anitato/popgen-notes

Population genetics notes

Population Genetics Notes

This is the latex source, images, and R code for the population genetics notes by Graham Coop. A fuller description of this resource is available at my website http://gcbias.org/population-genetics-notes/

Theses notes, code, and all of the figures are released under the Creative Commons Attribution 3.0 Unported License.So if you do reuse these you don’t need my permission, you just need to acknowledge where oyu got them from. My intention is that these notes can provide a resource for others to write their own versions of these notes.

There are still many typos in these notes, but I hope to fix them over time, and feel free to contact me or leave a comment here.

I hope to develop these notes into a fuller resource over the coming years, to create an up to date open source population genetics textbook.

Graham

Notes on Building the Site

You need latexmk and pandoc. Then use:

$ make clean site

.eps images will not work — be sure to convert all .eps files to .png and use the .png versions in LaTeX files.

$ find  . -name '*.eps' -type f | xargs -n1 -I{} basename {} .eps | xargs -n1 -I{} convert {}.eps {}.png

Then to deploy, use:

$ make deploy

This pushes html/ with git subtree, e.g. like

$ git subtree push --prefix html upstream gh-pages

For reference, this deploy.sh is used to deploy to the gh-pages branch. I've modified this version accordingly (e.g. works with BSD ls, by using -A instead of --almost-all)