check_info: Function to check randtip's files.

In iramosgutierrez/randtip: A generalized framework to expand incomplete phylogenies with taxonomic information

Function to check randtip's files.

Description

Function to account for the PUT status of the species in 'info', spelling errors, putative MDCCs and the phyletic nature of groups of PPCR species.

Usage

my.check <- check_info(info = my.info, tree = tree, sim = 0.85,
                   search.typos = TRUE, find.phyleticity = TRUE,
                   verbose = TRUE, parallelize = TRUE, ncores = 2 )

Arguments

info	An 'info' object.
tree	The original backbone tree.
sim	Name similarity threshold to detect possible misspellings on tip labels. Default value is 0.85. Similarity is obtained with stringsim function from stringdist package. See stringsim for details.
find.phyleticity	Logical. Should or not the phyletic nature o the taxonomic ranks be evaluated.
search.typos	Logical. Should or not the function search for possible misspelling on tip labels. This match lookup will be performed for all PUTs using all tree tips.
verbose	Logical. Should or not progress be printed.
parallelize	Logical. If TRUE it allows the function to look for phyletic status using multiple processing cores.
ncores	Number of cores to use in parallelization. If no number is provided it defaults to all but one of system logical cores.

Value

A data frame containing possible typographic errors, taxonomic ranks extracted from 'info' and the phyletic nature of each of them.

Author(s)

Ignacio Ramos-Gutierrez, Rafael Molina-Venegas, Herlander Lima

Examples

catspecies <- c("Lynx_lynx", "Panthera_uncia",
"Panthera_onca", "Felis_catus", "Puma_concolor",
"Lynx_canadensis", "Panthera_tigris", "Panthera_leo",
"Felis_silvestris")

cats.info <- build_info(species=catspecies, tree= cats,
     find.ranks=TRUE, db="ncbi", mode="backbone")

cats.checked <- check_info(info=cats.info, tree=cats, sim=0.75, parallelize = FALSE)

iramosgutierrez/randtip documentation built on March 19, 2024, 6:35 p.m.