Variation of Effective population size¶
VarEff is a R package.
This package estimates the effective population sizes from actual (sampling date) to ancestral time with a coalescent approach.
It works on microsatellites data.
VarEff contains several function as TMRCA (Temporal Most Recent Ancestral) estimating the time of detected bottleneck.
Two manuals are available in the Documents tab (Manuals of VarEff):
- Detailed Manual (classical CRAN manual)
- Summary to start and to use VarEff (description of all steps to use VarEff)
VarEff was archived on CRAN.
The package VarEff can be download from "Files" menu bar on this website.
This VarEff file (.zip for dos or .tar for mac) can be install on R manually using "Packages -> Install package(s) from local zip files" from menu bar.
Please install the package "mcmc" before installing VarEff :
-Nikolic N, Chevalet C 2014. Detecting past changes of effective population size. Evolutionary Applications. DOI: 10.1111/eva.12170
-Chevalet C & Nikolic N. 2010. Distribution of coalescent times and distances between microsatellite alleles with changing effective population size. Theoretical Population Biology. Volume 77, Issue 3: 152-163