Stdpopsim: Default 'flat' recombination maps

Created on 29 Nov 2019  路  5Comments  路  Source: popsim-consortium/stdpopsim

Most of the API/help for the recombination inputs say something like this (which I took from the CLI help)

  -g , --genetic-map    Specify a particular genetic map. If no genetic map is
                        specified use a flat map by default. Available maps:

A flat map is a uniform recombination rate, right? It's not clear where users can find out what this uniform rate is.

Subissue of #215 and #137

All 5 comments

We could say "By default, we use a chromosome-specific uniform recombination rate." The recombination rates for each chromosome are in the catalog and online docs.

"flat map" is not a good choice of terminology though, we should change it.

Okay, I'll do this.

What's the status of this @gtsambos?

Sorry, haven't gotten round to this yet. I can submit a mini pull request and change a few lines of wording later tonight so we can close this --

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