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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 geomorph 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

1,397

Version

1.3.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/mlcollyer/RRPP

Maintainer

Michael Collyer

Last Published

June 21st, 2022

Functions in RRPP (1.3.0)

Convert RRPP plots to ggplot objects

model.matrix.lm.rrpp

Extract the model design matrix from an lm.rrpp object

model.frame.lm.rrpp

Extract model frame from a lm.rrpp object

Simulated motion paths

na.omit.rrpp.data.frame

Handle missing values in rrpp.data.frame objects

Plot Function for RRPP

Plot Function for RRPP

print.model.comparison

Print/Summary Function for RRPP

Print/Summary Function for RRPP

plot.model.comparison

Plot Function for RRPP

print.coef.lm.rrpp

Print/Summary Function for RRPP

Extract the terms from an lm.rrpp object

Extract fitted values

summary.anova.lm.rrpp

Print/Summary Function for RRPP

trajectory.analysis

Quantify and compare shape change trajectories

print.anova.lm.rrpp

Print/Summary Function for RRPP

summary.coef.lm.rrpp

Print/Summary Function for RRPP

Plot Function for RRPP

Print/Summary Function for RRPP

Linear Model Evaluation with a Randomized Residual Permutation Procedure

MANOVA update for lm.rrpp model fits

print.summary.manova.lm.rrpp

Print/Summary Function for RRPP

summary.predict.lm.rrpp

Print/Summary Function for RRPP

Diagnostic cross-validation tool for ordination based on fitted values

print.summary.trajectory.analysis

Print/Summary Function for RRPP

Calculate the log-likelihood of a lm.rrpp fit

plot.predict.lm.rrpp

Plot Function for RRPP

plot.trajectory.analysis

Plot Function for RRPP

print.trajectory.analysis

Print/Summary Function for RRPP

model.comparison

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

print.summary.lm.rrpp

Print/Summary Function for RRPP

Ordination tool for data aligned to another matrix

summary.trajectory.analysis

Print/Summary Function for RRPP

Support function for RRPP

Linear discriminant function for lm.rrpp model fits

print.summary.ordinate

Print/Summary Function for RRPP

summary.lm.rrpp

Print/Summary Function for RRPP

predict.lm.rrpp

predict for lm.rrpp model fits

Pairwise comparisons of lm.rrpp fits

rrpp.data.frame

Create a data frame for lm.rrpp analysis

Print/Summary Function for RRPP

print.summary.pairwise

Print/Summary Function for RRPP

summary.ordinate

Print/Summary Function for RRPP

Print/Summary Function for RRPP

Scaling of a Covariance Matrix

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

residuals.lm.rrpp

Extract residuals

summary.manova.lm.rrpp

Print/Summary Function for RRPP

summary.model.comparison

Print/Summary Function for RRPP

summary.pairwise

Print/Summary Function for RRPP

Landmarks on pupfish

Landmarks on pupfish heads

Linear Model Evaluation with Randomized Residual Permutation Procedures

Plot tool to add phylogenetic trees to ordination plots

add.trajectories

Plot Function for RRPP

coef for lm.rrpp model fits

Plethodon comparative morphological data

ANOVA for lm.rrpp model fits

Deprecated functions in RRPP