R/WriteOut.R

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

WriteOut <- function(x, type = "all") {
    
    if (!is.spgeoOUT(x)) {
        switch(type, all = {
            .NexusOut(x)
            for (i in 1:length(x)) {
                .WriteTablesSpGeo(x[[i]], prefix = names(x)[i])
                Spgc2BioGeoBEARS(x[[i]], file = paste(names(x)[i], "_BioGeoBEARS.txt", 
                  sep = ""))
                .OutBayArea(x[[i]], prefix = names(x)[i])
                .OutPlotSpPoly(x[[i]], prefix = names(x)[i])
                .OutBarChartPoly(x[[i]], prefix = names(x)[i])
                .OutBarChartSpec(x[[i]], prefix = names(x)[i])
                .OutMapAll(x[[i]], prefix = names(x)[i])
                .OutMapPerSpecies(x[[i]], prefix = names(x)[i])
                .OutMapPerPoly(x[[i]], prefix = names(x)[i])
            }
        }, graphs = {
            for (i in 1:length(x)) {
                .OutPlotSpPoly(x[[i]], prefix = names(x)[i])
                .OutBarChartPoly(x[[i]], prefix = names(x)[i])
                .OutBarChartSpec(x[[i]], prefix = names(x)[i])
            }
        }, maps = {
            for (i in 1:length(x)) {
                .OutMapAll(x[[i]], prefix = names(x)[i])
                .OutMapPerSpecies(x[[i]], prefix = names(x)[i])
                .OutMapPerPoly(x[[i]], prefix = names(x)[i])
            }
        }, stats = {
            for (i in 1:length(x)) {
                .WriteTablesSpGeo(x[[i]], prefix = names(x)[i])
            }
        }, BioGeoBEARS = {
            for (i in 1:length(x)) {
                Spgc2BioGeoBEARS(x, file = paste(names(x)[i], "_BioGeoBEARS.txt", 
                  sep = ""))
            }
        }, BayArea = .OutBayArea(x, prefix = names(x)[i]), nexus = {
            .NexusOut(x)
        })
    } else {
        switch(type, all = {
            .NexusOut(x)
            .WriteTablesSpGeo(x)
            suppressMessages(Spgc2BioGeoBEARS(x, file = "BioGeoBEARS.txt"))
            .OutBayArea(x, prefix = "")
            .OutPlotSpPoly(x, prefix = "")
            .OutBarChartPoly(x, prefix = "")
            .OutBarChartSpec(x, prefix = "")
            .OutMapAll(x, prefix = "")
            .OutMapPerSpecies(x, prefix = "")
            .OutMapPerPoly(x, prefix = "")
        }, graphs = {
            .OutPlotSpPoly(x, prefix = "")
            .OutBarChartPoly(x, prefix = "")
            .OutBarChartSpec(x, prefix = "")
        }, maps = {
            .OutMapAll(x, prefix = "")
            .OutMapPerSpecies(x, prefix = "")
            .OutMapPerPoly(x, prefix = "")
        }, stats = {
            .WriteTablesSpGeo(x)
        }, nexus = {
            .NexusOut(x)
        }, BioGeoBEARS = {
            Spgc2BioGeoBEARS(x, file = "BioGeoBEARS.txt")
        }, BayArea = .OutBayArea(x, prefix = ""))
    }
}