinates and environmental
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
66 if (map) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
67 data_xy <- data_num[, c(collat, collong)]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
68 colnames(data_xy) <- c("latitude", "longitude")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
69 # Data for environment
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
70 data_env <- data_num[, c(colloc, collat, collong)]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
71 colnames(data_env) <- c("site", "latitude", "longitude")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
72 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
73
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
74 # Data with only species and their abundance
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
75 data_spe <- data_num[, nb_col:ncol(data_num)]
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
76 rownames(data_spe) <- paste0(data_num[, colloc], " - ", data_num[, coldate])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
77
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
78 #####Your analysis
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
79
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
80 # Computation beta.div {adespatial}
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
81 # Beta.div on Hellinger-transformed species data
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
82 data_beta <- adespatial::beta.div(data_spe, method = "hellinger", nperm = 9999)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
83
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
84 save(data_beta, file = "beta_diversity.Rdata")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
85 cat("##############################################################################",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
86 "\n########################### Beta Diversity Summary ###########################",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
87 "\n##############################################################################",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
88 "\n\n### All data ###",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
89 "\nBeta diversity: ", data_beta$beta[[2]],
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
90 "\nSum of Squares: ", data_beta$beta[[1]],
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
91 "\n\n### Vector of Local Contributions to Beta Diversity (LCBD) for the sites each date ###",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
92 "\n", capture.output(data_beta$LCBD),
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
93 "\n\n### Vector of P-values associated with the LCBD indices ###",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
94 "\n", capture.output(data_beta$p.LCBD),
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
95 "\n\n### Vector of Corrected P-values for the LCBD indices, Holm correction ###",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
96 "\n", capture.output(data_beta$p.adj),
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
97 "\n\n### Vector of Species contributions to beta diversity (SCBD) ###",
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
98 "\n", capture.output(data_beta$SCBD), file = "LCBD.txt", fill = 1, append = TRUE)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
99
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
100 # Which species have a SCBD larger than the mean SCBD?
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
101 scbd <- capture.output(data_beta$SCBD[data_beta$SCBD >= mean(data_beta$SCBD)])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
102 write(scbd, "SCBD.txt")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
103
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
104 ##1st fonction
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
105 beta_div_ext <- function(data_beta, data_xy, data_env) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
106 data_beta_ext <- data.frame(data_xy, data_env, LCBD = data_beta$LCBD * 100, p.LCBD = data_beta$p.LCBD, signif = data_beta$p.LCBD < 0.05)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
107
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
108 graph_beta_ext <- ggplot2::ggplot(data = data_beta_ext, ggplot2::aes(x = latitude, y = longitude, size = LCBD, col = signif)) +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
109 ggplot2::geom_point() +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
110 ggplot2::scale_colour_manual(values = c("#57bce0", "#ce0b0b"), labels = c("Non significant", "Significant"), name = "Significance at 0.05") +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
111 ggplot2::xlab("Longitude") + ggplot2::ylab("Latitude")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
112
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
113 ggplot2::ggsave("Beta_diversity_through_space.png", graph_beta_ext)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
114 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
115
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
116 ## Boyé et al. 2017 JSR Fig R
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
117 ####################################################
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
118
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
119 ####LCBD####
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
120 lcbd_site <- adespatial::beta.div(data_spe, "hellinger", nperm = 999)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
121
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
122 compute_lcbd <- function(data_beta, data_spe, data_num) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
123
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
124 #############
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
125 mat_lcbd_site <- data.frame(data_spe, LCBD = data_beta$LCBD * 100, p.LCBD = data_beta$p.LCBD, signif = data_beta$p.LCBD < 0.05, site = data_num[, colloc], date = data_num[, coldate])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
126
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
127 ## Map spatio-temp
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
128 ##################
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
129 p1 <- ggplot2::qplot(date, site, size = LCBD, col = signif, data = mat_lcbd_site)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
130 p1 <- p1 + ggplot2::scale_colour_manual(values = c("#57bce0", "#ce0b0b"), labels = c("Non significant", "Significant"), name = "Significance at 0.05")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
131 p1 <- p1 + ggplot2::theme_bw() + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90)) + ggplot2::xlab("Date") + ggplot2::ylab("Site")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
132
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
133 ggplot2::ggsave("LCBD_sites_time.png", p1)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
134
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
135
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
136 ## Par années
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
137 #############
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
138 mean_time <- tapply(mat_lcbd_site$LCBD, mat_lcbd_site$date, mean)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
139 sd_time <- tapply(mat_lcbd_site$LCBD, mat_lcbd_site$date, sd)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
140 date <- unique(mat_lcbd_site$date)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
141
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
142 data <- data.frame(date, mean_time, sd_time)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
143
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
144 time <- ggplot2::ggplot() + ggplot2::geom_pointrange(ggplot2::aes(x = date, y = mean_time, ymin = mean_time - sd_time, ymax = mean_time + sd_time), data = data)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
145 time <- time + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90), axis.line.y = ggplot2::element_line(size = 0.5)) + ggplot2::ylab("mean LCBD")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
146
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
147 ggplot2::ggsave("Mean_LCBD_through_time.png", time)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
148 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
149
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
150 ## Choose another graph
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
151 #######################
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
152 compute_lcbd2 <- function(data_beta, data_spe, data_num) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
153
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
154 #############
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
155 mat_lcbd_site <- data.frame(data_spe, LCBD = data_beta$LCBD * 100, p.LCBD = data_beta$p.LCBD, signif = data_beta$p.LCBD < 0.05, site = data_num[, colloc], date = data_num[, coldate], variable = data_num[, colvar])
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
156
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
157 p1 <- ggplot2::qplot(date, variable, size = LCBD, col = signif, data = mat_lcbd_site)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
158 p1 <- p1 + ggplot2::scale_colour_manual(values = c("#57bce0", "#ce0b0b"), labels = c("Non significant", "Significant"), name = "Significance at 0.05")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
159 p1 <- p1 + ggplot2::theme_bw() + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90)) + ggplot2::xlab("Date") + ggplot2::ylab(colvar)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
160
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
161 ggplot2::ggsave(paste0("LCBD_per_", colvar, "_through_time.png"), p1)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
162 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
163
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
164 ####SCBD###
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
165 # Function to compute SCBD
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
166 library(dplyr)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
167 make_scbd_uvc <- function(data_spe, z, data_beta) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
168 # Computation using beta.div {adespatial} on
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
169 # Hellinger-transformed species data
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
170
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
171 # Which species have a SCBD larger than the mean SCBD?
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
172 spe_scbd <- data_beta$SCBD[data_beta$SCBD >= mean(data_beta$SCBD)] %>%
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
173 as.data.frame() %>%
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
174 tibble::rownames_to_column(var = "Taxon") %>%
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
175 dplyr::mutate("Methode" = z)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
176
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
177 return(spe_scbd)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
178 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
179
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
180 # Function to make a radar plot
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
181
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
182 coord_radar <- function(theta = "x", start = 0, direction = 1) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
183 theta <- match.arg(theta, c("x", "y"))
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
184 r <- if (theta == "x") "y" else "x"
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
185 ggplot2::ggproto("CordRadar", ggplot2::coord_polar(theta = theta, start = start,
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
186 direction = sign(direction)),
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
187 is_linear = function(coord) TRUE)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
188 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
189
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
190 # Make the radar plot
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
191 radar_plot <- function(scbd_uvc_tc) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
192 uvc_rd_plot_data <- scbd_uvc_tc %>%
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
193 rename(scbd_score = ".")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
194
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
195 rad_uvc <- ggplot2::ggplot(uvc_rd_plot_data, ggplot2::aes(x = Taxon, y = scbd_score, group = Methode)) +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
196 ggplot2::geom_line() +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
197 ggplot2::geom_point(size = 3) +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
198 coord_radar() +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
199 ggplot2::theme_bw() +
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
200 ggplot2::theme(axis.text.x = ggplot2::element_text(size = 10),
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
201 legend.position = "bottom")
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
202
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
203 ggplot2::ggsave("SCBD_Species_Radar_plot.png", rad_uvc)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
204 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
205
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
206 ## LCBD
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
207
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
208 if (map) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
209 #Beta diversity
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
210 beta_div_ext(data_beta, data_xy, data_env)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
211 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
212
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
213 #Lcbd per places and time
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
214 compute_lcbd(data_beta, data_spe, data_num)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
215
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
216 #Lcbd of your choice
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
217 if (sepa) {
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
218 compute_lcbd2(data_beta, data_spe, data_num)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
219 }
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
220
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
221 ##SCBD
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
222
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
223 scbd_uvc_tc <- make_scbd_uvc(data_spe, z = "TC", data_beta)
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
224
9a2e0195bb43 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
parents:
diff changeset
225 radar_plot(scbd_uvc_tc)