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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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3.1
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Install
install.packages('PopGenReport')
Monthly Downloads
1,624
Version
2.0
License
GPL
Maintainer
Bernd Gruber
Last Published
July 4th, 2014
Functions in PopGenReport (2.0)
Search functions
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)