NEWS
waddR 1.6.1 (2021-05-28)
- Updates Documentation
- Updates Citation
- Updates Fields of output
waddR 1.3.1 (2020-03-16)
- Re-introduction of the eva package (archived version)
- Updates to Documentation
waddR 1.1.4 (2020-03-16)
- Fixes a build fail due to erronous merge in the previous commit 267f84b
waddR 1.1.3 (2020-03-12)
waddR 1.1.2 (2020-03-11)
- Fixes critical bug:
o Removed the usage of the unavailable package 'eva', which caused builds to fail
waddR 1.1.1 (2019-10-28)
- P-value reproducibility feature:
o Now using nextRNGstream to generate independent seeds for each gene
o Setting the seed (with set.seed()) only in .testWass
o Removed use of seeds and the seed argument everywhere in WassersteinTest.R
waddR 0.99.5 (2019-10-14)
- P-value reproducibility feature for the permutation procedure:
o as described [here](https://github.com/Bioconductor/Contributions/issues/1218#issuecomment-53710763), a seed argument has been added to the functions wasserstein.test and wasserstein.sc.
- Fix:
o Checks for the validity of the "method" argument in wasserstein.sc and wasserstein.test that have become unnecessary with the use of match.arg have been removed
waddR 0.99.4 (2019-10-01)
- Fixes:
o Fixed a bug in .wassersteinTestSp where the names in the output vector were changed unexpectedly and added a test for this bug
- Bioc Review I:
o vignette: Added SessionInfo() to each vignettes
o vignette/README: Changed the install instructions
o unit tests: removed unused and commented-out code
o R: Changed to switch statements to dispatch different methods in wasserstein.test and wasserstein.sc
o R: Changed the order of arguments in wasserstein.test and wasserstein.sc and added default methods
o R: wasserstein.test.sp has been renamed to .wassersteinTestSp; wassersetin.test.asy has been renamed to .wassersteinTestAsy -> both are now private
o R/NAMESPACE: removed the previously private functions .fishersCombinedPval and .combinePVal from NAMESPACE by removing @export decorators
waddR 0.99.3 (2019-08-30)
- Fixes:
o Fixed a bug in wasserstein.test that led to NAs during gpd fitting
o Fixed a bug in .gpdFittedPValue that led to NAs during gpd fitting
- Modified wasserstein.sc tests and added new tests to reproduce the bugs and challenge the fixes
- Change in squared_wass_decomp: If the standard deviation of one condition is 0, quantile-quantile corelation is not computed, since the shape term would be zero anyway. Previously, NAs were produced in some cases.
- Swapped 'true' and 'test' values in call to .relativeError
waddR 0.99.2 (2019-08-27)
- Changes to DESCRIPTION:
o removed the "Maintainer" field in favor of "Authors@R" to address build warnings
o Changed roles: 'cre' = Maintainer, 'aut' = author
waddR 0.99.0 (2019-08-27)
- Version Bump for BioC Submission
- Vignettes:
o Added introduction section and sessionInfo() to main vignette
o Added link to main vignette
- Code style:
o renaming where possible to conform with BioC convention
o file renaming to uniform upper camel-case
o comments edited
o additional helper functions introduced
waddR 0.2.8 (2019-08-19)
- R Code redesign:
o new unexported functions to help avoiding repeats
o Redesign of all single-cell methods as S4 methods that are also capable to take SingleCellExperiment objects as input
o Bioc-style function naming implemented
o Now using the cpp decomp functions instead computations in R
- Output names changed
- Descriptions changed to match altered code
waddR 0.2.7 (2019-08-13)
- Bug fix in interval table / wasserstein_metric causing wasserstein.sc runs to fail
- Tests for that bug added
waddR 0.2.6 (2019-08-08)
- Fix in wasserstein_metric where a result was squared
- Work on CPP implementations:
o Rework on the quantile computation in CPP that now produces more accurate approximations
o Removal of obsolete parameter "p" in approximation functions
- Now using wasserstein_metric in two sample testing procedures
waddR 0.2.5 (2019-08-06)
- Fixing R CMD check size error by reducing package size: Brownian bridge
distribution, used in the asymptotic implementation of wasserstein.test
now is downloaded into a local cache during the first run of
wasserstein.test. From there it is loaded in all subsequent runs.
- Fixed Bug in wasserstein.test
waddR 0.2.4 (2019-07-31)
- Added Vignettes for wasserstein distance, wasserstein.test, and wasserstein.sc
- Fixed examples and unparsable comments
- Adressing Notes of R CMD BiocCheck ...:
o Removed use of 1:... in favor of seq() or seq_len()
o Removed use of set.seed(), which changed the signature of testing functions
o Using 4 spaces instead of tabs and multiples of 4 spaces for indentation
waddR 0.2.3 (2019-07-29)
- Adressing Notes and Warnings of R CMD check ...:
o Reverted changes of BiocParallel from Import to Enhancement
o Removed redundant imports of arm, eva, BiocParallel
o Removed CITATION, as it could be formatted to satisfy the checks without naming a paper
waddR 0.2.2 (2019-07-29)
- Added this NEWS file for change announcements
- Added a file inst/CITATION that is supposed to hold the citation (after publication)
- DESCRIPTION file:
o Title and Description improved and shortened
o Added bioView Categories: StatisticalMethod, SingleCell, DifferentialExpression
o Added BugReports and URL in DESCRIPTION
o Changed the former Import BiocParallel to an Enhancement
- Changes to NAMESPACE:
o Explicitly declare the functions that should be imported from the packages arm, eva, and BiocParallel
- Changed all code files in the package to have max. 80 Character per line