COR_detaDd: Function to calculate pairwise detaD and correlation between...

In xinghuq/HierDpart: Partitioning Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

Function to calculate pairwise detaD and correlation between genetic differentiation (deta D) and geographic distance

Description

This function calculates new pairwise genetic differentication, deta D (Oscar E, et al, 2018), as well as the correlation between genetic differentiation (deta D) and geographic distance.

Usage

COR_detaDd(f, d, ncode)

Arguments

f	A genetic data files, the format is genepop format.
d	Pairwise geographic distance for calculating correlations. If no actual geographic distance, d=FALSE. If TRUE, the geographic distance should be a matrix that corresponds to the pairwise genetic differentiation matrix.
ncode	The coding type of your genetic data

Details

This function returns to lists of pairwise deta D matrix, and a matrix of theorical geographical distance if d is FALSE, as well as their correlation coefficient.

Value

PairwiseDetaD	The pairwise genetic differentiation-detaD matrix.
Dgeo	The pairwise geographical distance matrix.
CordetaDd	Person correlation coefficient between genetic differentiation (deta D) and geographic distance.

Author(s)

[e-mail]

References

Gaggiotti, O. E., Chao, A., Peres-Neto, P., Chiu, C. H., Edwards, C., Fortin, M. J., ... & Selkoe, K. A. (2018). Diversity from genes to ecosystems: A unifying framework to study variation across biological metrics and scales. Evolutionary Applications.

See Also

COR_Fst

Examples

infile <- system.file('extdata', 'Island.gen',package='HierDpart')
locinfile <- 'Island.gen' ## file in user's directory not in R's extdata directory
check <- file.copy(infile,locinfile,overwrite=TRUE)
d1=COR_detaDd(infile,d=FALSE,ncode=3)
print(d1)

xinghuq/HierDpart documentation built on March 21, 2023, 6:43 p.m.