Nothing
NEWS.md
In RRPP: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure
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.
OTHER CHANGES
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 functionsadd.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 functiontrajectory.analysis functionreveal.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.rcoef.lm.rrpp.rlm.rrpp.rpredict.lm.rrpp.rRRPP.support.code.r-
RRPP.utils.r
-
Added a NEWS.md file to track changes to the package.
Try the RRPP package in your browser
Any scripts or data that you put into this service are public.
RRPP documentation built on Aug. 16, 2023, 1:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
CHANGES IN RRPP 1.4.0
NEW FEATURES
- Added arguments for restricted resampling to
lm.rrppandpredict.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
verbosearguments to most analytical functions to reduce dense results. - Added utility functions (
getANOVAStats,getPermInfo,getTerms, andgetModels) to accommodateverbosefunction 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 ofplot.measurement.error, to focus attention on specific plot details.
BUG FIXES
- Fixed SSCP issue in
summary.lm.rrppthat produces matrices of 0s. The issue was inherent tolm.rrpp, from erroneous assignment of models, only for output (not for mechanics). - Attempted fix of
predict.lm.rrppfor QR-truncated design matrices. - Fixed illogical
print.progessconditions inpairwise. - Fixed potential problem with reliance on
Matrix::qrQ, using rather,Matrix::qr.Q. - Fixed GLS estimation issue with
pairwise.
OTHER CHANGES
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.ordinateto better work withplot.default.
BUG FIXES
- Fixed S4 issue with GLS for
plot.lm.rrppdiagnostic plots.
OTHER CHANGES
CHANGES IN RRPP 1.3.0
NEW FEATURES
- New S3 function,
logLik.lm.rrppto obtain log-likelihood from anlm.rrppobject. - New function,
scaleCovto 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.comparisonto include Z scores calculated from log-likelihoods.
CHANGES IN RRPP 1.2.3
BUG FIXES
- Fixed a bug in
predict.lm.rrppfor new data frames with only one observation. - Fixed a bug in
SS.iter.mainthat incidentally wrapped RSS.model by rows rather than columns. - Fixed a bug in
summary.lm.rrppthat did not properly index a matrix ofRSS.model.
CHANGES IN RRPP 1.2.2
BUG FIXES
- Fixed a typo in
plot.lm.rrppfor diagnostic plots, which forced an error.
CHANGES IN RRPP 1.2.1
NEW FEATURES
- Updated many functions to be able to use
Matrixclass matrices for more efficient computation, when needed. - Updated
checkersfunction 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.BMfor singleton nodes.
OTHER CHANGES
- Updated
lm.rrppto 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.frameobjects.
CHANGES IN RRPP 1.1.1
BUG FIXES
- Fixed issue in
lm.args.from.formulafor intercept only models with covariance matrices. - Fixed issue with non-full rank design matrices and dropped terms in
lm.rrppsupport functions. - Fixed issue in
logLsupport function for non-full rank design matrices.
CHANGES IN RRPP 1.1.0
NEW FEATURES
na.omit.rrpp.data.frameadded for handling missing data.looCVfunction added as diagnostic tool.
OTHER CHANGES
coef.lm.rrppupdated to provide results based onSS.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 ontolm). - Fixed some
as.matrixnames dropping in support code.
CHANGES IN RRPP 1.0.0 (Major Release)
NEW FEATURES
- Computation of sums of squares in
lm.rrppusingMatrixpackage and sparse matrix calculations. This speeds up computation time and requires far less memory allocation. - The
lm.rrppfunction 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 coercingRRPPplots 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.rrppso that functions in formulae are permissible.
OTHER CHANGES
- Adapted
summary.pairwiseto perform degree transformations rather thanprint.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.updatepc dimension issue (output) - Fixed
xlimandylimto be adjustable inplot.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.updateto have more efficient code and better notes. - Fixed a bug in
summary.manova.lm.rrppthat mixed up rows and columns of a matrix of random stats. - Fixed a bug that eliminated row names for
lm.rrppdata when converting a vector of data to a matrix. - Added a step to coerce single-column matrices to vectors in
rrpp.data.frameto prevent downstream issues. - Made it possible to use
trajectory.analysiswith univariate response data, omitting vector correlations output.
CHANGES IN RRPP 0.6.0 (Minor Release)
NEW FEATURES
ordinatefunction.summary.ordinateandplot.ordinateS3 functionsadd.treefunction (for plotting withplot.ordinate)
OTHER CHANGES
- Updated support functions for
lm.rrppto provide better flexibility for different formulas. - Changed
$LM$datainlm.rrppto be a model frame rather than a data frame, consistent with$modelfromlm.
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.ldaA new function to generate arguments forldain theMASSlibrary.
OTHER CHANGES
classifydeprecated (in favor ofprep.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
verboseoption withmanova.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.rrppfunction.
CHANGES IN RRPP 0.4.2 (Patch Release)
NEW FEATURES
OTHER CHANGES
- Added
tolandpc.noarguments tomodel.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.rrppto 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.analysistraj.list issue, to not use grep for sorting trajectories. (Now lexical ordering of interactions is used.) - Changed
dettodeterminantin 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.updatefunctiontrajectory.analysisfunctionreveal.model.designsfunction- New vignette for
ANOVA versus MANOVA in RRPP
OTHER CHANGES
- Added a pairwise variance comparison for the
pairwisefunction.
BUG FIXES
- Tuned F-stat calculations to allow for model-specific residual variances, for multiple terms.
- Updated
procD.lmto 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.comparisonfunction. - 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 alm.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.rrpptests 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.rcoef.lm.rrpp.rlm.rrpp.rpredict.lm.rrpp.rRRPP.support.code.r-
RRPP.utils.r -
Added a
NEWS.mdfile to track changes to the package.
Try the RRPP package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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