markfreq.condense {mixstock} | R Documentation

## 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))

[Package mixstock version 0.9.2 Index]