Nothing
WriteOut <- function(x, writetype = c("all", "BioGeoBEARS", "coexistence", "graphs",
"maps", "nexus", "statistics"), areanames = NULL) {
match.arg(writetype)
if (class(x) == "list") {
if (length(areanames) == 0) {
areanam <- x[[1]]$areanam
} else {
areanam <- areanames
}
if (writetype[1] == "all") {
.NexusOut(x)
for (i in 1:length(x)) {
.WriteTablesSpGeo(x[[i]], prefix = names(x)[i])
}
if (length(dim(x[[1]]$coexistence_classified)) == 0) {
warning("no coexistence matrix found")
} else {
for (i in 1:length(x)) {
.OutHeatCoEx(x[[i]], prefix = names(x)[i])
}
}
for (i in 1:length(x)) {
Spgc2BioGeoBEARS(x[[i]], file = paste(names(x)[i], "_BioGeoBEARS.txt",
sep = ""))
.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])
}
}
if (writetype[1] == "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])
}
}
if (writetype[1] == "maps") {
for (i in 1:length(x)) {
.OutMapAll(x[[i]], prefix = names(x)[i])
.OutMapPerSpecies(x[[i]], prefix = names(x)[i])
.OutMapPerPoly(x[[i]], areanames = areanames, prefix = names(x)[i])
}
}
if (writetype[1] == "statistics") {
for (i in 1:length(x)) {
.WriteTablesSpGeo(x[[i]], prefix = names(x)[i])
}
}
if (writetype[1] == "BioGeoBEARS") {
for (i in 1:length(x)) {
Spgc2BioGeoBEARS(x, file = paste(names(x)[i], "BioGeoBEARS.txt", sep = ""))
}
}
if (writetype[1] == "nexus") {
.NexusOut(x)
}
if (writetype[1] == "coexistence") {
if (length(dim(x[[1]]$coexistence_classified)) == 0) {
print("No coexistence matrix found")
} else {
for (i in 1:length(x)) {
.OutHeatCoEx(x[[i]], prefix = names(x)[i])
}
}
}
} else {
if (length(areanames) == 0) {
areanam <- x$areanam
} else {
areanam <- areanames
}
if (writetype[1] == "all") {
.NexusOut(x)
.WriteTablesSpGeo(x)
if (length(dim(x$coexistence_classified)) == 0) {
warning("No coexistence matrix found")
} else {
.OutHeatCoEx(x, prefix = "")
}
Spgc2BioGeoBEARS(x, file = "BioGeoBEARS.txt")
.OutPlotSpPoly(x, prefix = "")
.OutBarChartPoly(x, prefix = "")
.OutBarChartSpec(x, prefix = "")
.OutMapAll(x, prefix = "")
.OutMapPerSpecies(x, prefix = "")
.OutMapPerPoly(x, areanames = areanam, prefix = "")
}
if (writetype[1] == "graphs") {
.OutPlotSpPoly(x, prefix = "")
.OutBarChartPoly(x, prefix = "")
.OutBarChartSpec(x, prefix = "")
.OutMapAll(x, prefix = "")
.OutMapPerSpecies(x, prefix = "")
.OutMapPerPoly(x, areanames = areanam, prefix = "")
}
if (writetype[1] == "maps") {
.OutMapAll(x, prefix = "")
.OutMapPerSpecies(x, prefix = "")
.OutMapPerPoly(x, areanames = areanames, prefix = "")
}
if (writetype[1] == "statistics") {
.WriteTablesSpGeo(x)
}
if (writetype[1] == "nexus") {
.NexusOut(x)
}
if (writetype[1] == "BioGeoBEARS") {
Spgc2BioGeoBEARS(x, file = "BioGeoBEARS.txt")
}
if (writetype[1] == "coexistence") {
if (length(dim(x$coexistence_classified)) == 0) {
print("No coexistence matrix found")
} else {
.OutHeatCoEx(x, prefix = "")
}
}
}
}
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