NEWS.md

In RRPP: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

CHANGES IN RRPP 2.0.3

NEW FEATURES

• New function, QRforX, which produces consistent QR decomposition results despite differences betweenbase::qr and Matrix::qr functions.

BUG FIXES

• Fixed an important issue with removeRedundant and getRank to properly remove axes based on a base::qr pivot strategy, but still avoiding the making of large, dense matrices before using base::qr.

OTHER CHANGES

• Expanded function tests for CRAN checks.
• Updated R-dependency to >= 4.4.0

CHANGES IN RRPP 2.0.2

BUG FIXES

• Fixed an important issue with checkers function that assumed sparse-matrix (Matrix) format of an object without coercing this format.

CHANGES IN RRPP 2.0.1

NEW FEATURES

• Updated all QR decompositions that forced dense-matrix methods when not needed.
• Added functions to remove design matrix parameter redundancies without using QR decomposition.

BUG FIXES

• Fixed issues with model matrices for new data in predict.lm.rrpp and made the code more universal for different model formulae.
• Fixed standard error method for intercepts in .coef.lm.rrpp.
• Fixed some circularity issues with .lm.rrpp associated with covariance matrices (causing non-adjusted matrices).
• Fixed some issues with multiple functions that misused the logical subTest output from lm.rrpp.ws.
• Fixed issues with anova.multi.model and logL related to missing Pcov when GLS models are used.

CHANGES IN RRPP 2.0.0

NEW FEATURES

• Added arguments for restricted resampling to lm.rrpp and predict.lm.rrpp, and permutation of full model residuals (with restrictions) to lm.rrpp.
• Added new function, measurement.error.
• Added new function, lm.rrpp.ws.
• Added verbose arguments to most analytical functions to reduce dense results.
• Added utility functions (getANOVAStats, getPermInfo, getTerms, and getModels) to accommodate verbose function choices, plus allow users to easily extract objects as output.
• Added new function, ICCstats, for calculating ICC statistics for lm.rrpp fits.
• Added S3 generic functions for measurement.error, but also added a plot utility function, focusMEonSubjects, which builds off of plot.measurement.error, to focus attention on specific plot details.
• Added function, interSubVar, a utility function to use along with measurement.error, to visualize how variation between replicate measures, within subjects, can affect inter-subject variation.

BUG FIXES

• Fixed SSCP issue in summary.lm.rrpp that produces matrices of 0s. The issue was inherent to lm.rrpp, from erroneous assignment of models, only for output (not for mechanics).
• Attempted fix of predict.lm.rrpp for QR-truncated design matrices.
• Fixed illogical print.progess conditions in pairwise.
• Fixed potential problem with reliance on Matrix::qrQ, using rather, Matrix::qr.Q.
• Fixed GLS estimation issue with pairwise.

OTHER CHANGES

• argument SE added to coef.lm.rrpp for calculating bootstrap standard error.

CHANGES IN RRPP 1.3.1

NEW FEATURES

• Added ability to use either Pearson or normalized residuals in residual plots for plot.lm.rrpp
• Updated arguments for plot.ordinate to better work with plot.default.

BUG FIXES

• Fixed S4 issue with GLS for plot.lm.rrpp diagnostic plots.

OTHER CHANGES

CHANGES IN RRPP 1.3.0

NEW FEATURES

• New S3 function, logLik.lm.rrpp to obtain log-likelihood from an lm.rrpp object.
• New function, scaleCov to scale covariance matrices with linear or exponential scalars.

BUG FIXES

• Various lingering bugs from version 1.2 associated with sparse matrix calculation issues were removed.

OTHER CHANGES

• Updated model.comparison to include Z scores calculated from log-likelihoods.

CHANGES IN RRPP 1.2.3

BUG FIXES

• Fixed a bug in predict.lm.rrpp for new data frames with only one observation.
• Fixed a bug in SS.iter.main that incidentally wrapped RSS.model by rows rather than columns.
• Fixed a bug in summary.lm.rrpp that did not properly index a matrix of RSS.model.

CHANGES IN RRPP 1.2.2

BUG FIXES

• Fixed a typo in plot.lm.rrpp for diagnostic plots, which forced an error.

CHANGES IN RRPP 1.2.1

NEW FEATURES

• Updated many functions to be able to use Matrix class matrices for more efficient computation, when needed.
• Updated checkers function to use better algorithms to switch among different class matrices, to better save memory and increase computation time efficiency.

BUG FIXES

• Added catch to anc.BM for singleton nodes.

OTHER CHANGES

• Updated lm.rrpp to have less detritus during use. Also adjusted/updated support functions to work with updates.

CHANGES IN RRPP 1.1.2

BUG FIXES

• Fixed a few issues with dropped names when working with data.frame objects.

CHANGES IN RRPP 1.1.1

BUG FIXES

• Fixed issue in lm.args.from.formula for intercept only models with covariance matrices.
• Fixed issue with non-full rank design matrices and dropped terms in lm.rrpp support functions.
• Fixed issue in logL support function for non-full rank design matrices.

CHANGES IN RRPP 1.1.0

NEW FEATURES

• na.omit.rrpp.data.frame added for handling missing data.
• looCV function added as diagnostic tool.

OTHER CHANGES

• coef.lm.rrpp updated to provide results based on SS.type, rather than type III SS, only.
• Complete scanning and updating of code to identify and fix names lost due to matrix calculations or vector/matrix conversions in R.

BUG FIXES

• Fixed missing coefficients for GLS estimation in coef.lm.rrpp
• Fixed missing data issue in lm.rrpp (passed onto lm).
• Fixed some as.matrix names dropping in support code.

CHANGES IN RRPP 1.0.0 (Major Release)

NEW FEATURES

• Computation of sums of squares in lm.rrpp using Matrix package and sparse matrix calculations. This speeds up computation time and requires far less memory allocation.
• The lm.rrpp function now has a an argument, turbo, which can suppress calculating coefficients in random permutations, if unneeded, which can speed up analysis of large data sets.
• More options for parallel processing.
• New function, convert2ggplot, for coercing RRPP plots into ggplot objects.

CHANGES IN RRPP 0.6.2 (Patch Release)

NEW FEATURES

• Added option to add abscissa to plot.predict.lm.rrpp.
• Added Box-Cox transformation to effect.size.
• Added option to flip axes in plot.ordinate.
• Updated predict.lm.rrpp so that functions in formulae are permissible.

OTHER CHANGES

• Adapted summary.pairwise to perform degree transformations rather than print.summary.pairwise, so that objects saved are the same as objects printed.
• Removed error trap from pairwise for n = 1 groups.

BUG FIXES

• Fixed class check on model.comparison.
• Fixed manova.update pc dimension issue (output)
• Fixed xlim and ylim to be adjustable in plot.ordinate.
• Added transform logical output to ordinate.
• Fixed intercept only model issue in lm.rrpp.

CHANGES IN RRPP 0.6.1 (Patch Release)

NEW FEATURES

OTHER CHANGES

BUG FIXES

• Refined manova.update to have more efficient code and better notes.
• Fixed a bug in summary.manova.lm.rrpp that mixed up rows and columns of a matrix of random stats.
• Fixed a bug that eliminated row names for lm.rrpp data when converting a vector of data to a matrix.
• Added a step to coerce single-column matrices to vectors in rrpp.data.frame to prevent downstream issues.
• Made it possible to use trajectory.analysis with univariate response data, omitting vector correlations output.

CHANGES IN RRPP 0.6.0 (Minor Release)

NEW FEATURES

• ordinate function.
• summary.ordinate and plot.ordinate S3 functions
• add.tree function (for plotting with plot.ordinate)

OTHER CHANGES

• Updated support functions for lm.rrpp to provide better flexibility for different formulas.
• Changed $LM$data in lm.rrpp to be a model frame rather than a data frame, consistent with $model from lm.

BUG FIXES

• Fixed issue with transformation of dependent variable -- e.g., log(y) -- in formula for lm.rrpp. The bug was a failure to transform the variable(s).

CHANGES IN RRPP 0.5.2 (Patch Release)

BUG FIXES

• Fixed issue with GLS estimation of coefficients in pairwise (used GLS residuals instead of transformed residuals, by mistake).

CHANGES IN RRPP 0.5.1 (Patch Release)

BUG FIXES

• Fixed data.frame error in lm.rrpp for within-formula transformations (like log or poly).
• Arranged effect.type argument options in lm.rrpp to match anova.lm.rrpp).

CHANGES IN RRPP 0.5.0 (Minor Release)

NEW FEATURES

• prep.lda A new function to generate arguments for lda in the MASS library.

OTHER CHANGES

• classify deprecated (in favor of prep.lda)
• Changed the output structure for lm.rrpp objects. Either OLS or GLS statistics are returned, not both. There is no longer differentiation between GLS and weighted stats, as weighted stats are GLS estimated stats. The difference is obvious with the inclusion of weights or Cov matrix.
• No longer a verbose option with manova.update. The function was optimized to provide verbose output without having to slow down computation time.

BUG FIXES

• Fixed some issues with linear model weights and offset, throughout many functions.
• Sweeping changes to be CRAN 4.0 compliant

CHANGES IN RRPP 0.4.3 (Patch Release)

NEW FEATURES

OTHER CHANGES

BUG FIXES

• Fixed a parallel processing issue with internal function, SS.iter (produced incorrect RSS).
• Fixed multi-model anova TSS issue.
• Fixed an issue with the centering of trajectories in trajectoty.analysis.
• Fixed an issue for calculating fitted values for GLS in the lm.rrpp function.

CHANGES IN RRPP 0.4.2 (Patch Release)

NEW FEATURES

OTHER CHANGES

• Added tol and pc.no arguments to model.comparison (were fixed before) so that users have more control of the analysis.

BUG FIXES

• Tweaked logL tolerance calculation to be consistent with prcomp.
• Tweaked support code for lm.rrpp to work better with missing data frames.
• Fixed absolute eigenvalue issue with Cov.proj.
• Added forgotten code from last update to fix non-full rank design matrices.
• Fixed trajectory.analysis traj.list issue, to not use grep for sorting trajectories. (Now lexical ordering of interactions is used.)
• Changed det to determinant in all needing functions, to use modulus for near-singular matrices
• Fixed bug in plot.lm.rrpp (code lines out of order)

CHANGES IN RRPP VERSION 0.4.1 (Patch release)

NEW FEATURES

OTHER CHANGES

• Updated source in Description.

BUG FIXES

• Fixed univariate data issue with model.comparison
• Fixed xlab flexibility issue for regression plots in plot.procD.lm

CHANGES IN RRPP VERSION 0.4.0 (Minor release)

NEW FEATURES

• manova.update function
• trajectory.analysis function
• reveal.model.designs function
• New vignette for ANOVA versus MANOVA in RRPP

OTHER CHANGES

• Added a pairwise variance comparison for the pairwise function.

BUG FIXES

• Tuned F-stat calculations to allow for model-specific residual variances, for multiple terms.
• Updated procD.lm to better work with data in the global environment rather than a data frame.

CHANGES IN RRPP VERSION 0.3.0 (Minor release)

NEW FEATURES

• Added print.summary.pairwise.
• Added model.comparison function.
• Added classify function.

OTHER CHANGES

• Added an update to allow classify to work on univariate data.

BUG FIXES

• Tuned criterion for assessing whether generalized inverse should be performed.
• Fixed bug with GLS variance estimation in pairwise.
• Fixed some issues with univariate data for classify.
• Fixed some issues with univariate data for pairwise.
• Fixed the logL function within model.comparisons for GLS determinants (was returning 0).
• Fixed some issues with the aov.multimodel subfunction of anova.lm.rrpp, related to GLS permutations and intercept only models.
• Added random SS output to aov.multimodel subfunction of anova.lm.rrpp, so that it can be called by other functions/packages.

CHANGES IN RRPP VERSION 0.2.0 (Minor release)

NEW FEATURES

• pairwise function: allows pairwise comparison of means or slopes for a lm.rrpp fit.
• A vignette for using RRPP, which is the same as Appendix S2 in Collyer and Adams (2008). RRPP: An R package for fitting linear models to high-dimensional data using residual randomization. Methods in Ecology and Evolution. (submitted)

OTHER CHANGES

• Added multi-model inference capability to anova.lm.rrpp

BUG FIXES

• Fixed issue for coef.lm.rrpp tests when type II or type III SS is chosen, to make sure that appropriate coefficients are used.

CHANGES IN RRPP VERSION 0.1.0 (Major release)

New Release!

New features

• anova.lm.rrpp.r
• coef.lm.rrpp.r
• lm.rrpp.r
• predict.lm.rrpp.r
• RRPP.support.code.r

• RRPP.utils.r

• Added a NEWS.md file to track changes to the package.

RRPP documentation built on June 22, 2024, 6:45 p.m.