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 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

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.