geneticResampling {PAICE}

Simulate genetic sampling effort reduction

Description

A reduction of the resolution of the genealogy by supressing a variable position in the genealogy. It simulates a lower level of genetic sampling.

Usage

geneticResampling(data, network, position)

Arguments

data

a data frame containing the occurrence matrix of haplotypes in the islands of an archipelago (applicable to any island-like system). The two first columns indicate islands and populations sampled. Successive columns indicate haplotype occurrences (one column per haplotype). If present, missing haplotypes must also be included (i.e. columns without occurrences).

network

a data frame containing the genealogy of haplotypes. The first column indicates the haplotype, the second column indicates its ancestral haplotype and the third column indicates the variable position changed between an haplotype and its ancestral haplotype. If present, missing haplotypes must also be included. The ancestral haplotype must be connected to an outgroup named "OUT", located in the first row of the data frame, and has a variable position not shared with other connections.

position

numeric. Indicates the variable position that will be deleted in the simplified data.

Details

To simulate a lower level of genetic sampling, this function deletes a variable position from the original data and thus simplifies the genealogy. geneticResampling generates a new occurrence matrix of haplotypes and a new genealogy without the variable position previously indicated and merging ancestral and derived haplotypes separated by this variable position. If more than one connection are defined by the variable position indicated, this function deletes all connections with this variable position. This function works for both observed and missing haplotypes.

Value

geneticResampling returns a list containing the new occurrence matrix of haplotypes and the new genealogy after deleting the variable position indicated. The returned object contains the following components:

data

a data frame containing the new occurrence matrix of haplotypes after removing the variable position indicated.

network

a data frame containing the new genealogy after removing the variable position indicated.

Note

If the variable position corresponds to the connection between the ancestral haplotype in the archipelago and the outgroup (denoted as "OUT"), no change is effected as the ancestral haplotype stays connected to the outgroup.

This function works inside rarecol.

See Also

rarecol to build a rarefaction curve of colonization events.

Examples

data(CmonsData)
data(CmonsNetwork)
# Delete position 462 of Cistus monspeliensis data
newdata <- geneticResampling(CmonsData, CmonsNetwork, 462)
newdata$data # New presences matrix of haplotypes
newdata$network # New genealogy