Changes in 1.1.4 (2020-03-16) + Fixes a build fail due to erronous merge in the previous commit 267f84b Changes in 1.1.3 (2020-03-12) + Updates to Documentation Changes in 1.1.2 (2020-03-11) + Fixes critical bug: o Removed the usage of the unavailable package 'eva', which caused builds to fail Changes in 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 Changes in 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 Changes in 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 Changes in 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 Changes in 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 Changes in 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 Changes in 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 Changes in 0.2.7 (2019-08-13) + Bug fix in interval table / wasserstein_metric causing wasserstein.sc runs to fail + Tests for that bug added Changes in 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 Changes in 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 Changes in 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 Changes in 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 Changes in 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