R/Subsetselection.R

In MaxentVariableSelection: Selecting the Best Set of Relevant Environmental Variables along with the Optimal Regularization Multiplier for Maxent Niche Modeling

Subsetselection <-
function(outdir){
    Resulttable <- read.csv(paste(outdir,"/maxentResults.csv",sep=""),sep=",",header=TRUE)
    # Select those columns where the column names contain the word "contribution"
    variable.contributions <- Resulttable[length(Resulttable[,1]),# This extracts the last (average) contributions
                                          (colnames(Resulttable) %in% grep("contribution",colnames(Resulttable),value=T))]
    # remove the '.contribution' tag from the result names
    colnames(variable.contributions) <- gsub(".contribution","",colnames(variable.contributions))
    # order the variable contributions so that the most influential variable is the first one
    variable.contributions <- variable.contributions[,order(variable.contributions,decreasing=TRUE)]
    return(variable.contributions)
    }