#' Parse a data.frame imported from a SORTIE-ND OUT File.
#'
#' This function takes the data.frame generated by \code{\link{getOutFile}} and
#' reformats it so that Step, Subplot, and Species are the first 3 columns,
#' followed by values for Absolute Densities and Basal Areas. By default, this
#' function removes any columns labeled "NR" or "Total".
#' @param df The data.frame generated by \code{\link{getOutFile}}.
#' @param removeSpp Optional, already set to remove "NR" and "Total" columns
#' from reformatting, so you can deal with those separately or regenerate them
#' yourself.
#' @note This function cannot handle the relative density or basal areas
#' statistics provided by SORTIE-ND, possibly because "rel" or some form of it
#' is a protected word for the \code{\link{grep}} family of functions that I
#' use.
#' @examples
#' #dat <- getOutFile("test.out")
#' #head(parseOutFile(dat))
#' @export
parseOutFile <- function(df, removeSpp=c("Total")){
#return(df)
repeatcols <- df[, 1:2]
for(i in 1:length(removeSpp)){
df <- df[, -grep(removeSpp[i], colnames(df), value=F)]
}
SdlAbsDen <- changeColsBySpp(df, "Sdl.Abs.Den..")
SaplAbsDen <- changeColsBySpp(df, "Sapl.Abs.Den..")
AdultAbsDen <- changeColsBySpp(df, "Adult.Abs.Den..")
SaplAbsBA <- changeColsBySpp(df, "Sapl.Abs.BA..")
AdultAbsBA <- changeColsBySpp(df, "Adult.Abs.BA..")
newdf <- data.frame(Step=repeatcols[, 1],
Subplot=repeatcols[, 2],
Species=SdlAbsDen[,1],
SdlAbsDen=SdlAbsDen[,2],
SaplAbsDen=SaplAbsDen[,2],
AdultAbsDen=AdultAbsDen[,2],
SaplAbsBA=SaplAbsBA[,2],
AdultAbsBA=AdultAbsBA[,2]
)
return(newdf)
}
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