Erick Matsen issues

Results 15 issues of


                                            Erick Matsen

Fix "Langeving" typo in sampling.rst

# Thank you for opening a PR! A few important guidelines and requirements before we can merge your PR: - [ ] *If I add a new sampler*, there is...

More elegant failure with faulty place files

When parsing a problematic place file, such as one produced in the presence of zero length branch lengths leading to `-nan` and `-inf` values, guppy does not fail especially beautifully,...

improve convexify documentation

https://matsengrp.slack.com/archives/D09UWH1EF/p1442330490000036

have `-help` spit out a link to online docs

Would be easy and nice!

easy

flesh out ADCL documentation and link to arxiv

have the informative branch length prior depend on edge position

add note about n_keep and n_pitches to FAQ

Re Sean Conlan's question

test out default values of parameters

Including: - --prior-lower

examples

We should put together a collection of "cookbook" example scripts so novices can get up to speed quickly. I have made an "examples" directory. In examples/SConstruct.drop_seq, I don't understand everything,...

Ability to count reversions

Our biologist collaborators hate seeing reversions in trees, and feel that they are a clear signal of a problem in the tree. @WSDeWitt correctly points out that under simple models,...