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PopGenReport (version 2.0)

PopGen: A simple way to analyse and visualize population genetic data

Description

This package provides an easy way to analyse population genetic data

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Version

Install

install.packages('PopGenReport')

Monthly Downloads

1,484

Version

2.0

License

GPL

Maintainer

Bernd Gruber

Last Published

July 4th, 2014

Functions in PopGenReport (2.0)

allel.rich

Calculates the allelic richness for a genind object
gd.smouse

Individual genetic distance calculation based on Smouse and Peakall 1999
landgen

A simulated genind data set with spatial coordinates
fric.raster

a simulated friction map
bilby

Bilby data set
PopGen-package

Analysing population genetic data within a standardised framework
genleastcost

Least-cost path analysis based on a friction matrix
lgrMMRR

Multiple Matrix Regression with Randomization analysis
wassermann

Partial Mantel tests on costdistance matrices
spautocor

Spatial autocorrelation following Smouse and Pekall 1999
null.all

Checks for the presence of and determine the frequency of null alleles
landgenreport

Create a landscape genetic report
popgenreport

This is the main function of the package. It analyses an object of class genind and then creates a report containing the results of the analysis. There are several routines that can be optionally included in the analysis and there are multip output options including a PDF with the report, R-code and an object (fname.results) containing all of the results, which can be used for further analyses.
allele.dist

Counts and visualises allele frequencies across loci and subpopulations
gd.kosman

Individual genetic distance calculation based on Kosman & Leonhard 2005
read.genetable

Function to convert textfiles into a genind object (the format required for popgenreport)