edits for AKs comments

[petrelharp]

Andy said:

1) In figure 3, the bottom left image of the intervals is a bit confusing. In particular its not clear why the nodes are at different points on the X axis.

2) Algorithm W. It would be helpful to state what P’_j is before going all the way through the algo. Also it seemed to us that the “if” statement at W5 should be it’s own line.

3) Figure 5. It was unclear to us where the red numbering of nodes after simplification came from. Is there a method behind the ordering that is important?

4) Figure 6 was really confusing. It took us a long while to work through and we still had questions. One thing that would help a lot— change the color of coalesced chromosome to something other than white. Also it took us a long time to figure out what was happening with the “side bars” showing the coalesced regions— this could be made more clear. Also I would label the spatial extents of the chromosomes shown such that the 0 end and the 1 end are shown. I also noted that we couldn’t in the end figure out why nodes D and E were colored as they were, but I can’t remember now what exactly the issue was.

5) Lastly it would be great if you guys could lay out in a bit more detail what would be needed by an outside simulation to hook up to the API. As I told Kevin last night, this is something I’m keen on, but after reading the preprint it wasn’t clear exactly what I needed to provide.

I've done something about everything except (4); not sure about (4) yet.

[petrelharp]

OK, I added some more words to the caption of (4). I do wonder if we're hand-holding too much by even providing Figure 6: really to understand one should do it themselves. I think these changes are all good with the possible exception of the new paragraph added for (5) - not sure if we want that one or not.

[jeromekelleher]

OK, I added some more words to the caption of (4). I do wonder if we're hand-holding too much by even providing Figure 6: really to understand one should do it themselves. I think these changes are all good with the possible exception of the new paragraph added for (5) - not sure if we want that one or not.

It looks good to me, bar a minor correction re sortedness. I'm also wondering whether the paint-pot figure is helping. On the one hand it gives a good visual overview of what's going on. On the other hand, it is a bit tricky to trace back what actually happened if you go though it in detail.

Perhaps a very simple (ie., minimal) example would be better? We don't have to use the same example as the previous figure. I don't have a strong opinion here, I'm just putting out suggestions if you feel like updating this @petrelharp. It's perfectly good as it is if you don't!

[petrelharp]

I've fixed the sorting thing (by removing it). And it's a good idea to put in a simpler example, but my vote is to see what the reviewers say.

[petrelharp]

Thanks @ashander - I updated in the most recent commit. (and added USFWS to funding)