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PopGenReport (version 3.0.0)

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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Install

install.packages('PopGenReport')

Monthly Downloads

1,173

Version

3.0.0

License

GPL

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Repository

https://github.com/green-striped-gecko/PopGenReport

Maintainer

Bernd Gruber

Last Published

February 1st, 2017

Functions in PopGenReport (3.0.0)

Calculates cost distances for a given landscape (resistance matrix)

Least-cost path analysis based on a friction matrix

Individual genetic distance calculation based on Kosman & Leonhard 2005

Function to add a polygon to a landscape

Function to add lines to landscape

Function to execute emigration on a pops object

Counts and visualises allele frequencies across loci and subpopulations

Calculates the allelic richness for a genind object

Individual genetic distance calculation based on Smouse and Peakall 1999

Create a landscape genetic report

Multiple Matrix Regression with Randomization analysis

Calculates pairwise fsts using a genind object (very fast)

Initialise a spatial meta-population for a popgen simulation

pairwise.propShared

Calculates proportion of shared alleles per pairs of populations

A simulated genind data set with spatial coordinates

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

Function to execute mutation on a pop data.frame

Function to calculate dispersal distances based on cost distances

Function for optimising a landscape genetic analysis based on resistance layers

Function converts pops to a genind object

Spatial autocorrelation following Smouse and Pekall 1999

A raster file [proportion of treeScrub per cell in Hawke Bay, NZ]

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

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

Partial Mantel tests on costdistance matrices

Function to execute reproduction on a pop data.frame

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.

Run a time-forward popgen simulation