R/prepNHMData.R

In JCur96/sfe: Adds Useful Tools for Ecologists to the sf Package

#' Reads a .csv file and converts it to a filtered sf object (a data frame)
#'
#' \code{prepNHMData} Reads in old format geospatial data taking user input.
#' Terminal prompts ask for path to data and layer type, once entered
#' prepIUCNData is read in and reformated to 'sf' format. Spaces in the
#' \code{binomial} column are replaced with \code{_}
#'

#' @param x a csv file containing NHM records
#' @param indexToChange if the index you need to change is already known please
#' enter it here to save time. Including this mostly to make the vignette run
#' properly as it doesn't like terminal input. Default of \code{NULL} as in
#' most cases I would assume the index is unknown and this function works fine
#' outside of the vignette.
#' @return An object of class sf (a data frame) with a column renamed to
#' \code{binomial}, with binomial names underscorred, filtered to exclude NA
#' values.
#' @examples
#' data.frame <- prepNHMData()
#' 'please enter path'
#' path/to/your/data
#' 'please enter column index to rename'
#' YourIndexHere
#'
#' @export
prepNHMData <- function(x, indexToChange = NULL) {
  suppressMessages(library(dplyr))
  #print(colnames(x))
  if (is.null(indexToChange)) {
    colToChange <- readline(prompt = 'please enter column index to rename to binomial: ')
    colToChange <- as.numeric(colToChange)
    colnames(x)[colToChange] <- 'binomial'
  } else{
    colToChange <- as.numeric(indexToChange)
    colnames(x)[colToChange] <- 'binomial'
  }
  # colToChange <- readline(prompt = 'please enter column index to rename to Locality: ')
  # colToChange <- as.numeric(colToChange)
  # colnames(x)[colToChange] <- 'Locality'
  x <- x %>%
    filter(Longitude != is.na(Longitude)
           & Latitude !=is.na(Latitude) & Locality !='' & binomial != '')
  x$binomial <- gsub(' ', '_', x$binomial)
  x <- st_as_sf(x, coords = c("Longitude", "Latitude"), crs = 4326)
  return(x)
  # dfName <- readline(prompt = 'please enter your df name: ')
  # assign(dfName,df,envir=.GlobalEnv)
}