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annotate brt.R @ 0:52d4151e00d8 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
author ecology
date Wed, 28 May 2025 10:12:06 +0000
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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1 #16/02/2023
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2 ## Analyse BRT data
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3
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4 ### Clean environment
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5 rm(list = ls(all.names = TRUE))
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6 options(warn=1)
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7
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8 ### load packages
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9
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10 library(dismo, warn.conflicts = FALSE)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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11 library(gbm, warn.conflicts = FALSE)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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12 library(ggplot2, warn.conflicts = FALSE)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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13
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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15 #load arguments
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16 args = commandArgs(trailingOnly=TRUE)
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17 if (length(args)==0)
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18 {
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19 stop("This tool needs at least one argument")
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20 }else{
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21 enviro <- args[1]
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22 species_files <- args[2]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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23 abio_para <- args[3]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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24 dec_env <- ifelse(args[8]=="Dot", ".", ",")
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25 dec_species <- ifelse(args[9]=="Dot", ".", ",")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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26 }
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28 ### load data
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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29
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30 env = read.table(enviro, dec = dec_env, header = TRUE, sep="\t", na.strings = "-9999")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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31 pred_vars = strsplit(abio_para, ",")[[1]]
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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32 data_files = strsplit(species_files,",")
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33
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34 pred.vars <- character(length(pred_vars))
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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35
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36 for (i in seq_along(pred_vars)) {
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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37 pred_var_col <- as.numeric(pred_vars[i])
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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38 pred.vars[i] <- names(env)[pred_var_col]}
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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39
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40 #environemental parameters
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41 #Carbo,Grav,Maxbearing,Maxmagnit,Meancurmag,Meansal,Meantheta,Mud,Prof,Rugosity,Sand,Seaice_prod,Sili,Slope,Standcurmag,Standsal,Standtheta
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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42
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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43 #Load functions
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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44
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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45 make.brt <- function(spe,data,pred.vars,env,nb_file){
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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46 cat(paste(" ", spe,":\n -> optimising BRT model ",sep=""))
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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47 lr <- 0.05
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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48 no.trees <- 0
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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49 while ( no.trees < 1000 & lr > 0.0005 ) {
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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50 cat(".")
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51 try(brt_step <- gbm.step(data= data, gbm.x = pred.vars, gbm.y = spe, family = "bernoulli", tree.complexity = 2, learning.rate = lr,max.trees = 10000, plot.main = F))
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52 # if the gbm does not converge, the return object is null or of size 0
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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53 if (!is.null(brt_step) ) {
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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54 if (object.size(brt_step) > 0 ) {
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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55 no.trees <- brt_step$gbm.call$best.trees
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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56 print(no.trees)
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57 }
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58 } else {
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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59 no.trees <- 0
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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60 print(no.trees)
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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61 }
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62
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63 # decrease the learning rate
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64 lr <- lr / 2
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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65 print(lr)
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66 }
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67 #plot
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68 if (is.null(brt_step)==FALSE){
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69 pdf(file = paste("BRT-",spe,".pdf"))
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70 gbm.plot(brt_step, write.title = T,show.contrib = T, y.label = "fitted function",plot.layout = c(3,3))
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71 dev.off()
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72 #total deviance explained as (Leathwick et al., 2006)
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73 total_deviance <- brt_step$self.statistics$mean.null
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74 cross_validated_residual_deviance <- brt_step$cv.statistics$deviance.mean
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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75 total_deviance_explained <- (total_deviance - cross_validated_residual_deviance)/total_deviance
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76 #Validation file
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77 valid = cbind(spe,brt_step$cv.statistics$discrimination.mean,brt_step$gbm.call$tree.complexity,total_deviance_explained)
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78 write.table(valid, paste(nb_file,"_brts_validation_ceamarc.tsv",sep=""), quote=FALSE, dec=".",sep="\t" ,row.names=F, col.names=F,append = T)}
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79
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80 return(brt_step)
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81 }
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82
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83 make.prediction.brt <- function(brt_step){
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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84 #predictions
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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85 preds <- predict.gbm(brt_step,env,n.trees=brt_step$gbm.call$best.trees, type="response")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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86 preds <- as.data.frame(cbind(env$lat,env$long,preds))
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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87 colnames(preds) <- c("lat","long","Prediction.index")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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88 #carto
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89 ggplot()+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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90 geom_raster(data = preds , aes(x = long, y = lat, fill = Prediction.index))+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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91 geom_raster(data = preds , aes(x = long, y = lat, alpha = Prediction.index))+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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92 scale_alpha(range = c(0,1), guide = "none")+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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93 scale_fill_viridis_c(
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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94 alpha = 1,
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95 begin = 0,
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96 end = 1,
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97 direction = -1,
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98 option = "D",
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99 values = NULL,
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100 space = "Lab",
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101 na.value = "grey50",
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102 guide = "colourbar",
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103 aesthetics = "fill")+
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104 xlab("Longitude") + ylab("Latitude")+ ggtitle(paste(spe,"Plot of BRT predictions"))+
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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105 theme(plot.title = element_text(size = 10))+
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106 theme(axis.title.y = element_text(size = 10))+
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107 theme(axis.title.x = element_text(size = 10))+
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108 theme(axis.text.y = element_text(size = 10))+
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109 theme(axis.text.x = element_text(size = 10))+
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110 theme(legend.text = element_text(size = 10))+
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111 theme(legend.title = element_text(size = 10))+
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112 coord_quickmap()
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113 output_directory <- ggsave(paste("BRT-",spe,"_pred_plot.png"))
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114
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115 #Write prediction in a file
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116 preds <- cbind(preds,spe)
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117 write.table(preds, paste(nb_file,"_brts_pred_ceamarc.tsv",sep=""), quote=FALSE, dec=".", row.names=F, col.names=!file.exists(paste(nb_file,"_brts_pred_ceamarc.tsv",sep="")),append = T,sep="\t")
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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118 }
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119
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120 #### RUN BRT ####
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121 nb_file = 0
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122
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123 # Creating the %!in% operator
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124 `%!in%` <- Negate(`%in%`)
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125
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126 # Data file browsing
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127 for (file in data_files[[1]]) {
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128
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129 # Reading the file
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130 species_data <- read.table(file, dec = dec_species, sep = "\t", header = TRUE, na.strings = "NA", colClasses = "numeric")
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131 nb_file = nb_file + 1
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132
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133 # List to store species to predict
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134 sp = list()
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135
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136 # Selection of columns that are not in 'env' and that are not coordinates or stations
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137 for (n in names(species_data)) {
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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138 if (n %!in% names(env) && n != 'station' && n != 'decimalLatitude' && n != 'decimalLongitude' && n!='lat' && n!='long'){
52d4151e00d8 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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139 sp = c(sp,n)
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140 }
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141 }
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142 # Making predictions for each species
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143 for (spe in sp){
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144 try(make.prediction.brt(make.brt(spe,species_data,pred.vars,env,nb_file)))
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145 }
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146 }
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147
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148 #Display of abiotic parameters
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149 cat("Here is the list of your abiotic parameters:\n")
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150 cat(paste(pred.vars, collapse = ", "), "\n")
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151
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152