Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / richelbilderbeek/pirouette issues and pull requests

#433 - pirouette cleans up too much?

Issue - State: open - Opened by richelbilderbeek about 1 year ago

#432 - Fix CRAN issues

Issue - State: closed - Opened by richelbilderbeek about 2 years ago - 1 comment

#431 - Fix CRAN issues

Issue - State: closed - Opened by richelbilderbeek about 2 years ago - 1 comment

#430 - Use feast to do DNA sequence simulation

Issue - State: closed - Opened by richelbilderbeek over 3 years ago - 1 comment

#429 - Fix CRAN Windows build

Issue - State: closed - Opened by richelbilderbeek almost 4 years ago - 1 comment

#428 - Update nodeSub::sim_dual_linked

Issue - State: closed - Opened by richelbilderbeek about 4 years ago - 1 comment

#427 - Let all pirouette examples use 'create_exemplary_dd_tree'

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

#426 - Prepare version for pirouette article

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

#425 - 'create_exemplary_dd_tree' must match all pirouette examples code

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

#424 - Fix pir_plot

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

#423 - Check that values from files are correctly classified

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

#422 - Fix facet title

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

#421 - Use correct number of bins

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

#420 - Reduce waste in pir_plots

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

#419 - Improve speed of pir_plot_from_files

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

#418 - aa

Pull Request - State: closed - Opened by Giappo over 4 years ago

#417 - aaa

Pull Request - State: closed - Opened by Giappo over 4 years ago

#416 - Lose dependency upon becosys

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

#415 - Develop

Pull Request - State: closed - Opened by Giappo over 4 years ago

#414 - Creating an exemplary DD tree

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

#413 - Develop

Pull Request - State: closed - Opened by Giappo over 4 years ago

#412 - Giovanni

Pull Request - State: closed - Opened by Giappo over 4 years ago

#411 - create_std_pir_params is slow

Issue - State: closed - Opened by Giappo over 4 years ago - 12 comments
Labels: medium priority

#410 - Develop

Pull Request - State: closed - Opened by Giappo over 4 years ago

#409 - Develop

Pull Request - State: closed - Opened by Giappo over 4 years ago

#408 - Why is `create_std_pir_paramses` slow?

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

#407 - 'pir_params$twinning_params$twin_evidence_filename' must be NA if there is no evidences estimated

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

#406 - 'create_pir_params_twin' obsolete?

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

#404 - 'pir_params$evidence_filename' absent in 'get_pir_params_filenames'

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

#403 - Add 'pir_rename_to_std' to create standard names

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

#402 - 'check_experiments' does not detect duplicate error filenames

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

#401 - Giovanni

Pull Request - State: closed - Opened by Giappo over 4 years ago

#400 - Cache folder name on Windows?

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

#399 - Develop

Pull Request - State: closed - Opened by Giappo over 4 years ago

#398 - Add 'renum_rng_seeds'

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

#396 - 'get_pir_params_filenames' results differ between 'flat' and 'oldskool'

Issue - State: closed - Opened by richelbilderbeek over 4 years ago
Labels: high priority

#395 - 'get_pir_params_filenames' does not return all files

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

#394 - Write 'pir_rename'

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

#393 - Develop

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

#392 - Richel

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

#391 - Remove geiger

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

#390 - Add 'create_all_bd_experiments'

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

#389 - Write pir_run_distribution

Issue - State: closed - Opened by Giappo almost 5 years ago - 6 comments
Labels: low priority

#388 - Why does 'create_dd_tree' pick a tree from the best 5% percentile?

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

#387 - Develop

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

#386 - fixed pir_runs + implemented collect_pir_outs

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

#385 - Giovanni

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

#384 - Develop

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

#383 - Add: create_dd_tree

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

#382 - [ANALYSE] Check the effect of MCMC chain length on ESS estimation

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

#381 - fixato lo stile, si spera

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

#380 - Giovanni

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

#379 - Develop

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

#378 - Add 'get_sim_yule_twin_tree_fun'

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

#377 - Re-run pirouette example 3

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

#376 - Remove sapply

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

#375 - update to latest version

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

#374 - Feature request: more error functions

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

#373 - Add example to reproduce Sarver et al., 2019

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

#372 - Add example to reproduce Revell et al., 2015

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

#371 - Add functionality to implement multiple error functions

Issue - State: closed - Opened by thijsjanzen almost 5 years ago - 13 comments

#370 - Update Thijs Branch

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

#369 - Replace 'true_alignment' by 'tral', 'twin_alignment' by 'twal'

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

#368 - Giovanni

Pull Request - State: closed - Opened by Giappo almost 5 years ago - 1 comment

#367 - Put pirouette ms on BioRxiv

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

#366 - Rename 'lambda' and 'mu' to 'speciation_rate' and 'extinction_rate'

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

#365 - Develop

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

#364 - Do short run with unusual logging intervals

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

#363 - Twin alignment is not saved

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

#362 - Rename `(un)linked_node_sub` to `uns` and `lns`

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

#361 - How come coalescent models are so often picked?

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

#360 - Check pirouette on Windows

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

#359 - Richel

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

#358 - update

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

#357 - test-sim_twin_alignment does not pass locally on Windows

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

#355 - Merge pull request #354 from richelbilderbeek/master

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

#354 - pushback

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

#353 - pirouette::sim_bd_twin_tree must have no 'seed' argument

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

#352 - razzo must use the new babette interface

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

#351 - peregrine must use new babette interface

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

#348 - A twin tree function should return an ultrametric tree

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

#346 - Twin tree must have the same number of taxa

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

#345 - Twin tree must have the same labels

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

#344 - Rename 'create_sim_bd_twin_tree_fun' to 'get_sim_bd_twin_tree_fun'

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

#343 - Deprecate error_measure_params$burn_in_fraction

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

#342 - Cannot create branching times for a Yule tree

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

#341 - All candidate experiments must work on the same BEAST2 input file

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

#337 - Add MacOS to Travis again

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

#334 - Feature request: add Pigot's delta-r to the error measurement functions

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

#333 - Feature request: add the log-transformed nLTT as an error function

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

#332 - Feature request: allow custom true alignment function

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

#330 - Feature request: Add option for twin alignment has the same mutation rate

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

#328 - Add 'update_pirouette'

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

#325 - Skip style test until lintr is fixed

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