Package: RRPP 2.0.3.999

Michael Collyer

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

Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. This packaged is described by Collyer & Adams (2018). Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.

Authors:Michael Collyer [aut, cre], Dean Adams [aut]

RRPP_2.0.3.999.tar.gz
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RRPP.pdf |RRPP.html✨
RRPP/json (API)
NEWS

# Install 'RRPP' in R:
install.packages('RRPP', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mlcollyer/rrpp/issues

Datasets:

On CRAN:

51 exports 4 stars 3.86 score 31 dependencies 7 dependents 16 mentions 157 scripts 1.4k downloads

Last updated 8 hours agofrom:49ed1516a0. Checks:OK: 1 WARNING: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 07 2024
R-4.5-winWARNINGSep 07 2024
R-4.5-linuxWARNINGSep 07 2024
R-4.4-winWARNINGSep 07 2024
R-4.4-macWARNINGSep 07 2024

Exports:add.trajectoriesadd.treeanova.lm.rrppanova.measurement.errorclassifyconvert2ggploteffect.sizefocusMEonSubjectsgetANOVAStatsgetModelCovgetModelsgetPermInfogetResCovgetTermsICCstatsinterSubVarlm.rrpplm.rrpp.wslooCVlr_testmahal_distmanova.updatemeasurement.errormodel.comparisonordinatepairwiseplot.lm.rrppplot.predict.lm.rrppprep.ldaprint.anova.lm.rrppprint.coef.lm.rrppprint.lm.rrppprint.pairwiseprint.predict.lm.rrppprint.summary.lm.rrppprint.summary.pairwiseprint.summary.trajectory.analysisprint.trajectory.analysispvalQRforXreveal.model.designsrrpp.data.framescaleCovsummary.anova.lm.rrppsummary.coef.lm.rrppsummary.lm.rrppsummary.pairwisesummary.predict.lm.rrppsummary.trajectory.analysistrajectory.analysisvec.cor.matrix

Dependencies:apeclicolorspacedigestfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr

ANOVA versus MANOVA in RRPP

Michael L. Collyer

Rendered fromANOVA.vs.MANOVA.Rmdusingknitr::rmarkdownon Sep 07 2024.

Last update: 2024-06-02
Started: 2019-02-23

Using RRPP

Rendered fromUsing.RRPP.Rmdusingknitr::rmarkdownon Sep 07 2024.

Last update: 2024-06-12
Started: 2019-02-23

Readme and manuals

Help Manual

Help pageTopics
Plot Function for RRPPadd.trajectories
Plot tool to add phylogenetic trees to ordination plotsadd.tree
ANOVA for lm.rrpp model fitsanova.lm.rrpp
ANOVA for lm.rrpp model fits used in measurement.erroranova.measurement.error
Deprecated functions in RRPPclassify
coef for lm.rrpp model fitscoef.lm.rrpp
Convert RRPP plots to ggplot objectsconvert2ggplot
Obtain Effect-size from a vector of valueseffect.size
Simulated fish data for measurement error analysisfishy
Extract fitted valuesfitted.lm.rrpp
Plot Function for RRPPfocusMEonSubjects
Utility Function for RRPPgetANOVAStats
Utility Function for RRPPgetModelCov
Utility Function for RRPPgetModels
Utility Function for RRPPgetPermInfo
Utility Function for RRPPgetResCov
Utility Function for RRPPgetTerms
Intraclass correlation statistics from an lm.rrpp model fitsICCstats
Reveal the inter-subject variability from a measurement error analysisinterSubVar
Linear Model Evaluation with a Randomized Residual Permutation Procedurelm.rrpp
Linear Model Evaluation with RRPP performed within subjectslm.rrpp.ws
Calculate the log-likelihood of a lm.rrpp fitlogLik.lm.rrpp
Diagnostic cross-validation tool for ordination based on fitted valueslooCV
Likelihood ratio test for a linear model, based on RRPPlr_test
Calculate the pairwise Mahalanobis distances between observationsmahal_dist
MANOVA update for lm.rrpp model fitsmanova.update
Evaluation of measurement error for two or more multivariate measurements, for common research subjectsmeasurement.error
Model Comparisons, in terms of the log-likelihood, covariance trace, or Z-score.model.comparison
Extract model frame from a lm.rrpp objectmodel.frame.lm.rrpp
Extract the model design matrix from an lm.rrpp objectmodel.matrix.lm.rrpp
Simulated motion pathsmotionpaths
Handle missing values in rrpp.data.frame objectsna.omit.rrpp.data.frame
Ordination tool for data aligned to another matrixordinate
Pairwise comparisons of lm.rrpp fitspairwise
Plethodon comparative morphological dataPlethMorph
Plot Function for RRPPplot.interSubVar
Plot Function for RRPPplot.lm.rrpp
Plot Function for RRPPplot.looCV
Plot Function for RRPPplot.measurement.error
Plot Function for RRPPplot.model.comparison
Plot Function for RRPPplot.ordinate
Plot Function for RRPPplot.predict.lm.rrpp
Plot Function for RRPPplot.trajectory.analysis
predict for lm.rrpp model fitspredict.lm.rrpp
Linear discriminant function for lm.rrpp model fitsprep.lda
Print/Summary Function for RRPPprint.anova.lm.rrpp
Print/Summary Function for RRPPprint.coef.lm.rrpp
Print/Summary Function for RRPPprint.ICCstats
Print/Summary Function for RRPPprint.lm.rrpp
Print/Summary Function for RRPPprint.looCV
Print/Summary Function for RRPPprint.lr_test
Print/Summary Function for RRPPprint.measurement.error
Print/Summary Function for RRPPprint.model.comparison
Print/Summary Function for RRPPprint.ordinate
Print/Summary Function for RRPPprint.pairwise
Print/Summary Function for RRPPprint.predict.lm.rrpp
Print/Summary Function for RRPPprint.summary.lm.rrpp
Print/Summary Function for RRPPprint.summary.manova.lm.rrpp
Print/Summary Function for RRPPprint.summary.ordinate
Print/Summary Function for RRPPprint.summary.pairwise
Print/Summary Function for RRPPprint.summary.trajectory.analysis
Print/Summary Function for RRPPprint.trajectory.analysis
Landmarks on pupfishPupfish
Landmarks on pupfish headsPupfishHeads
Obtain P-value from a vector of valuespval
QR decomposition of linear model design matricesQRforX
Extract residualsresiduals.lm.rrpp
Reveal model designs used in lm.rrpp fitreveal.model.designs
Create a data frame for lm.rrpp analysisrrpp.data.frame
Scaling of a Covariance MatrixscaleCov
Print/Summary Function for RRPPsummary.anova.lm.rrpp
Print/Summary Function for RRPPsummary.coef.lm.rrpp
Print/Summary Function for RRPPsummary.ICCstats
Print/Summary Function for RRPPsummary.lm.rrpp
Print/Summary Function for RRPPsummary.looCV
Print/Summary Function for RRPPsummary.lr_test
Print/Summary Function for RRPPsummary.manova.lm.rrpp
Print/Summary Function for RRPPsummary.measurement.error
Print/Summary Function for RRPPsummary.model.comparison
Print/Summary Function for RRPPsummary.ordinate
Print/Summary Function for RRPPsummary.pairwise
Print/Summary Function for RRPPsummary.predict.lm.rrpp
Print/Summary Function for RRPPsummary.trajectory.analysis
Extract the terms from an lm.rrpp objectterms.lm.rrpp
Quantify and compare shape change trajectoriestrajectory.analysis
Support function for RRPPvec.cor.matrix