RRPP - Patch Release 2.0.3

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

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Published by mlcollyer about 2 years ago

RRPP - Patch Release 2.0.2

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.

- R
Published by mlcollyer about 2 years ago

RRPP - Patch Release 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.

- R
Published by mlcollyer about 2 years ago

RRPP - Major Release 2.0.0

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.

- R
Published by mlcollyer over 2 years ago

RRPP - Minor Release v1.4.0

CHANGES IN RRPP 1.4.0

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 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.

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.

- R
Published by mlcollyer almost 3 years ago

RRPP - Minor Release

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.

- R
Published by mlcollyer almost 4 years ago

RRPP - Minor Release v1.3.0

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.

- R
Published by mlcollyer about 4 years ago

RRPP - Patch Release v1.2.3

- R
Published by mlcollyer over 4 years ago

RRPP - Patch Release v1.2.2

Fixes one programming bug in plot.lm.rrpp

- R
Published by mlcollyer over 4 years ago

RRPP - Minor Release v1.2.1

This is a minor release that mostly updates algorithms to switch to sparse matrix use to save computation time.

- R
Published by mlcollyer over 4 years ago

RRPP - Release v1.1.1

Patch release, for bug fixes for v1.1.0

- R
Published by mlcollyer over 4 years ago

RRPP - Minor Release

This is a minor release, 1.1.0, that includes two new functions: looCV and na.omit.rrpp.data.frame. All support code was also updated to be consistent with R 4.1.

- R
Published by mlcollyer almost 5 years ago

RRPP - RRPP v1.0.0

This is a major release, adding sparse linear algebra and algorithms to choose among most efficient computation strategies. Additionally, convert2ggplot is a new function to convert RRPP plots to amenable ggplot plots.

- R
Published by mlcollyer over 5 years ago

RRPP - 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.

- R
Published by mlcollyer over 5 years ago

RRPP - Patch Release

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.

- R
Published by mlcollyer about 6 years ago

RRPP - 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).

- R
Published by mlcollyer about 6 years ago

RRPP - Patch Release

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).

- R
Published by mlcollyer over 6 years ago

RRPP - Patch Release

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).

- R
Published by mlcollyer over 6 years ago

RRPP - Minor Release

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 ouput 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

- R
Published by mlcollyer over 6 years ago

RRPP - 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 eigen 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)

- R
Published by mlcollyer about 7 years ago

RRPP - Patch Release

NEW FEATURES

• NA

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

- R
Published by mlcollyer over 7 years ago

RRPP - 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.

- R
Published by mlcollyer over 7 years ago