NEWS.md
In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny
News
Newest versions at top.
pirouette 1.6.8 (2023-09-29)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- New CRAN submission
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.7 (2023-09-25)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use new CITATION style
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.6 (submitted to CRAN)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.5 (unreleased)
NEW FEATURES
- None
MINOR IMPROVEMENTS
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.4 (2020-11-24)
NEW FEATURES
- Added
check_pir_paramses to check a list of pir_params for validity
- Add
create_std_pir_paramses and create_std_pir_params to easily create
one or more pir_params in a standard way
- Add
shorten_pir_params and shorten_pir_paramses to shorten run-time
(for example, on Travis CI) easily
- Add
pir_save to save all pirouette output in a standarized way
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.3 (2020-02-26)
NEW FEATURES
- Added
pir_rename_to_std to conformize all files created by a pirouette run
- Added 'pir_rename' to rename all files created by a pirouette run
- Depend on beautier v2.3.5 (for
rename_mcmc_filenames)
MINOR IMPROVEMENTS
- Use at-least versions of packages, instead of exact versions
- Check if there is need for an evidence file. Will stop if there
is an evidence filename specified without needing one and vice versa
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Use new
nodeSube v0.5 (2020-01-13) default arguments
pirouette 1.6.2 (2020-01-06)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Process
goodpractice feedback
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.1 (2020-01-01)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Improved documentation
- Increased code coverage
- Removed dead code
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6 (2019-10-13)
NEW FEATURES
- Can create a twin tree that is a copy, by using
copy_tree as the
method used in create_twin_tree
- Can use node substitution model, by using
linked_node_sub (lns)
or unlinked_node_sub (uns) as the site_model used in create_alignment
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.5.1 (2019-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use
mcbette version in which a higher number of particles in
Nested Sampling does result in a better marginal likelihood
estimation
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.5 (2019-08-19)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Checks that all experiments have a unique inference model
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.4.1 (2019-08-19)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Table with evidences for twin models works
DEPRECATED AND DEFUNCT
- None
pirouette 1.4 (2019-08-18)
NEW FEATURES
- Evidence estimations shows estimated error of evidence
- Evidence estimations shows effective sample size in estimating the evidence
MINOR IMPROVEMENTS
- Better error message when using a CBS site model and too few taxa
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.3 (2019-08-15)
NEW FEATURES
- Removed duplicate
evidence_epsilon argument from est_evidences:
use the epsilon supplied in the experiments' est_evidence_mcmc$epsilon
MINOR IMPROVEMENTS
- Better error message when using a CBS site model and too few taxa
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
News
Newest versions at top.
pirouette 1.6.8 (2023-09-29)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- New CRAN submission
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.7 (2023-09-25)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use new CITATION style
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.6 (submitted to CRAN)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.5 (unreleased)
NEW FEATURES
- None
MINOR IMPROVEMENTS
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.4 (2020-11-24)
NEW FEATURES
- Added
check_pir_paramsesto check a list ofpir_paramsfor validity - Add
create_std_pir_paramsesandcreate_std_pir_paramsto easily create one or morepir_paramsin a standard way - Add
shorten_pir_paramsandshorten_pir_paramsesto shorten run-time (for example, on Travis CI) easily - Add
pir_saveto save all pirouette output in a standarized way
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.3 (2020-02-26)
NEW FEATURES
- Added
pir_rename_to_stdto conformize all files created by a pirouette run - Added 'pir_rename' to rename all files created by a pirouette run
- Depend on beautier v2.3.5 (for
rename_mcmc_filenames)
MINOR IMPROVEMENTS
- Use at-least versions of packages, instead of exact versions
- Check if there is need for an evidence file. Will stop if there is an evidence filename specified without needing one and vice versa
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Use new
nodeSubev0.5 (2020-01-13) default arguments
pirouette 1.6.2 (2020-01-06)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Process
goodpracticefeedback
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6.1 (2020-01-01)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Improved documentation
- Increased code coverage
- Removed dead code
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.6 (2019-10-13)
NEW FEATURES
- Can create a twin tree that is a copy, by using
copy_treeas themethodused increate_twin_tree - Can use node substitution model, by using
linked_node_sub (lns)orunlinked_node_sub (uns)as thesite_modelused increate_alignment
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.5.1 (2019-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use
mcbetteversion in which a higher number of particles in Nested Sampling does result in a better marginal likelihood estimation
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.5 (2019-08-19)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Checks that all experiments have a unique inference model
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.4.1 (2019-08-19)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Table with evidences for twin models works
DEPRECATED AND DEFUNCT
- None
pirouette 1.4 (2019-08-18)
NEW FEATURES
- Evidence estimations shows estimated error of evidence
- Evidence estimations shows effective sample size in estimating the evidence
MINOR IMPROVEMENTS
- Better error message when using a CBS site model and too few taxa
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
pirouette 1.3 (2019-08-15)
NEW FEATURES
- Removed duplicate
evidence_epsilonargument fromest_evidences: use theepsilonsupplied in the experiments'est_evidence_mcmc$epsilon
MINOR IMPROVEMENTS
- Better error message when using a CBS site model and too few taxa
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.