RRPP2.1.2 package

Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

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

model.matrix.lm.rrpp

Extract the model design matrix from an lm.rrpp object

na.omit.rrpp.data.frame

Handle missing values in rrpp.data.frame objects

ordinate

Ordination tool for data aligned to another matrix

pairwise.model.Z

Pairwise comparisons of model effects

pairwise

Pairwise comparisons of lm.rrpp fits

plot.interSubVar

Plot Function for RRPP

plot.kcomp

Plot Function for RRPP

pval

Obtain P-value from a vector of values

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

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

model.frame.lm.rrpp

Extract model frame from a lm.rrpp object

print.pairwise

Print/Summary Function for RRPP

measurement.error

Evaluation of measurement error for two or more multivariate measureme...

model.comparison

Model Comparisons, in terms of the log-likelihood, covariance trace, o...

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

print.predict.lm.rrpp

Print/Summary Function for RRPP

convert2ggplot

Convert RRPP plots to ggplot objects

effect.size

Obtain Effect-size from a vector of values

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

print.summary.betaTest

Print/Summary Function for RRPP

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 Procedu...

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

print.summary.lm.rrpp

Print/Summary 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.model.Z

Print/Summary Function for RRPP

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-package

RRPP: Linear Model Evaluation with Randomized Residuals in a Permutati...

rrpp.data.frame

Create a data frame for lm.rrpp analysis

summary.trajectory.analysis

Print/Summary Function for RRPP

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.model.Z

Print/Summary Function for RRPP

summary.pairwise

Print/Summary Function for RRPP

summary.predict.lm.rrpp

Print/Summary Function for RRPP

Download source packageRead PDF manual

Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.