Kevin Keenan's academic CV

A basic look at the differences in 95% CI calculated by bootstrapping across individuals vs loci, when calculating pairwise differentiation from genetic data

A documentation of the binning process for a suite of microsatellite loci in brown trout from Lough Neagh, Northern Ireland.

A notebook demonstrating how to bootstrap species density to estimate parameter error.

Visualising individual similarity coefficients in R.

A notebook documenting the simulations and analyses reported in Sundqvist et al. 2015. All code is reproducible, providing the instructions in the README file at https://github.com/kkeenan02/Sundqvist_et_al_2015 have been followed.

What is the fastest method for tabulating genotype counts in R

Using the divMigrate function from diveRsity (v1.9.5+) to test for significant directional differentiation

Convert large SNP matrices into genepop format files using the diveRsity package in R.

This document demonstrates the use of the polyIn function in the diveRsity package to rank loci of any ploidy on the basis of both their global informativeness for the inference of ancestry, and their consensus pairwise informativeness.

This document demonstrate how the divBasic function in the diveRsity package can be used in 'batch mode'.

highlighting an alleged postdoc scam

A demo of how the diveRsity function, divBasic can be used to test for differences in the levels of inbreeding between population pairs.

A description of how to access some of the output structure of the fastDivPart function from the diveRsity package, within R. Some plotting methods are also demonstrated.

This function will take an R markdown input file and write an R script to file. The R script contains all of the original R Markdown content which can be compiled to a Markdown HTML using knitr. The R script can be sourced to the console also.

Describes an amended version of the pmfSamplingDistYiN function, which allows the calculation of binomial coefficients for large integers.

A simplistic exploration of the effect of locus polymorphism on the clustering of individuals based on multilocus genotype data.

Describes two methods for running a BLAST (Basic Local Alignment Search Tool) search from R.

A tutorial for the divMigrate function in the diveRity R package

An outline of the programs used in Fung & Keenan 2013, originally written for Mathematica and converted to R.

An outline of the programs used in Fung & Keenan 2013, originally written for Mathematica and converted to R.