R/suggestNamesBio.R

In alexology/biomonitorweb:

#' @importFrom utils select.list
#' @importFrom hunspell dictionary hunspell_check hunspell_suggest

suggestNamesBio <- function( x , custom = F , group = group , ... ){

  # set the path of the dictionary. If group is mi or mf the dictionary is stored in the package path
  # while if group is set to custom the dictionary is created in the user directory.
  # the check of the names relies on the package hunspell
  if( custom == F ){
    if( group == "mi" ){
      dic.path <- system.file( "dict" , "mi_dictionary.txt", package = "biomonitorweb" )
      # very important to set cache equal to FALSE, otherwise suggestNames will provide inconsistent results.
      dictio <- dictionary( dic.path, cache = F )
    }
    if( group == "mf" ){
      dic.path <- system.file( "dict" , "mf_dictionary.txt" , package = "biomonitorweb" )
      dictio <- dictionary( dic.path , cache = F )
    }
    if( group == "fi" ){
      dic.path <- system.file( "dict" , "fi_dictionary.txt" , package = "biomonitorweb" )
      dictio <- dictionary( dic.path , cache = F )
    }
  }
  if( custom == T ){
    dic.path <- c( paste(getwd() , "/custom_dictio.dic" , sep = "" ) )
    dictio <- dictionary( dic.path , cache = F )
  }

  # get unique names present in the taxa list
  taxaCar <- unique( as.character( x ) )


  # replace space with underscore to be compatible with hunspell
  taxaCar <- gsub( " " , '_' , taxaCar )

  # nameCheck and nameSuggest check for the wrong names and suggest for correct names.
  # hunspell_check and hunspell_suggest are from the package hunspell
  nameCheck <- hunspell_check( taxaCar , dict = dictio )
  nameSuggest <- hunspell_suggest( taxaCar , dict = dictio )

  # This part of the function change the wrong names to correct
  # the user is provided with an interactive selection interface with select.list

  wrongName <- as.list( taxaCar ) # vector of wrong taxa names

  for( i in 1:length( nameSuggest ) ){
    nameSuggest[[ i ]] <- c( wrongName[[ i ]] , nameSuggest[[ i ]]  )
    nameSuggest[[i]] <- gsub("_", " ", unlist(nameSuggest[[i]]))
  }

  nameSuggest

}