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#' Detect file format of taxon file
#' @description Detect file format of the total taxon list (molecular, morphological, and stratigraphic) and maximum age of fossil, see RevBayes total
#' -evidence fossil file for an example of this.
#' @param dataf A data frame with one column containing the taxon name of tips in phylogenetic tree. Optionally, a second column can indicate the maximum age of the tip. If the tip is extant, use 0.0 as the age. Can be CSV or TSV.
#' @return tax_frame Dataframe containing the total set of tips on the tree
#' @importFrom utils read.csv
#' @examples
#' \dontrun{tax_frame <- dataf_parsr(dataf)}
#' @export
dataf_parsr <- function(dataf) {
fileformat(dataf)
if (endsWith(dataf, ".tsv") == TRUE) {
message(".tsv file ending detected.")
df <- read.csv(file = dataf, sep = "\t")
} else if (endsWith(dataf, ".csv") == TRUE){
message(".csv file ending detected.")
df <- read.csv(file = dataf)
}
if (ncol(df) == 2){
names(df) <- c("taxon", "age")
tax_frame <- df
message("File processing complete.")
} else if (ncol(df) == 1) {
names(df) <- "taxon"
tax_frame <- df
message("File processing complete.")
} else {
stop("Dataframes should either one or two columns, minimally a taxon
column")
}
taxon_testr(tax_frame)
tax_frame <- as.data.frame(tax_frame)
return(tax_frame)
}
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