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FinePop (version 1.5.2)

Fine-Scale Population Analysis

Description

Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.

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Install

install.packages('FinePop')

Monthly Downloads

228

Version

1.5.2

License

GPL (>= 2.0)

Maintainer

Reiichiro Nakamichi

Last Published

March 15th, 2024

Functions in FinePop (1.5.2)

FinePop-package

tools:::Rd_package_title("FinePop")
DJ

Jost's D
FstBoot

Bootstrap sampler of Fst
GstNC

Nei and Chesser's Gst
FstEnv

Regression analysis of environmental factors on genetic differentiation
read.genepop

Create a genotype data object of populations from a GENEPOP format file.
GstN

Nei's Gst.
EBDJ

Empirical Bayes estimator of Jost's D
EBFST

Empirical Bayes estimator of Fst.
GstH

Hedrick's G'st
EBGstH

Empirical Bayes estimator of Hedrick's G'st
jsmackerel

An example dataset of Japanese Spanich mackerel in GENEPOP and frequency format.
clip.genepop

Remove designated markers from a GENEPOP file.
read.frequency

Create an allele (haplotype) frequency data object of populations from a frequency format file.
thetaWC.pair

Weir and Cockerham's theta adapted for pairwise Fst.
herring

An example dataset of Atlantic herring.