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PopGenReport (version 3.1)

A Simple Framework to Analyse Population and Landscape Genetic Data

Description

Provides beginner friendly framework to analyse population genetic data. Based on 'adegenet' objects it uses 'knitr' to create comprehensive reports on spatial genetic data. For detailed information how to use the package refer to the comprehensive tutorials or visit .

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Version

Install

install.packages('PopGenReport')

Monthly Downloads

1,312

Version

3.1

License

GPL

Issues

7

Pull Requests

0

Stars

5

Forks

5

Maintainer

Bernd Gruber

Last Published

October 11th, 2023

Functions in PopGenReport (3.1)

mutation

Function to execute mutation on a pop data.frame
pairwise.propShared

Calculates proportion of shared alleles per pairs of populations
null.all

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

Create a landscape genetic report
pairwise.fstb

Calculates pairwise fsts using a genind object (very fast)
lgrMMRR

Multiple Matrix Regression with Randomization analysis
init.popgensim

Initialise a spatial meta-population for a popgen simulation
landgen

A simulated genind data set with spatial coordinates
p2p

Function to calculate dispersal distances based on cost distances
opt.landgen

Function for optimising a landscape genetic analysis based on resistance layers
spautocor

Spatial autocorrelation following Smouse and Pekall 1999
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 multiple 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.
read.genetable

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

Function to execute reproduction on a pop data.frame
run.popgensim

Run a time-forward popgen simulation
possums

A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]
pops2genind

Function converts pops to a genind object
wassermann

Partial Mantel tests on costdistance matrices
bilby

Bilby data set
emigration

Function to execute emigration on a pops object
costdistances

Calculates cost distances for a given landscape (resistance matrix)
gd.smouse

Individual genetic distance calculation based on Smouse and Peakall 1999
allel.rich

Calculates the allelic richness for a genind object
allele.dist

Counts and visualises allele frequencies across loci and subpopulations
addline

Function to add lines to landscape
addpoly

Function to add a polygon to a landscape
gd.kosman

Individual genetic distance calculation based on Kosman & Leonhard 2005
genleastcost

Least-cost path analysis based on a friction matrix