markfreq.condense: condense marker frequency list

In bbolker/mixstock: Functions for Mixed Stock Analysis

condense marker frequency list

Description

"condenses" standard marker-frequency-list data (marker samples from sources and mixed stocks) by removing unrepresented markers, lumping markers where that removes no information, etc.

Usage

markfreq.condense(sourcesamp=NULL, mixsamp=NULL, debug=FALSE, exclude.nomix=FALSE)

Arguments

sourcesamp	Turtle data in standard form: list of sourcesamp (see below) and mixsamp OR matrix of source genotype samples (sources=columns, markers=rows)
mixsamp	Vector of mixed stock marker samples
debug	Print out debugging information?
exclude.nomix	Exclude markers not found in the mixed stock?

Details

Criteria:

• any marker found in the mixed stock but not in any of the sources is deleted from both: it provides no further information about the source contributions (although it does contribute to goodness-of-fit tests)

• any set of markers found in only one source (and possibly also in the mixed stock, although not necessarily) is lumped together

• "exclude.nomix" determines whether to exclude markers not found in the mixed stock

Value

"Standard" mixed stock analysis data set, suitably condensed.

sourcesamp	source samples
mixsamp	mixed stock samples
err	was there an error in attempting to lump?

Author(s)

Ben Bolker

Examples

data(lahanas98raw,package="mixstock")
lahan98c <- markfreq.condense(as.mixstock.data(lahanas98raw))

bbolker/mixstock documentation built on July 23, 2024, 12:18 p.m.