check_pop_levels: Check the use of pop.levels, pop.labels and pop.select...

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Check the use of pop.levels, pop.labels and pop.select arguments.

Description

Check that pop.levels and pop.labels and pop.select arguments are used correctly and that the values are cleaned for spaces.

Usage

check_pop_levels(pop.levels = NULL, pop.labels = NULL, pop.select = NULL)

Arguments

pop.levels	(optional, string) This refers to the levels in a factor. In this case, the id of the pop. Use this argument to have the pop ordered your way instead of the default alphabetical or numerical order. e.g. pop.levels = c("QUE", "ONT", "ALB") instead of the default pop.levels = c("ALB", "ONT", "QUE"). White spaces in population names are replaced by underscore. Default: pop.levels = NULL.
pop.labels	(optional, string) Use this argument to rename/relabel your pop or combine your pop. e.g. To combine "QUE" and "ONT" into a new pop called "NEW": (1) First, define the levels for your pop with pop.levels argument: pop.levels = c("QUE", "ONT", "ALB"). (2) then, use pop.labels argument: pop.labels = c("NEW", "NEW", "ALB"). To rename "QUE" to "TAS": pop.labels = c("TAS", "ONT", "ALB"). Default: pop.labels = NULL. If you find this too complicated, there is also the strata argument that can do the same thing, see below. White spaces in population names are replaced by underscore.
pop.select	(optional, string) Selected list of populations for the analysis. e.g. pop.select = c("QUE", "ONT") to select QUE and ONT population samples (out of 20 pops). Default: pop.select = NULL

Author(s)

Thierry Gosselin [e-mail]

thierrygosselin/radiator documentation built on April 25, 2024, 3:20 a.m.