richelbilderbeek/pirouette_article issues and pull requests

#102 - Process point Giovanni

Issue - State: closed - Opened by richelbilderbeek over 4 years ago - 2 comments

#101 - Process feedback response letter Rampal

Issue - State: closed - Opened by richelbilderbeek over 4 years ago - 3 comments

#100 - Words "importance" and "error"

Issue - State: closed - Opened by Giappo over 4 years ago - 1 comment

#99 - FYI: Richel read this!

Issue - State: closed - Opened by Giappo over 4 years ago - 2 comments

#98 - sections 8.7 through 8.14 of the Supplementary materials need a description

Issue - State: closed - Opened by Giappo over 4 years ago - 6 comments

#97 - Process feedback article before June 29th

Issue - State: closed - Opened by richelbilderbeek over 4 years ago - 3 comments

#96 - Update

Pull Request - State: closed - Opened by richelbilderbeek almost 5 years ago

#95 - [SCRIPTING] 27: non-standard clock model (17 with replicates)

Issue - State: closed - Opened by richelbilderbeek almost 5 years ago - 1 comment

#94 - [RUNNING] 19: effect of halving DNA sequence length

Issue - State: closed - Opened by richelbilderbeek almost 5 years ago - 1 comment

#93 - 29: Check 'The effect of MCMC chain length'

Issue - State: closed - Opened by richelbilderbeek almost 5 years ago - 1 comment

#92 - Fix bug in `pir_to_pics`

Issue - State: closed - Opened by richelbilderbeek almost 5 years ago - 6 comments
Labels: medium priority

#91 - Cannot create evidence file in subsubsub folder

Issue - State: closed - Opened by richelbilderbeek almost 5 years ago - 2 comments
Labels: high priority

#90 - Updates from Overleaf

Pull Request - State: closed - Opened by richelbilderbeek about 5 years ago

#89 - [RUNNING] 28: Run a distribution of DD trees with same DD settings as exemplary one

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 8 comments
Labels: high priority

#88 - Make video how to run a pirouette example on Peregrine

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#87 - [RUNNING] 17: Interpret and improve subsection 'The effect of non-clock like models'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 3 comments

#86 - Correct capitalization of references

Issue - State: closed - Opened by richelbilderbeek about 5 years ago

#85 - More gently introduce the set of inference models we use

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 1 comment

#84 - Call a site model a site model

Issue - State: closed - Opened by richelbilderbeek about 5 years ago

#83 - Sort values in Table 1 alphabetically

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 6 comments

#82 - Add reference to TESS package

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 6 comments

#81 - Add reference to DDD package

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 5 comments

#80 - Describe nLTT statistic in main text

Issue - State: closed - Opened by richelbilderbeek about 5 years ago

#79 - Describe DD in main text

Issue - State: closed - Opened by richelbilderbeek about 5 years ago

#78 - Use nice DD tree in main text's example code

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 4 comments

#77 - Add literature to section 'Does error scale with tree size?' in Appendix

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 1 comment
Labels: depends

#76 - Plot tree in article nicely

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 13 comments

#75 - Pick one tree for our main example

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 18 comments

#74 - Shorten to application

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 1 comment

#73 - Add empiricists guidelines in the appendix

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 1 comment

#72 - Shorten main text to one example

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 1 comment

#71 - Updates from Overleaf

Pull Request - State: closed - Opened by richelbilderbeek about 5 years ago

#70 - Interpret and improve subsection 'The effect of mutation rate'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#69 - Interpret and improve subsection 'The effect of equal or equalized mutation rate in the twin' alignment'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#68 - Interpret and improve subsection 'The effect of differently common diversity-dependent trees'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 33 comments

#67 - Interpret and improve subsection 'The effect of assuming a Yule tree prior on a BD tree'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#66 - Interpret and improve subsection 'The effect of assuming a Yule tree prior on a Yule tree'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#65 - Interpret and improve subsection 'The effect of non-clock like models'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#64 - [RUNNING] 21: Interpret and improve subsection 'The effect of DNA sequence length'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#63 - [RUNNING] 20: Interpret and improve subsection 'The effect of the number of taxa'

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 3 comments
Labels: high priority

#62 - pirouette: add pir_plots

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 1 comment

#61 - Explore RPANDA::JSDtree

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 8 comments
Labels: depends

#60 - pirouette: add `pir_runs`

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 3 comments

#59 - Experiment: different mutation rates

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 4 comments

#58 - Experiment: DD with BD

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 6 comments

#57 - Experiment: Yule on Yule

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 3 comments

#56 - Experiment: alignment size

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 7 comments

#55 - Experiment: effect of number of taxa

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 3 comments

#54 - Write response letter

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 3 comments

#53 - Indeed an Application?

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 2 comments

#52 - Process feedback reviewers

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 2 comments

#51 - Publication on MEE: complete checklist

Issue - State: closed - Opened by Giappo over 5 years ago - 11 comments

#50 - Count words properly

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 1 comment

#49 - Pick different RNG seed

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 1 comment

#48 - Separate final plot

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 3 comments

#47 - Fix RQE 2 code

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 3 comments
Labels: medium priority

#46 - Process feedback Rampal #2

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 5 comments
Labels: high priority

#45 - Measure effect of alignment on twinning

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 2 comments

#44 - pirouette fails too often, due to mcbette

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 8 comments

#43 - Cite newer BEAST2 article?

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 1 comment

#42 - Implement feedback Rampal #1

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 2 comments
Labels: medium priority

#41 - Run example_3 in parallel

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 23 comments
Labels: medium priority

#40 - Fix create_test_pir_out

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 1 comment

#39 - Plot to 95% quantile

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 1 comment

#38 - Better pir_plot

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 3 comments

#37 - Better plotting on Peregrine

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 1 comment

#36 - pir_plot: show models names' abbreviations

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 1 comment

#35 - Review description

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago

#34 - Review introduction

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 1 comment

#33 - Review abstract

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 1 comment

#32 - pirouette_article: the choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

Issue - State: closed - Opened by richelbilderbeek almost 6 years ago - 2 comments

GitHub / richelbilderbeek/pirouette_article issues and pull requests