R/GetSpNames.R

In TrashBirdEcology/bbsRDM: Calculate regime detection metrics using bird communities

# Read in list of species names, from SpeciesList.txt, and then extract list of where the data is kept
#' @title Download species names
#' @description Read in list of species names, from SpeciesList.txt, and then extract list of where the data is kept
#' @param Dir ftp URL for directory with data files
#' @return A dataframe
#' @export GetSpNames
#'
GetSpNames <- function(Dir="ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/DataFiles/") {
  File <- paste0(Dir, "SpeciesList.txt")

  All <- scan(File, what="character", sep="\n", encoding="latin1")
  Delimiter <- grep("^-", All)

  ColNames <- strsplit(All[Delimiter-1], split='[[:blank:]]+')[[1]]
  Widths <- nchar(strsplit(All[Delimiter], split='[[:blank:]]+')[[1]])

  Lines <- sapply(All[-(1:Delimiter)], function(str, w) {
    trimws(substring(str, c(1,cumsum(w[-length(w)])), cumsum(w)))
  }, w=Widths+1)
  colnames(Lines) <- NULL
  rownames(Lines) <- ColNames

  Lines.df <- as.data.frame(t(Lines), stringsAsFactors = FALSE)
  Lines.df$Seq <- as.numeric(Lines.df$Seq)
  Lines.df$AOU <- as.numeric(Lines.df$AOU)
  names(Lines.df) <- c("seq", "aou", "commonName","frenchCommonName", "scientificName", "order", "family","genus", "species")

  Lines.df

 }