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RRPP

RRPP is a software package for evaluating linear models with residual randomization in a permutation procedure. S3 Generic used for the lm function can also be used with lm.rrpp, with the chief difference being that lm coefficients, fitted values, and residuals are estimated many times with random permutations of data.

To install the current RRPP R-package from CRAN:

Within R:

install.packages("RRPP")

To install the current version of the RRPP R-package from Github using devtools:

Within R:

install.packages("pak")

pak::pkg_install("mlcollyer/RRPP")

The version on github is updated regularly, especially if errors or programming bugs are discovered.

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Version

Install

install.packages('RRPP')

Monthly Downloads

2,919

Version

2.2.5

License

GPL (>= 3)

Issues

0

Pull Requests

0

Stars

4

Forks

1

Maintainer

Michael Collyer

Last Published

November 8th, 2026

Functions in RRPP (2.2.5)

anova.measurement.error

ANOVA for lm.rrpp model fits used in measurement.error
classify

Deprecated functions in RRPP
convert2ggplot

Convert RRPP plots to ggplot objects
add.tree

Plot tool to add phylogenetic trees to ordination plots
coef.lmm.rrpp

coef for lmm.rrpp model fits
fishy

Simulated Fish Data for Measurement Error Analysis
betaTest

Test of beta parameters for lm.rrpp model fits
effect.size

Obtain Effect-size from a vector of values
anova.lm.rrpp

ANOVA for lm.rrpp model fits
coef.lm.rrpp

coef for lm.rrpp model fits
getModels

Utility Function for RRPP
fixef.lmm.rrpp

fixef for lmm.rrpp model fits
focusMEonSubjects

Plot Function for RRPP
fitted.lm.rrpp

Extract fitted values
getPermInfo

Utility Function for RRPP
getResCov

Utility Function for RRPP
flower

Flower Production and Temperature
getANOVAStats

Utility Function for RRPP
getModelCov

Utility Function for RRPP
getTerms

Utility Function for RRPP
looCV

Diagnostic cross-validation tool including ordination based on fitted values
logLik.lm.rrpp

Calculate the log-likelihood of a lm.rrpp fit
looCV_table

Table for looCV comparisons
lr_test

Likelihood ratio test for a linear model, based on RRPP
mahal_dist

Calculate the pairwise Mahalanobis distances between observations
kcomp

K-component analysis
interSubVar

Reveal the inter-subject variability from a measurement error analysis
lmm.rrpp

Mixed Linear Model Evaluation with RRPP performed within subjects
lm.rrpp.ws

Linear Model Evaluation with RRPP performed within subjects
lm.rrpp

Linear Model Evaluation with a Randomized Residual Permutation Procedure
model.matrix.lm.rrpp

Extract the model design matrix from an lm.rrpp object
manova.update

MANOVA update for lm.rrpp model fits
model.frame.lm.rrpp

Extract model frame from a lm.rrpp object
na.omit.rrpp.data.frame

Handle missing values in rrpp.data.frame objects
mammalHRphy

Phylogenetic Data for the Mammal Home Range Data
motionpaths

Simulated motion paths
model.comparison

Model Comparisons, in terms of the log-likelihood, covariance trace, or Z-score.
ordinate

Ordination tool for data aligned to another matrix
mammalHR

Mammal Home Range Data
measurement.error

Evaluation of measurement error for two or more multivariate measurements, for common research subjects
phytoplankton

Phytoplankton Biomass and Eutrophication
plot.interSubVar

Plot Function for RRPP
pairwise.model.Z

Pairwise comparisons of model effects
pairwise

Pairwise comparisons of lm.rrpp fits
plot.kcomp

Plot Function for RRPP
plot.model.comparison

Plot Function for RRPP
plot.looCV

Plot Function for RRPP
plot.measurement.error

Plot Function for RRPP
plot.ordinate

Plot Function for RRPP
plot.lm.rrpp

Plot Function for RRPP
print.betaTest

Print/Summary Function for RRPP
podarcis

Podarcis Wall Lizards from the Mediterranean Basin
powerTrans

Power Transformation
print.ordinate

Print/Summary Function for RRPP
prep.lda

Linear discriminant function for lm.rrpp model fits
print.measurement.error

Print/Summary Function for RRPP
print.pairwise

Print/Summary Function for RRPP
predict.lm.rrpp

predict for lm.rrpp model fits
print.pairwise.model.Z

Print/Summary Function for RRPP
print.summary.trajectory.analysis

Print/Summary Function for RRPP
print.model.comparison

Print/Summary Function for RRPP
print.trajectory.analysis

Print/Summary Function for RRPP
print.looCV

Print/Summary Function for RRPP
print.anova.lm.rrpp

Print/Summary Function for RRPP
print.coef.lm.rrpp

Print/Summary Function for RRPP
print.ICCstats

Print/Summary Function for RRPP
summary.betaTest

Print/Summary Function for RRPP
print.lr_test

Print/Summary Function for RRPP
scaleCov

Scaling of a Covariance Matrix
pval

Obtain P-value from a vector of statistics
summary.coef.lm.rrpp

Print/Summary Function for RRPP
print.summary.betaTest

Print/Summary Function for RRPP
print.summary.pairwise

Print/Summary Function for RRPP
print.predict.lm.rrpp

Print/Summary Function for RRPP
snakeHS

Snake Head Size and Regional Variation
print.summary.lm.rrpp

Print/Summary Function for RRPP
summary.looCV

Print/Summary Function for RRPP
summary.lm.rrpp

Print/Summary Function for RRPP
summary.kcomp

Print/Summary Function for RRPP
summary.manova.lm.rrpp

Print/Summary Function for RRPP
summary.pairwise.model.Z

Print/Summary Function for RRPP
summary.pairwise

Print/Summary Function for RRPP
rrpp.data.frame

Create a data frame for lm.rrpp analysis
print.lm.rrpp

Print/Summary Function for RRPP
plot.trajectory.analysis

Plot Function for RRPP
summary.lr_test

Print/Summary Function for RRPP
print.kcomp

Print/Summary Function for RRPP
print.summary.manova.lm.rrpp

Print/Summary Function for RRPP
plot.predict.lm.rrpp

Plot Function for RRPP
summary.predict.lm.rrpp

Print/Summary Function for RRPP
reveal.model.designs

Reveal model designs used in lm.rrpp fit
summary.ordinate

Print/Summary Function for RRPP
vec.cor.matrix

Support function for RRPP
print.summary.ordinate

Print/Summary Function for RRPP
summary.trajectory.analysis

Print/Summary Function for RRPP
summary.measurement.error

Print/Summary Function for RRPP
summary.model.comparison

Print/Summary Function for RRPP
terms.lm.rrpp

Extract the terms from an lm.rrpp object
ranef.lmm.rrpp

ranef for lmm.rrpp model fits
summary.ICCstats

Print/Summary Function for RRPP
residuals.lm.rrpp

Extract residuals
summary.anova.lm.rrpp

Print/Summary Function for RRPP
trajectory.analysis

Quantify and compare shape change trajectories
QRforX

QR decomposition of linear model design matrices
PupfishHeads

Landmarks on pupfish heads
PupfishMR

Experimental metabolic rate data from pupfish
ReptAbund

Reptile Abundance Data in Western Australia
PlethCinHoff

Plethodon comparative SVL data
PlethMorph

Plethodon comparative morphological data
RRPP-package

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

Intraclass correlation statistics from an lm.rrpp model fits
Pupfish

Landmarks on pupfish
add.trajectories

Plot Function for RRPP