mahal_dist, which emulates the dist function but allows a covariance matrix to be used for generalized distances.pairwise suite of functions: stdist and mdist, for standardized and Malahanobis distances, respectively.groups.first, to measurement.error for ordering terms having subjects and groups in ANOVA.anc.BM.measurement.error.getLSmeans.QRforX for determining 0 values.Pcov issue in manova.update.QRforX, which produces consistent QR decomposition results despite differences betweenbase::qr and Matrix::qr functions.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.R-dependency to >= 4.4.0checkers function that assumed sparse-matrix (Matrix) format of an object without coercing this format.predict.lm.rrpp and made the code more universal for different model formulae..coef.lm.rrpp..lm.rrpp associated with covariance matrices (causing non-adjusted matrices).subTest output from lm.rrpp.ws.anova.multi.model and logL related to missing Pcov when GLS models are used.lm.rrpp and predict.lm.rrpp, and permutation of full model residuals (with restrictions) to lm.rrpp.measurement.error.lm.rrpp.ws.verbose arguments to most analytical functions to reduce dense results.getANOVAStats, getPermInfo, getTerms, and getModels) to accommodate verbose function choices, plus allow users to easily extract objects as output.ICCstats, for calculating ICC statistics for lm.rrpp fits.measurement.error, but also added a plot utility function, focusMEonSubjects, which builds off of plot.measurement.error, to focus attention on specific plot details.interSubVar, a utility function to use along with measurement.error,
to visualize how variation between replicate measures, within subjects, can affect inter-subject variation.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).predict.lm.rrpp for QR-truncated design matrices.print.progess conditions in pairwise.Matrix::qrQ, using rather, Matrix::qr.Q.pairwise.SE added to coef.lm.rrpp for calculating bootstrap standard error.plot.lm.rrppplot.ordinate to better work with plot.default.plot.lm.rrpp diagnostic plots.logLik.lm.rrpp to obtain log-likelihood from an lm.rrpp object.scaleCov to scale covariance matrices with linear or exponential scalars.model.comparison to include Z scores calculated from log-likelihoods.predict.lm.rrpp for new data frames with only one observation.SS.iter.main that incidentally wrapped RSS.model by rows rather than columns.summary.lm.rrpp that did not properly index a matrix of RSS.model.plot.lm.rrpp for diagnostic plots, which forced an error.Matrix class matrices for more efficient computation, when needed.checkers function to use better algorithms to switch among different class matrices, to better save memory and increase computation time efficiency.anc.BM for singleton nodes.lm.rrpp to have less detritus during use. Also adjusted/updated support functions to work with updates.data.frame objects.lm.args.from.formula for intercept only models with covariance matrices.lm.rrpp support functions.logL support function for non-full rank design matrices.na.omit.rrpp.data.frame added for handling missing data.looCV function added as diagnostic tool.coef.lm.rrpp updated to provide results based on SS.type, rather than
type III SS, only.R.coef.lm.rrpplm.rrpp (passed onto lm).as.matrix names dropping in support code.lm.rrpp using Matrix package and sparse matrix calculations. This speeds up computation time and requires far less memory allocation.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.convert2ggplot, for coercing RRPP plots into ggplot objects.plot.predict.lm.rrpp.effect.size.plot.ordinate.predict.lm.rrpp so that functions in formulae are permissible.summary.pairwise to perform degree transformations rather than print.summary.pairwise, so that objects saved are the same as objects printed.model.comparison.manova.update pc dimension issue (output)xlim and ylim to be adjustable in plot.ordinate.manova.update to have more efficient code and better notes.summary.manova.lm.rrpp that mixed up rows and columns of a matrix of random stats.lm.rrpp data when converting a vector of data to a matrix.rrpp.data.frame to prevent downstream issues.trajectory.analysis with univariate response data, omitting vector correlations output.ordinate function.summary.ordinate and plot.ordinate S3 functionsadd.tree function (for plotting with plot.ordinate)lm.rrpp to provide better flexibility for different formulas.$LM$data in lm.rrpp to be a model frame rather than a data frame, consistent with $model from lm.prep.lda A new function to generate arguments for lda in the MASS library.classify deprecated (in favor of prep.lda)verbose option with manova.update. The function was optimized to provide verbose output without having to slow down computation time.SS.iter (produced incorrect RSS).trajectoty.analysis.lm.rrpp function.tol and pc.no arguments to model.comparison (were fixed before) so that users have more control of the analysis.prcomp.lm.rrpp to work better with missing data frames.trajectory.analysis traj.list issue, to not use grep for sorting trajectories. (Now lexical ordering of interactions is used.)det to determinant in all needing functions, to use modulus for near-singular matricesplot.lm.rrpp (code lines out of order)model.comparisonplot.procD.lmmanova.update functiontrajectory.analysis functionreveal.model.designs functionANOVA versus MANOVA in RRPPpairwise function.procD.lm to better work with data in the global environment rather than a data frame.print.summary.pairwise.model.comparison function.classify.pairwise.anova.lm.rrpp, related to GLS permutations and intercept only models.anova.lm.rrpp, so that it can be called by other functions/packages.pairwise function: allows pairwise comparison of means or slopes for a lm.rrpp fit.anova.lm.rrppcoef.lm.rrpp tests when type II or type III SS is chosen, to make sure that appropriate coefficients are used.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.