pr2_taxo_check: Check taxonomy

In vaulot/dvutils: A set of utilities

Description

This check the taxonomy for the following conditions:

• No taxon has 2 different parents

• Not taxon appears at different ranks

Usage

pr2_taxo_check(pr2_taxo, taxo_levels = pr2.env$taxo_levels, dir_taxo = "")

Arguments

pr2_taxo	dataframe - should contain eight or nine columns kingdom -> species or domain -> species
taxo_levels	vector with taxo levels
dir_taxo	character - full path where file are saved (without final //)

Value

Write several files (see description)

Note

The input data frame does not need to be the whole pr2 taxo, can be taxo extracted from an Excel file. Several files are produced:

• taxo_list_(rank_number)_(rank_name).txt (7 files)

  • name of each taxon

  • taxa_number - number of species in this taxon

  • level of taxon - from 1 to 8 (1 for kingdom or domain)

  • id of the parent taxon (at rank i-1)

  • id of the taxon (from 1 to n for each rank)

• taxo_list_2_parents_(rank_number)_(rank_name).txt (7 files). This is an important file because it list all the taxa that have 2 parents. When all the files are completely empty, then the taxonomic list is OK.

  • name of the taxon

  • number of parents

• taxo_level_duplicates.txt. List the taxa that are found at different ranks. Fro example Cryptophyta can be in the Class column for one species and in the Division levels for all other species.

  • name

  • number of times found

  • taxa number

  • level at which found

  • id

  • id of the parent

• taxo_species_duplicates. List of species that appear at least twice in the species list.

Examples

pr2_taxo_check (taxo_list, "C:/Daniel/database")

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.