# Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

## Documentation for package ‘RRPP’ version 2.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

add.trajectories | Plot Function for RRPP
add.tree | Plot tool to add phylogenetic trees to ordination plots
anova.lm.rrpp | ANOVA for lm.rrpp model fits
anova.measurement.error | ANOVA for lm.rrpp model fits used in measurement.error
betaTest | Test of beta parameters for lm.rrpp model fits
classify | Deprecated functions in RRPP
coef.lm.rrpp | coef for lm.rrpp model fits
convert2ggplot | Convert RRPP plots to ggplot objects
effect.size | Obtain Effect-size from a vector of values
fishy | Simulated fish data for measurement error analysis
fitted.lm.rrpp | Extract fitted values
focusMEonSubjects | Plot Function for RRPP
getANOVAStats | Utility Function for RRPP
getModelCov | Utility Function for RRPP
getModels | Utility Function for RRPP
getPermInfo | Utility Function for RRPP
getResCov | Utility Function for RRPP
getTerms | Utility Function for RRPP
ICCstats | Intraclass correlation statistics from an lm.rrpp model fits
interSubVar | Reveal the inter-subject variability from a measurement error analysis
kcomp | K-component analysis
lm.rrpp | Linear Model Evaluation with a Randomized Residual Permutation Procedure
lm.rrpp.ws | Linear Model Evaluation with RRPP performed within subjects
logLik.lm.rrpp | Calculate the log-likelihood of a lm.rrpp fit
looCV | Diagnostic cross-validation tool for ordination based on fitted values
lr_test | Likelihood ratio test for a linear model, based on RRPP
mahal_dist | Calculate the pairwise Mahalanobis distances between observations
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
model.comparison | Model Comparisons, in terms of the log-likelihood, covariance trace, or Z-score.
model.frame.lm.rrpp | Extract model frame from a lm.rrpp object
model.matrix.lm.rrpp | Extract the model design matrix from an lm.rrpp object
motionpaths | Simulated motion paths
na.omit.rrpp.data.frame | Handle missing values in rrpp.data.frame objects
ordinate | Ordination tool for data aligned to another matrix
pairwise | Pairwise comparisons of lm.rrpp fits
pairwise.model.Z | Pairwise comparisons of model effects
PlethMorph | Plethodon comparative morphological data
plot.interSubVar | Plot Function for RRPP
plot.kcomp | Plot Function for RRPP
plot.lm.rrpp | Plot Function for RRPP
plot.looCV | Plot Function for RRPP
plot.measurement.error | Plot Function for RRPP
plot.model.comparison | Plot Function for RRPP
plot.ordinate | Plot Function for RRPP
plot.predict.lm.rrpp | Plot Function for RRPP
plot.trajectory.analysis | Plot Function for RRPP
predict.lm.rrpp | predict for lm.rrpp model fits
prep.lda | Linear discriminant function for lm.rrpp model fits
print.anova.lm.rrpp | Print/Summary Function for RRPP
print.betaTest | Print/Summary Function for RRPP
print.coef.lm.rrpp | Print/Summary Function for RRPP
print.ICCstats | Print/Summary Function for RRPP
print.kcomp | Print/Summary Function for RRPP
print.lm.rrpp | Print/Summary Function for RRPP
print.looCV | Print/Summary Function for RRPP
print.lr_test | Print/Summary Function for RRPP
print.measurement.error | Print/Summary Function for RRPP
print.model.comparison | Print/Summary Function for RRPP
print.ordinate | Print/Summary Function for RRPP
print.pairwise | Print/Summary Function for RRPP
print.pairwise.model.Z | Print/Summary Function for RRPP
print.predict.lm.rrpp | Print/Summary Function for RRPP
print.summary.betaTest | Print/Summary Function for RRPP
print.summary.lm.rrpp | Print/Summary Function for RRPP
print.summary.manova.lm.rrpp | Print/Summary Function for RRPP
print.summary.ordinate | Print/Summary Function for RRPP
print.summary.pairwise | Print/Summary Function for RRPP
print.summary.trajectory.analysis | Print/Summary Function for RRPP
print.trajectory.analysis | Print/Summary Function for RRPP
Pupfish | Landmarks on pupfish
PupfishHeads | Landmarks on pupfish heads
pval | Obtain P-value from a vector of values
QRforX | QR decomposition of linear model design matrices
residuals.lm.rrpp | Extract residuals
reveal.model.designs | Reveal model designs used in lm.rrpp fit
rrpp.data.frame | Create a data frame for lm.rrpp analysis
scaleCov | Scaling of a Covariance Matrix
summary.anova.lm.rrpp | Print/Summary Function for RRPP
summary.betaTest | Print/Summary Function for RRPP
summary.coef.lm.rrpp | Print/Summary Function for RRPP
summary.ICCstats | Print/Summary Function for RRPP
summary.kcomp | Print/Summary Function for RRPP
summary.lm.rrpp | Print/Summary Function for RRPP
summary.looCV | Print/Summary Function for RRPP
summary.lr_test | Print/Summary Function for RRPP
summary.manova.lm.rrpp | Print/Summary Function for RRPP
summary.measurement.error | Print/Summary Function for RRPP
summary.model.comparison | Print/Summary Function for RRPP
summary.ordinate | Print/Summary Function for RRPP
summary.pairwise | Print/Summary Function for RRPP
summary.pairwise.model.Z | Print/Summary Function for RRPP
summary.predict.lm.rrpp | Print/Summary Function for RRPP
summary.trajectory.analysis | Print/Summary Function for RRPP
terms.lm.rrpp | Extract the terms from an lm.rrpp object
trajectory.analysis | Quantify and compare shape change trajectories
vec.cor.matrix | Support function for RRPP