keepTaxon: Keep Items (Taxa, Populations, Samples, Morphological...

In MorphoTools2: Multivariate Morphometric Analysis

Keep Items (Taxa, Populations, Samples, Morphological Characters) in an Morphodata Object (and Remove Others)

Description

These functions keep only selected taxa, populations, samples or morphological characters in morphodata object. The samples can be kept by names using sampleName argument, or by the threshold. Each sample holding less or equal portion of missing data than the desired threshold (missingPercentage) will be kept. Only one parameter can be specified in one run.

Usage

keepTaxon(object, taxonName)

keepPopulation(object, populationName)

keepSample(object, sampleName = NULL, missingPercentage = NA)

keepCharacter(object, characterName)

Arguments

object	an object of class morphodata.
taxonName	vector of taxa to be kept.
populationName	vector of populations to be kept.
sampleName	vector of samples to be kept.
missingPercentage	a numeric, samples holding less or equal portion of missing data than specified by missingPercentage will be kept.
characterName	vector of characters to be kept.

Value

an object of class morphodata with the following elements:

ID	IDs of each row of data object.
Population	population membership of each row of data object.
Taxon	taxon membership of each row of data object.
data	data.frame of individuals (rows) and values of measured morphological characters (columns).

Examples

data(centaurea)

centaurea.hybr = keepTaxon(centaurea, "hybr")
centaurea.PhHybr = keepTaxon(centaurea, c("ph", "hybr"))

centaurea.PREL = keepPopulation(centaurea, "PREL")

centaurea.NA_0.1 = keepSample(centaurea, missingPercentage = 0.1)

centaurea.stem = keepCharacter(centaurea, c("SN", "SF", "ST"))

MorphoTools2 documentation built on Oct. 2, 2024, 5:07 p.m.