NEWS.md
In jackstraw: Statistical Inference for Unsupervised Learning

jackstraw 1.3.2 (2020-12-23)

Fixed lots of minor things that caused check errors
Vignette: minor edits to fix recent build errors
Moved external package imports from R code to DESCRIPTION, adding missing packages, and fixed namespaces.
Corrected function arguments and usage discrepancies.
Added this NEWS.md file to track changes to the package.

Overview:

Added unit tests to almost all functions
Basic uses are covered (default optional parameters), and some but not all advanced uses
Minor user-facing changes:
Moved mandatory arguments to the front (no backward-incompatible problems since these arguments had to be called by name unless the earlier optional arguments were also present and were passed unnamed (rare))
Added more informative error messages for missing mandatory arguments, objects with wrong classes, and covariate dimension disagreements
Minor bug fixes (some s = 1 edge cases)
Eliminated all non-error/warning verbosity when verbose = FALSE.

Additional details:

Function jackstraw_cluster
Added option pool (default TRUE) to calculate p-values by pooling null statistics (to match jackstraw_kmeans option and default). Previously the hardcoded behavior matched pool = FALSE.
Functions jackstraw_lfa, jackstraw_alstructure, jackstraw_pca, jackstraw_rpca, jackstraw_irlba, jackstraw_subspace:
Argument r is now second argument.
- lfa, alstructure, subspace versions: r does not have a default value and it is mandatory.
Functions jackstraw_kmeans, jackstraw_kmeanspp, jackstraw_MiniBatchKmeans, jackstraw_pam, jackstraw_cluster:
Debugged s = 1 edge case: null data used to be centered incorrectly. Bug only occurred in combination with center = TRUE (default).
Internal (unexported) function RSS now returns actual residual sum of squares. This change does not affect any exported functions that use it. Previously RSS calculated a normalized version (equal to 1 - R^2), but this normalization canceled out in FSTAT (its only downstream use), so the normalization had no user-facing effect.

Exclusive list of functions without unit tests (all are redundant with other packages, so they are candidates for removal in the near future):

Functions jackstraw_pca, jackstraw_rpca, jackstraw_irlba: Corrected documentation (parameter r1 was incorrectly described as PC in parts of the documentation. Thanks to Djordje Bajić (GitHub username djbajic) for reporting this error!
Removed option seed from all functions that had it. For the same behavior, call set.seed(seed) before calling the function.
Functions jackstraw_lfa and jackstraw_alstructure: removed devR option.
Removed redundant functions
lfa.corpcor: same as lfa::lfa with option override = TRUE
pi0est_bootstrap: redundant with qvalue::pi0est with option pi0.method = 'bootstrap'
dev.R (internal; functionality implemented in package gcatest)
devdiff_parallel (internal; redundant with gcatest::gcat.stat)
getp (internal; redundant with qvalue::empPvals)

Function jackstraw_lfa now accepts genotypes input as BEDMatrix objects. In this case, the function operates on a low-memory mode, keeping data on disk rather than memory as much as possible, and writes permuted data into temporary files as well. To enable this mode, the BEDMatrix and genio packages are now dependencies. Note only jackstraw_lfa supports BEDMatrix because lfa supports it too (most recent fork; see below).
Removed function devdiff, which is redundant (and replaced internally) with gcatest::delta_deviance_lf, a function that supports more special cases, including genotypes accessed through a BEDMatrix object. The only internal dependencies were jackstraw_lfa and jackstraw_alstructure.
Updated README.md to instruct users to install the most updated forks of lfa and gcatest on GitHub (under username alexviiia), rather than the Bioconductor versions that are lacking critical updates.

All jackstraw_* functions now return NA p-values for NA statistics.
Before NA statistics resulted in p-values of 1 instead, which is what qvalue::empPvals returns. Now an internal wrapper function ensures the desired behavior.
Removed two jackstraw_pam toy example unit tests that failed often due to colinearity.
Reformatted this NEWS.md slightly to improve its automatic parsing.

Temporary changes for CRAN resubmission
Removed jackstraw_alstructure because dependency alstructure is not on CRAN or Bioconductor.
Removed BEDMatrix functionality for function jackstraw_lfa because the latest versions of the dependencies lfa and gcatest on Bioconductor do not support BEDMatrix (the development versions that do support BEDMatrix are on GitHub only).
Removed lfa and gcatest devel version requirements.
Added internal functions delta_deviance_lf, delta_deviance_snp, delta_deviance_snp_lf, which are copies of the gcatest functions of the same name (available on development version only, hence this copying)
Made testing a bit more lenient towards some NA cases
Minor non-code edits
Spell checked documentation
Changed to single maintainer (Neo)
Removed VignetteBuilder: knitr since there's no vignette anymore
Fixed broken or outdated URLs

Temporarily removed exported function jackstraw_lfa and package dependencies lfa and gcatest, since lfa is having build errors on bioc-devel.
Also removed internal functions pseudo_Rsq, mcfadden_Rsq_snp, efron_Rsq, efron_Rsq_snp, delta_deviance_{lf,snp,snp_lf}.R (all depended on lfa)
Also removed package dependencies parallel and genio which are temporarily not being used.
Removed many package suggested dependencies (knitr, rmarkdown, ggplot2, mutoss, Matrix, gridExtra, cowplot, scales, formatR) that were only used in a vignette currently not being built.
Reduced example dimensions for jackstraw_irlba and jackstraw_rpca by 5 to keep their runtime low.