Package: RRPP 2.1.2.999

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. 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_2.1.2.999.tar.gz
RRPP_2.1.2.999.zip(r-4.7)RRPP_2.1.2.999.zip(r-4.6)RRPP_2.1.2.999.zip(r-4.5)
RRPP_2.1.2.999.tgz(r-4.6-any)RRPP_2.1.2.999.tgz(r-4.5-any)
RRPP_2.1.2.999.tar.gz(r-4.7-any)RRPP_2.1.2.999.tar.gz(r-4.6-any)
RRPP_2.1.2.999.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
RRPP/json (API)

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

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

Datasets:
  • fishy - Simulated Fish Data for Measurement Error Analysis
  • flower - Flower Production and Temperature
  • mammalHR - Mammal Home Range Data
  • mammalHRphy - Phylogenetic Data for the Mammal Home Range Data
  • motionpaths - Simulated motion paths
  • phytoplankton - Phytoplankton Biomass and Eutrophication
  • PlethCinHoff - Plethodon comparative SVL data
  • PlethMorph - Plethodon comparative morphological data
  • podarcis - Podarcis Wall Lizards from the Mediterranean Basin
  • Pupfish - Landmarks on pupfish
  • PupfishHeads - Landmarks on pupfish heads
  • PupfishMR - Experimental metabolic rate data from pupfish
  • ReptAbund - Reptile Abundance Data in Western Australia
  • snakeHS - Snake Head Size and Regional Variation

On CRAN:

Conda:

9.53 score 4 stars 5 packages 243 scripts 1.9k downloads 16 mentions 70 exports 32 dependencies

Last updated from:2f996b16b9. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK246
source / vignettesOK252
linux-release-x86_64OK203
macos-release-arm64OK168
macos-oldrel-arm64OK123
windows-develOK168
windows-releaseOK150
windows-oldrelOK165
wasm-releaseOK144

Exports:add.trajectoriesadd.treeanova.lm.rrppanova.measurement.errorbetaTestclassifyconvert2ggploteffect.sizefixef.lmm.rrppfocusMEonSubjectsgetANOVAStatsgetModelCovgetModelsgetPermInfogetResCovgetTermsICCstatsinterSubVarkcomplm.rrpplm.rrpp.wslmm.rrpplooCVlooCV_tablelr_testmahal_distmanova.updatemeasurement.errormodel.comparisonordinatepairwisepairwise.model.Zplot.kcompplot.lm.rrppplot.ordinateplot.predict.lm.rrpppowerTransprep.ldaprint.anova.lm.rrppprint.betaTestprint.coef.lm.rrppprint.ICCstatsprint.lm.rrppprint.model.comparisonprint.pairwiseprint.pairwise.model.Zprint.predict.lm.rrppprint.summary.betaTestprint.summary.lm.rrppprint.summary.pairwiseprint.summary.trajectory.analysisprint.trajectory.analysispvalQRforXranef.lmm.rrppreveal.model.designsrrpp.data.framescaleCovsummary.anova.lm.rrppsummary.betaTestsummary.coef.lm.rrppsummary.ICCstatssummary.lm.rrppsummary.model.comparisonsummary.pairwisesummary.pairwise.model.Zsummary.predict.lm.rrppsummary.trajectory.analysistrajectory.analysisvec.cor.matrix

Dependencies:apebootclicpp11digestfarverggplot2gluegtableisobandlabelinglatticelifecyclelme4MASSMatrixminqanlmenloptrR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangS7scalesvctrsviridisLitewithr

Using RRPP
APPENDIX S2

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

ANOVA versus MANOVA in RRPP
Preliminaries | What is ANOVA? | What is ANOVA in RRPP? | What is MANOVA? | MANOVA in RRPP | Example of ANOVA and MANOVA in RRPP | Dimensionality Warning for MANOVA on high-dimensional data | Conclusions and Suggestions

Last update: 2024-06-02
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
Test of beta parameters for lm.rrpp model fitsbetaTest
Deprecated functions in RRPPclassify
coef for lm.rrpp model fitscoef.lm.rrpp
coef for lmm.rrpp model fitscoef.lmm.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
fixef for lmm.rrpp model fitsfixef.lmm.rrpp
Flower Production and Temperatureflower
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
K-component analysiskcomp
Linear Model Evaluation with a Randomized Residual Permutation Procedurelm.rrpp
Linear Model Evaluation with RRPP performed within subjectslm.rrpp.ws
Mixed Linear Model Evaluation with RRPP performed within subjectslmm.rrpp
Calculate the log-likelihood of a lm.rrpp fitlogLik.lm.rrpp
Diagnostic cross-validation tool including ordination based on fitted valueslooCV
Table for looCV comparisonslooCV_table
Likelihood ratio test for a linear model, based on RRPPlr_test
Calculate the pairwise Mahalanobis distances between observationsmahal_dist
Mammal Home Range DatamammalHR
Phylogenetic Data for the Mammal Home Range DatamammalHRphy
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
Pairwise comparisons of model effectspairwise.model.Z
Phytoplankton Biomass and Eutrophicationphytoplankton
Plethodon comparative SVL dataPlethCinHoff
Plethodon comparative morphological dataPlethMorph
Plot Function for RRPPplot.interSubVar
Plot Function for RRPPplot.kcomp
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
Podarcis Wall Lizards from the Mediterranean Basinpodarcis
Power TransformationpowerTrans
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.betaTest
Print/Summary Function for RRPPprint.coef.lm.rrpp
Print/Summary Function for RRPPprint.ICCstats
Print/Summary Function for RRPPprint.kcomp
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.pairwise.model.Z
Print/Summary Function for RRPPprint.predict.lm.rrpp
Print/Summary Function for RRPPprint.summary.betaTest
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
Experimental metabolic rate data from pupfishPupfishMR
Obtain P-value from a vector of statisticspval
QR decomposition of linear model design matricesQRforX
ranef for lmm.rrpp model fitsranef.lmm.rrpp
Reptile Abundance Data in Western AustraliaReptAbund
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
Snake Head Size and Regional VariationsnakeHS
Print/Summary Function for RRPPsummary.anova.lm.rrpp
Print/Summary Function for RRPPsummary.betaTest
Print/Summary Function for RRPPsummary.coef.lm.rrpp
Print/Summary Function for RRPPsummary.ICCstats
Print/Summary Function for RRPPsummary.kcomp
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.pairwise.model.Z
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