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PopGenReport (version 2.2.2)

A Simple Framework to Analyse Population Genetic Data

Description

Provides beginner friendly framework to analyse population genetic data. 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 www.popgenreport.org.

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Install

install.packages('PopGenReport')

Monthly Downloads

1,173

Version

2.2.2

License

GPL

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Repository

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

Maintainer

Bernd Gruber

Last Published

May 11th, 2016

Functions in PopGenReport (2.2.2)

Calculates the allelic richness for a genind object

Calculates pairwise fsts using a genind object (very fast)

Multiple Matrix Regression with Randomization analysis

Function for optimising a landscape genetic analysis based on resistance layers

A simulated genind data set with spatial coordinates

Function to add a polygon to a landscape

Function to execute emigration on a pops object

Individual genetic distance calculation based on Kosman & Leonhard 2005

Function converts pops to a genind object

Partial Mantel tests on costdistance matrices

Function to calculate dispersal distances based on cost distances

Analysing population genetic data within a simple framework

Run forward step generations a popgen simulation

Least-cost path analysis based on a friction matrix

Function to add lines to landscape

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

Counts and visualises allele frequencies across loci and subpopulations

Spatial autocorrelation following Smouse and Pekall 1999

Initialise a pops object fo a a popgen simulation

Calculates cost distances for a given landscape (resistance matrix)

Function to execute mutation on a pop data.frame

a simulated friction map

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

Individual genetic distance calculation based on Smouse and Peakall 1999

Function to execute reproduction on a pop data.frame

Create a landscape genetic report

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.