| Previous changeset 0:5cde56683579 (2024-03-21) Next changeset 2:ace69a8ec1c3 (2024-10-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097 |
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modified:
GeoNearestNeighbor.xml brt.R test-data/Summary_of_taxa_model.tsv test-data/cnidaria_filtered.tsv |
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| diff -r 5cde56683579 -r 36637718c51d GeoNearestNeighbor.xml --- a/GeoNearestNeighbor.xml Thu Mar 21 14:05:01 2024 +0000 +++ b/GeoNearestNeighbor.xml Wed Sep 11 09:19:58 2024 +0000 |
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| @@ -132,4 +132,9 @@ | ... | ... | ... | ... | ... | ... | ... | ... | +----------+-----------+------------------------+-----------+---------+------+--------------+-----+ ]]></help> + <citations> + <citation type="doi">10.32614/RJ-2018-009</citation> + <citation type="doi">10.32614/CRAN.package.dplyr</citation> + <citation type="doi">10.32614/CRAN.package.sf</citation> + </citations> </tool> |
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| diff -r 5cde56683579 -r 36637718c51d brt.R --- a/brt.R Thu Mar 21 14:05:01 2024 +0000 +++ b/brt.R Wed Sep 11 09:19:58 2024 +0000 |
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| @@ -3,7 +3,7 @@ ### Clean environment rm(list = ls(all.names = TRUE)) -options(warn=-1) +options(warn=1) ### load packages @@ -43,7 +43,27 @@ #Load functions make.brt <- function(spe,data,pred.vars,env,nb_file){ - brt_step <- gbm.step(data= data, gbm.x = pred.vars, gbm.y = spe, family = "bernoulli", tree.complexity = 2, learning.rate = 0.0001,max.trees = 10000,plot.main = F) + cat(paste(" ", spe,":\n -> optimising BRT model ",sep="")) + lr <- 0.05 + no.trees <- 0 + while ( no.trees < 1000 & lr > 0.0005 ) { + cat(".") + 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)) + # if the gbm does not converge, the return object is null or of size 0 + if (!is.null(brt_step) ) { + if (object.size(brt_step) > 0 ) { + no.trees <- brt_step$gbm.call$best.trees + print(no.trees) + } + } else { + no.trees <- 0 + print(no.trees) + } + + # decrease the learning rate + lr <- lr / 2 + print(lr) + } #plot if (is.null(brt_step)==FALSE){ pdf(file = paste("BRT-",spe,".pdf")) @@ -94,27 +114,38 @@ #Write prediction in a file preds <- cbind(preds,spe) - write.table(preds, paste(nb_file,"_brts_pred_ceamarc.tsv",sep=""), quote=FALSE, dec=".", row.names=F, col.names=T,append = T,sep="\t") + 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") } #### RUN BRT #### nb_file = 0 +# Creating the %!in% operator +`%!in%` <- Negate(`%in%`) + +# Data file browsing for (file in data_files[[1]]) { + + # Reading the file species_data <- read.table(file, dec = dec_species, sep = "\t", header = TRUE, na.strings = "NA", colClasses = "numeric") nb_file = nb_file + 1 - `%!in%` <- Negate(`%in%`) + + # List to store species to predict sp = list() + + # Selection of columns that are not in 'env' and that are not coordinates or stations for (n in names(species_data)) { - if (n %!in% names(env) && n != 'station'){ - sp = cbind(sp,n) + if (n %!in% names(env) && n != 'station' && n != 'decimalLatitude' && n != 'decimalLongitude' && n!='lat' && n!='long'){ + sp = c(sp,n) } - } + } + # Making predictions for each species for (spe in sp){ try(make.prediction.brt(make.brt(spe,species_data,pred.vars,env,nb_file))) } } +#Display of abiotic parameters cat("Here is the list of your abiotic parameters:\n") cat(paste(pred.vars, collapse = ", "), "\n") |
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| diff -r 5cde56683579 -r 36637718c51d test-data/Summary_of_taxa_model.tsv --- a/test-data/Summary_of_taxa_model.tsv Thu Mar 21 14:05:01 2024 +0000 +++ b/test-data/Summary_of_taxa_model.tsv Wed Sep 11 09:19:58 2024 +0000 |
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| @@ -1,5 +1,4 @@ Taxa Model Occurences -Acanthogorgiidae No 0 Actiniaria Yes 50 Ainigmaptilon_edisto No 2 Alcyonacea No 43 |
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| diff -r 5cde56683579 -r 36637718c51d test-data/cnidaria_filtered.tsv --- a/test-data/cnidaria_filtered.tsv Thu Mar 21 14:05:01 2024 +0000 +++ b/test-data/cnidaria_filtered.tsv Wed Sep 11 09:19:58 2024 +0000 |
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| b'@@ -1,64 +1,64 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|