1) Markdown file is cleanly parsed for the README, Atom had eaten some of my code
2) If loci is called with a missing value which was not run during a sites run, instead of the previous error message, loci now just calls changeMissing, generates the necessary files, and continues on.
In this way, one can run sites with whatever m value they want (the default value, for instance), but if they wish to run loci for a different value, they can run it directly without having to explicitly call changeMissing.
This pull request has just a few extra tweaks:
1) Markdown file is cleanly parsed for the README, Atom had eaten some of my code
2) If loci is called with a missing value which was not run during a sites run, instead of the previous error message, loci now just calls changeMissing, generates the necessary files, and continues on.
In this way, one can run sites with whatever m value they want (the default value, for instance), but if they wish to run loci for a different value, they can run it directly without having to explicitly call changeMissing.