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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

1,622

Version

2.1.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/mlcollyer/RRPP

Maintainer

Michael Collyer

Last Published

February 1st, 2025

Functions in RRPP (2.1.0)

Obtain Effect-size from a vector of values

Deprecated functions in RRPP

Convert RRPP plots to ggplot objects

Utility Function for RRPP

Utility Function for RRPP

Simulated fish data for measurement error analysis

focusMEonSubjects

Plot Function for RRPP

Extract fitted values

coef for lm.rrpp model fits

Test of beta parameters for lm.rrpp model fits

Utility Function for RRPP

Reveal the inter-subject variability from a measurement error analysis

Diagnostic cross-validation tool for ordination based on fitted values

Utility Function for RRPP

Calculate the log-likelihood of a lm.rrpp fit

Utility Function for RRPP

Utility Function for RRPP

K-component analysis

model.matrix.lm.rrpp

Extract the model design matrix from an lm.rrpp object

MANOVA update for lm.rrpp model fits

Simulated motion paths

measurement.error

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

Likelihood ratio test for a linear model, based on RRPP

Calculate the pairwise Mahalanobis distances between observations

model.comparison

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

na.omit.rrpp.data.frame

Handle missing values in rrpp.data.frame objects

model.frame.lm.rrpp

Extract model frame from a lm.rrpp object

pairwise.model.Z

Pairwise comparisons of model effects

Linear Model Evaluation with RRPP performed within subjects

Ordination tool for data aligned to another matrix

Pairwise comparisons of lm.rrpp fits

Linear Model Evaluation with a Randomized Residual Permutation Procedure

Plot Function for RRPP

Plot Function for RRPP

Print/Summary Function for RRPP

print.coef.lm.rrpp

Print/Summary Function for RRPP

Print/Summary Function for RRPP

plot.measurement.error

Plot Function for RRPP

print.summary.ordinate

Print/Summary Function for RRPP

plot.interSubVar

Plot Function for RRPP

Linear discriminant function for lm.rrpp model fits

print.anova.lm.rrpp

Print/Summary Function for RRPP

Print/Summary Function for RRPP

plot.model.comparison

Plot Function for RRPP

print.summary.manova.lm.rrpp

Print/Summary Function for RRPP

rrpp.data.frame

Create a data frame for lm.rrpp analysis

Scaling of a Covariance Matrix

Print/Summary Function for RRPP

print.pairwise.model.Z

Print/Summary Function for RRPP

Plot Function for RRPP

plot.predict.lm.rrpp

Plot Function for RRPP

Plot Function for RRPP

plot.trajectory.analysis

Plot Function for RRPP

predict.lm.rrpp

predict for lm.rrpp model fits

Print/Summary Function for RRPP

print.predict.lm.rrpp

Print/Summary Function for RRPP

Print/Summary Function for RRPP

reveal.model.designs

Reveal model designs used in lm.rrpp fit

Print/Summary Function for RRPP

print.measurement.error

Print/Summary Function for RRPP

summary.lm.rrpp

Print/Summary Function for RRPP

residuals.lm.rrpp

Extract residuals

Support function for RRPP

print.trajectory.analysis

Print/Summary Function for RRPP

Extract the terms from an lm.rrpp object

summary.lr_test

Print/Summary Function for RRPP

Print/Summary Function for RRPP

Print/Summary Function for RRPP

trajectory.analysis

Quantify and compare shape change trajectories

Obtain P-value from a vector of values

print.summary.lm.rrpp

Print/Summary Function for RRPP

summary.ordinate

Print/Summary Function for RRPP

summary.model.comparison

Print/Summary Function for RRPP

summary.betaTest

Print/Summary Function for RRPP

summary.ICCstats

Print/Summary Function for RRPP

print.model.comparison

Print/Summary Function for RRPP

Print/Summary Function for RRPP

summary.coef.lm.rrpp

Print/Summary Function for RRPP

summary.anova.lm.rrpp

Print/Summary Function for RRPP

print.summary.pairwise

Print/Summary Function for RRPP

summary.pairwise.model.Z

Print/Summary Function for RRPP

summary.pairwise

Print/Summary Function for RRPP

summary.manova.lm.rrpp

Print/Summary Function for RRPP

summary.measurement.error

Print/Summary Function for RRPP

print.summary.trajectory.analysis

Print/Summary Function for RRPP

summary.predict.lm.rrpp

Print/Summary Function for RRPP

summary.trajectory.analysis

Print/Summary Function for RRPP

add.trajectories

Plot Function for RRPP

Landmarks on pupfish heads

Plethodon comparative morphological data

anova.measurement.error

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

Plot tool to add phylogenetic trees to ordination plots

Landmarks on pupfish

QR decomposition of linear model design matrices

Intraclass correlation statistics from an lm.rrpp model fits

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

ANOVA for lm.rrpp model fits