# A Simple Framework to Analyse Population and Landscape Genetic Data

## Documentation for package ‘PopGenReport’ version 3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

addline | Function to add lines to landscape
addpoly | Function to add a polygon to a landscape
allel.rich | Calculates the allelic richness for a genind object
allele.dist | Counts and visualises allele frequencies across loci and subpopulations
bilby | Bilby data set
costdistances | Calculates cost distances for a given landscape (resistance matrix)
emigration | Function to execute emigration on a pops object
gd.kosman | Individual genetic distance calculation based on Kosman & Leonhard 2005
gd.smouse | Individual genetic distance calculation based on Smouse and Peakall 1999
genleastcost | Least-cost path analysis based on a friction matrix
init.popgensim | Initialise a spatial meta-population for a popgen simulation
landgen | A simulated genind data set with spatial coordinates
landgenreport | Create a landscape genetic report
lgrMMRR | Multiple Matrix Regression with Randomization analysis
mutation | Function to execute mutation on a pop data.frame
null.all | Checks for the presence of and determine the frequency of null alleles
opt.landgen | Function for optimising a landscape genetic analysis based on resistance layers
p2p | Function to calculate dispersal distances based on cost distances
pairwise.fstb | Calculates pairwise fsts using a genind object (very fast)
pairwise.propShared | Calculates proportion of shared alleles per pairs of populations

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.

pops2genind | Function converts pops to a genind object
possums | A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]
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
spautocor | Spatial autocorrelation following Smouse and Pekall 1999
wassermann | Partial Mantel tests on costdistance matrices