README.md

A bundle of functions we use in our daily routine here at the Ecology group (Department of biology, Biotechnical faculty, University of Ljubljana).

The package currently contains the following functions:

• readClumpp Read result of Clumpp into a data.frame.
• writeStructure Write a genind object to be analyzed using Structure.
• writeGenePop Write two genind objects to be analyzed using GENEPOP.
• writeGenPop Write a genind object to be analyzed using GENEPOP using strat/pop functionality. It can also write a list of genind objects as populations.
• subsetGenData Handle dropping levels in other slot.
• writeINEST Will write INEST file from a genind object.
• drawLoci Will draw alleles from a list of loci.
• findIntegerInterval Find a repeating sequence of integers.
• findSeason For a datum, find a season based on equinox/solstice.
• plotCircleOnMap Will plot circles on a map based for a given variable and its SE.
• Mratio Calculate Garza-Williamson M-ratio.
• genindSlidingWindow will take a genind object and create a list of smaller genind objects, subsetted on dates based on a sliding window.
• writeCoancestry Will write a file accepted by Coancestry software.
• goSlide A function in support of genindSlidingWindow to visualize years of cohorts (sliding windows).
• readColony Extract results from a Colony project. Useful for comparing matched genotypes from LC or LR runs.
• makeNGSfilter Based on a PCR plate template with tag-primer combination, name wells according to a layout file and account for the desired number of replicates.

Package installation

The easy way via devtools

To install the package using

library(devtools)
install_github("romunov/zvau")

you will need

• R
• Rtools (see http://cran.r-project.org/bin/windows/Rtools/) to build the package
• LaTeX (MiKTeX on Windows) to build documentation.

Via binary package

To install from a binary package, you can download the .zip file (may not be up to date!) by clicking Raw and saving it to a (known) location.

After you have a local copy, you can install the package from within R using

install.packages("zvau_*.zip", repos = NULL) # change filename according to the version