PopGenReport - a simple way to analyse population genetic data using R

**** New Version 2.0 is now including landscape genetic analysis using surface resistance layers ****

**** New Version 2.1 adds pairwise matrix plots to landgenreport, NN must now be specified ****

This document serves as a quick guide for the installation of R and Latex(optional but recommended) to run PopGenReport successfully. For a more detailed description of the installation process and a tutorial how to do an analysis download the tutorial PopGenReportTutorial (pdf).

In a nutshell

The main strength of PopGenReport is to simplify a population genetic analysis. The aim is to make the power of R and its functions to analyse population genetic data available to many more researchers by providing a low-level entry. Hence we aimed for simplicity. A general workflow includes only two steps.

  1. load your data into R using various file formats (genepop, structure or a simple text or Excel csv file)
  2. use the function popgenreport to analyse your data [and create a nicely layouted pdf of your analysis (optional)]
  3. (optional) use the output which are in the form of maps, figures and tables for your final publication
  4. (optional) use the provided R code to sophisticate and customize your analysis

Installation

To install PopGenReport you can either install it

  1. Local install

  2. USB stick /local folder (currently Windows only)

Test the installation by typing the following lines into your R console:

require(PopGenReport)
data(bilby) #this loads some sample data
popgenreport(bilby) #if you installed LaTeX
popgenreport(bilby, mk.pdf=FALSE) #if you did not install LaTeX

You should get the following output (if you installed LaTeX):

There is no figures folder. I am trying to create it otherwise create it manually.
Compiling report...
- Generall summary...

Analysing data ...
Creating pdf from: PopGenReport.rnw ...
Finished.
Check PopGenReport.pdf for results.
Files are saved under: C:\DOCUME~1\user\LOCALS~1\Temp\RtmpcTcsaf
Figures are available in the figures subfolder
Results are stored under PopGenReport.results as an R object

and the following output if you did not install LaTeX:

Compiling report...
- Generall summary...

Analysing data ...
Files are saved under: C:\DOCUME~1\user\LOCALS~1\Temp\RtmpcTcsaf
Figures are available in the figures subfolder
Results are stored under PopGenReport.results as an R object

You can check your output files by accessing the specified folder.
For further information on how to load your data into R type ?read.genetable and on how to do an analysis type ?popgenreport

Tutorial for beginners

Tutorial on how to install the package and do a first analysis using popgenreport .

Tutorial on how to use the least-cost path modelling functions (landgenreport).

Or simply type browseVignettes("PopGenReport") to access the tutorial from within the package (be aware the landscape tutorial is currently only available from here).

Have fun analysing your data using PopGenReport.

Please be aware that PopGenReport is a work in progress and it is likely to contain bugs. Therefore please do not hesitate to contact us via bernd.gruber@canberra.edu.au or aaron.adamack@canberra.edu.au, if you encounter problems, have a comment and/or have a feature request.

Version history and known bugs

PopGenReport 2.1

PopGenReport 2.0

PopGenReport 1.6.5

PopGenReport 1.6.1

 

PopGenReport 1.6