Revision pass

[trvrb]

@evogytis ---

This is a full pass except for Methods, which I'll attend to on Monday. Some notes:

• I changed "whilst" to "while" throughout. This was based on "whilst" sounding archaic to my ear and a brief Google shows that UK style guides are preferring "while" to "whilst".
• Include other examples besides Ebola here: https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R124
• "Population structure models" meant very little to me as a term, so I threw in a reference to the "structured coalescent" in the introduction: https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R136
• I thought it was important to report the differences in effective population size between humans and camels as this is what helps to power the model: https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R151.
• There were too many unnecessary details about the Monte Carlo method in Results. I went through a stripped out things I thought should be reserved for Methods (like omega): https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R209
• You should do model averaging to get a single range for R0 and introduction count across bias values: https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R224. This can be done by constructing a new sample with 10% of its values drawn from the bias=1 category, 45% of its values from the bias=2 category and 45% of its values from the bias=3 category.
• I thought it was much more clear talking about "viruses" instead of "tips" when discussing recombination figure. I think of tips as belonging to a single tree, easier to think of viruses as belonging to two different trees: https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R312
• Provide a summary of overlap shown in Figure 4A: https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R274
• First couple sentences of Discussion were too broad, should focus on pathogen transmission: https://github.com/blab/structured-mers/compare/tb-pass?expand=1#diff-f2787150bef52ad29edeb9b46defee69R360 or somehow improve the general story.
• I spent some time also doing a full pass on references and cleaning up things like capitalization and journal abbreviations.
• I've left \tbc{XXX} notes where numbers need filling in.
• I've left \tbc comments showing in the text for things that I do think need attending to.

I've carved out a few of the remaining larger issues into separate threads not included in this PR. These are issues #6, #7, #8.

[trvrb]

Here's a diffed PDF to make it easier to quickly review what's changed: diff.pdf

[trvrb]

@evogytis: Please merge this is you're comfortable with it.