R/internals.R

In ppendemic: A Glimpse at the Diversity of Peru's Endemic Plants

# Function to clean species list names
#' @keywords internal

standardize_names <- function(splist) {
  fixed1 <- simple_cap(trimws(splist)) # all up
  fixed2 <- gsub("cf\\.", "", fixed1)
  fixed3 <- gsub("aff\\.", "", fixed2)
  fixed4 <- trimws(fixed3) # remove trailing and leading space
  fixed5 <- gsub("_", " ", fixed4) # change names separated by _ to space

  # Hybrids
  fixed6 <- gsub("(^x )|( x$)|( x )", " ", fixed5)
  hybrids <- fixed5 == fixed6
  if (!all(hybrids)) {
    sp_hybrids <- splist[!hybrids]
    warning(paste("The 'x' sign indicating hybrids have been removed in the",
                  "following names before search:",
                  paste(paste0("'", sp_hybrids, "'"), collapse = ", ")),
            immediate. = TRUE, call. = FALSE)
  }
  # Merge multiple spaces
  fixed7 <- gsub("(?<=[\\s])\\s*|^\\s+|\\s+$", "", fixed6, perl = TRUE)
  return(fixed7)
}

#' @keywords internal
simple_cap <- function(x) {
  # Split each string into words, remove unnecessary white spaces, and convert to lowercase
  words <- sapply(strsplit(x, "\\s+"), function(words) paste(tolower(words), collapse = " "))

  # Capitalize the first letter of each word
  capitalized <- sapply(strsplit(words, ""), function(word) {
    if (length(word) > 0) {
      word[1] <- toupper(word[1])
    }
    paste(word, collapse = "")
  })

  return(capitalized)
}