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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("devtools")

devtools::install_github("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

1,438

Version

1.4.0

License

GPL (>= 3)

Issues

1

Pull Requests

0

Stars

4

Forks

1

Maintainer

Michael Collyer

Last Published

August 15th, 2023

Functions in RRPP (1.4.0)

fitted.lm.rrpp

Extract fitted values
getModelCov

Utility Function for RRPP
getResCov

Utility Function for RRPP
focusMEonSubjects

Plot Function for RRPP
interSubVar

Reveal the inter-subject variability from a measurement error analysis
getPermInfo

Utility Function for RRPP
getANOVAStats

Utility Function for RRPP
lm.rrpp

Linear Model Evaluation with a Randomized Residual Permutation Procedure
getModels

Utility Function for RRPP
getTerms

Utility Function for RRPP
model.frame.lm.rrpp

Extract model frame from a lm.rrpp object
looCV

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

Calculate the log-likelihood of a lm.rrpp fit
model.matrix.lm.rrpp

Extract the model design matrix from an lm.rrpp object
motionpaths

Simulated motion paths
lm.rrpp.ws

Linear Model Evaluation with RRPP performed within subjects
manova.update

MANOVA update for lm.rrpp model fits
measurement.error

Evaluation of measurement error for two or more multivariate measurements, for common research subjects
na.omit.rrpp.data.frame

Handle missing values in rrpp.data.frame objects
model.comparison

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

Ordination tool for data aligned to another matrix
pairwise

Pairwise comparisons of lm.rrpp fits
plot.ordinate

Plot Function for RRPP
plot.model.comparison

Plot Function for RRPP
plot.measurement.error

Plot Function for RRPP
rrpp.data.frame

Create a data frame for lm.rrpp analysis
plot.predict.lm.rrpp

Plot Function for RRPP
print.pairwise

Print/Summary Function for RRPP
reveal.model.designs

Reveal model designs used in lm.rrpp fit
print.lm.rrpp

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

Print/Summary Function for RRPP
print.looCV

Print/Summary Function for RRPP
plot.trajectory.analysis

Plot Function for RRPP
print.ordinate

Print/Summary Function for RRPP
summary.measurement.error

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

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

Print/Summary Function for RRPP
plot.interSubVar

Plot Function for RRPP
plot.looCV

Plot Function for RRPP
plot.lm.rrpp

Plot Function for RRPP
terms.lm.rrpp

Extract the terms from an lm.rrpp object
summary.pairwise

Print/Summary Function for RRPP
print.summary.ordinate

Print/Summary Function for RRPP
print.measurement.error

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

Print/Summary Function for RRPP
summary.ordinate

Print/Summary Function for RRPP
summary.model.comparison

Print/Summary Function for RRPP
print.model.comparison

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

Print/Summary Function for RRPP
summary.lm.rrpp

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

Print/Summary Function for RRPP
predict.lm.rrpp

predict for lm.rrpp model fits
prep.lda

Linear discriminant function for lm.rrpp model fits
summary.looCV

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

Print/Summary Function for RRPP
trajectory.analysis

Quantify and compare shape change trajectories
print.trajectory.analysis

Print/Summary Function for RRPP
residuals.lm.rrpp

Extract residuals
vec.cor.matrix

Support function for RRPP
print.summary.trajectory.analysis

Print/Summary Function for RRPP
scaleCov

Scaling of a Covariance Matrix
summary.anova.lm.rrpp

Print/Summary Function for RRPP
print.summary.pairwise

Print/Summary Function for RRPP
summary.trajectory.analysis

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

Print/Summary Function for RRPP
RRPP-package

Linear Model Evaluation with Randomized Residual Permutation Procedures
anova.lm.rrpp

ANOVA for lm.rrpp model fits
PupfishHeads

Landmarks on pupfish heads
classify

Deprecated functions in RRPP
convert2ggplot

Convert RRPP plots to ggplot objects
coef.lm.rrpp

coef for lm.rrpp model fits
PlethMorph

Plethodon comparative morphological data
Pupfish

Landmarks on pupfish
add.trajectories

Plot Function for RRPP
add.tree

Plot tool to add phylogenetic trees to ordination plots