richelbilderbeek/razzo issues and pull requests

#401 - add coarsegrain to nltts

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

#400 - new info added in collect_all_data

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

#399 - Giovanni

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

#398 - kl

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

#397 - Create CODE_OF_CONDUCT.md

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

#396 - Giovanni

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

#395 - push on master YOLO

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

#394 - Send data again, so I can reproduce the figure

Issue - State: closed - Opened by Giappo about 5 years ago - 1 comment
Labels: high

#393 - Develop

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

#392 - Add pirouette example: the effect of MCMC chain length on ESS

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

#391 - Just do the full runs [RE-RUNNING FAILED RUNS]

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 15 comments
Labels: high

#390 - Why: longer chain length, lower ESS?

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

#389 - Modify 'razzo_project/scripts/99_zip.sh' to also zip 'parameters.RDa' files

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

#388 - Do https://github.com/richelbilderbeek/pirouette/issues/378

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

#387 - Giovanni

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

#386 - Develop

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

#385 - collect_esses must ignore ESSes of marginal likelihood estimations

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 10 comments

#384 - Fix pilot runs [MAYBE DONE]

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 9 comments
Labels: high

#383 - Use Jensen-Shannon divergence between true and twin tree?

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

#382 - Use babette from CRAN

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

#381 - Measure required time for strongest mbdness parsettings. 20200128

Issue - State: open - Opened by Giappo about 5 years ago - 11 comments

#380 - Need to redo the 'collect_' functions, as these may have given incorrect results

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

#379 - Add raztr repo

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

#378 - Regenerate data

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

#377 - Use tagged versions for razzo experiment

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

#376 - Evidence files must be created in the right folder

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

#375 - Regen example data

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

#374 - 'pirouette::est_evidences' should use filenames in MCMC

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

#373 - Check select_candidate_evidences

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

#372 - Put pirouette manuscript on BioRxiv

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

#371 - Get test run to work again

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 16 comments
Labels: high

#370 - Decide: DNA sequence length: 1000 or 5000?

Issue - State: closed - Opened by richelbilderbeek about 5 years ago - 4 comments
Labels: medium, decision

#369 - Gather info: Proportion invariant in DNA: 0.0, 0.5 or estimate?

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

#368 - Fix build, fix #366

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

#367 - Do a full run with the Giappo params, 20200126

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

#366 - Fix develop branch

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

#365 - Develop

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

#364 - Show detailed testthat log on Travis

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

#363 - Develop

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

#362 - Giovanni

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

#361 - Develop

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

#360 - Process feedback pirouette manuscript

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

#359 - Develop

Pull Request - State: closed - Opened by Giappo over 5 years ago

#358 - Vote for pirouette logo

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

#357 - Update beautier and beastier to provide for correct MCMC lengths

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

#356 - Develop

Pull Request - State: closed - Opened by Giappo over 5 years ago

#355 - Determine n_replicates for n_params_max

Issue - State: open - Opened by richelbilderbeek over 5 years ago - 4 comments

#354 - Add runtime to detailed overview

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

#353 - Give last info for presentation

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 8 comments

#352 - Check validity of our current conclusions

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

#351 - Multiple TODO's in a chronolocal order

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

#350 - Check pirouette MCMC chain length

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 19 comments
Labels: high, bug

#349 - Check mbd.SimTrees

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

#348 - Check ESSes versus number of taxa

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

#347 - Rerun Giappo run: more qs

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 5 comments
Labels: high, depends

#346 - Run Giappo params, crown age 8, 2 replicates, 10x MCMC chain length. 20200127

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 9 comments

#345 - Rerun: Giappo params, crown age 8, 20 replicates

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

#344 - ooo

Pull Request - State: closed - Opened by Giappo over 5 years ago

#343 - Allow nodeSub to be used in pirouette properly

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

#342 - mbd.TaxaAndMbdness loose dependency on razzo

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

#341 - [RUNNING] Run with DNA length of 1000 again

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

#340 - [RUNNING] Run with 20 replicates

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

#339 - [RUNNING] Run with longer chain length, to increase ESS

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

#338 - Add critereria to 'check_taxa_and_mbd_ness'

Issue - State: open - Opened by richelbilderbeek over 5 years ago
Labels: low

#337 - Fix bug in 90_... script that produced a too high failure rate

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

#336 - [CREATE FIGURES] Do Giappo run

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 10 comments

#335 - Develop

Pull Request - State: closed - Opened by Giappo over 5 years ago

#334 - [CREATE FIGURES] Run razzo with crown age = 6

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

#333 - [CREATE FIGURES] Run razzo with crown age = 5

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

#332 - [CREATE FIGURES] Run razzo with crown age = 4

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

#331 - [CREATE FIGURES] Run razzo with crown age = 3

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

#330 - [CREATE FIGURES] Run razzo with crown age = 2

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

#329 - [CREATE FIGURES] Run razzo with crown age = 1

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

#328 - Make verdict per parameter setting

Issue - State: closed - Opened by Giappo over 5 years ago - 2 comments
Labels: medium

#327 - Check ESSes versus MBD params

Issue - State: closed - Opened by Giappo over 5 years ago - 6 comments
Labels: medium

#326 - [Conclusion: more taxa, lower ESS] Check ESSes versus number of taxa

Issue - State: closed - Opened by Giappo over 5 years ago - 4 comments

#325 - Delete run 20190801

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

#324 - Run: Giappo params for range of different tree sizes

Issue - State: open - Opened by richelbilderbeek over 5 years ago - 1 comment
Labels: medium, depends

#323 - Do not vary q if nu == 0

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

#322 - Determine optimal parameter settings

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

#321 - Show percentage of failed simulations in overview

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

#320 - Pirouette: last check and resubmission

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

#319 - Show mutation rate in overview

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

#318 - Show nus in overview

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

#317 - Illustrate pirouette by doing an experiment with a Yule tree prior on BD tree

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

#316 - Decide: do run with Yule generative and twin tree for zero extinction rate?

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 2 comments
Labels: medium, decision

#315 - Do run with shorter DNA alignment of 500 nucleotides

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

#313 - Process feedback Rampal on pirouette_article

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

#303 - Make pilot run schedule

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

#302 - Do run with new mus [RUNNING]

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

#298 - Do run with lower mutation rate [RUNNING]

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

#295 - Pirouette: Fix high cyclomatic complexity

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

#294 - Run: one Giappo param setting with range of NS epsilons

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 5 comments
Labels: depends, upstream

#292 - Determine optimal crown age

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 8 comments

#277 - Show best models

Issue - State: open - Opened by richelbilderbeek over 5 years ago
Labels: medium

#276 - Create fig 1: separate generative from best

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

#272 - Are results results?

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

#270 - Check twinning params seeds are all unique

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

#244 - Check article and code matches

Issue - State: open - Opened by richelbilderbeek over 5 years ago - 8 comments
Labels: low

#242 - Estimate error in marginal likelihood estimation

Issue - State: closed - Opened by richelbilderbeek over 5 years ago - 21 comments
Labels: depends, upstream

GitHub / richelbilderbeek/razzo issues and pull requests