R/Spgc2BioGeoBEARS.R

In azizka/speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

Spgc2BioGeoBEARS <- function(x, phyl = NULL, file = NULL, true.areas = TRUE, true.species = TRUE) {
    
    # reformat input
    dat <- x$spec_table
    dat <- data.frame(dat[!names(dat) == "not_classified"])
    
    # set occurrences to logical
    dat[dat >= 1] <- 1
    
    # check for redundant areas
    if (true.areas) {
        if (sum(colSums(dat) == 0) > 0) {
            warning(sprintf("%s areas with zeros species removed", sum(!colSums(dat) > 
                0)))
        }
        
        dat <- data.frame(dat[, colSums(dat) > 0])
    }
    
    # check for redundant species
    if (true.species) {
        if (sum(rowSums(dat) == 0) > 0) {
            warning(sprintf("%s species with zeros occurrences removed", sum(!rowSums(dat) > 
                0)))
        }
        
        dat <- data.frame(dat[rowSums(dat) > 0, ])
    }
    
    # treat phylogeny if provided
    if (!is.null(phyl)) {
        tr <- phyl
        data <- geiger::treedata(tr, dat, warnings = FALSE)
        tr <- data$phy
        dat <- data$data
        ape::write.tree(tr, file = paste(file, ".tre", sep = ""))
    }
    
    # prepare output files
    length_dat <- length(dat[, 1])
    if (length(dat[1, ]) > 26) {
        stop(sprintf("%s areas; More than 26 exceed function limits", length(dat[1, 
            ])))
    }
    letters_data <- paste("(", paste(letters[1:length(dat[1, ])], collapse = " "), 
        ")", sep = "")
    command_string <- paste(length_dat, length(dat[1, ]), letters_data, sep = "\t")
    
    # write output file
    if (!is.null(file)) {
        write(command_string, file)
        write.table(dat, file = file, append = TRUE, quote = FALSE, sep = "", 
            col.names = FALSE, row.names = paste(rownames(dat), "\t"))
        
        names(dat) <- c(paste(letters[1:length(names(dat))], names(dat), sep = "_"))
    }
    # return(list(BioGeoBEARS_command = command_string, BioGeoBEARS_matrix =
    # dat))
}