cleansp {divDyn} | R Documentation

## Cleanse Species Name Vector

### Description

This function will take a vector of binomial names with various qualifiers of open nomenclatures, and removes them form the vector entries. Only the the genus and species names will remain.

### Usage

    cleansp(x, debug = FALSE, collapse = "_", subgenera = FALSE,
      misspells = TRUE, stems = TRUE)

### Arguments

`x` | `(character)`: the vector containing species names with qualifiers of open taxonomy.
`debug` | `(logical)`: `FALSE` will return the cleaned species name vector, `TRUE` returns a data table that allows one by one checking.
`collapse` | `(character)`: This argument will be passed to the paste function's argument of the same name. The character value to be inserted between the genus and species names.
`subgenera` | `(logical)`: `FALSE` omits subgenus information (in parentheses) and will construct a unique binomen based on the genus and species names alone. `TRUE` will promote the subgenus names and it will create a new binomen based on the subgenus rather than the genus name.
`misspells` | `logical`: Resolution of common spelling mistakes, such as diphtongs and alternate spellings: 'ue' is replaced with 'u', 'ae' is replaced with 'e', 'll' with 'l', 'ss' with 's'and 'y' with 'i'.
`stems` | `(logical)`: Setting this to `TRUE` will omit the adjective declination suffices from the species names.

### Details

This version will not keep subgenera, and will assign species to the base genus. The following qualifiers will be omitted: "n.", "sp.", "?", "gen.", "aff.", "cf.", "ex gr.", "subgen.", "spp" and informal species designated with letters. Entries with "informal" and "indet." in them will also be invalidated.

Functions called by the `misspells` and `stems` arguments were written by Gwen Antell.

### Examples

    examp <- c("Genus cf. species", "Genus spp.", "Family indet.",
      "Mygenus yourspecies", "Okgenus ? questionsp",
      "Genus (cf. Subgenus) aff. species")
    cleansp(examp)

[Package divDyn version 0.8.0 Index]