mvabund: Statistical Methods for Analysing Multivariate Abundance Data
Version 3.10.5

A set of tools for displaying, modeling and analysing multivariate abundance data in community ecology. See 'mvabund-package.Rd' for details of overall package organization. The package is implemented with the Gnu Scientific Library (http://www.gnu.org/software/gsl/) and Rcpp (http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.

Browse man pages Browse package API and functions Browse package files

AuthorYi Wang, Ulrike Naumann, Stephen Wright and David Warton
Date of publication2015-08-17 02:08:55
MaintainerDavid Warton <David.Warton@unsw.edu.au>
LicenseLGPL (>= 2.1)
Version3.10.5
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("mvabund", repos="http://R-Forge.R-project.org")

Man pages

anova.manyany: Analysis of Deviance for Many Univariate Models Fitted to...
anova.manyglm: Analysis of Deviance for Multivariate Generalized Linear...
anova.manylm: ANOVA for Linear Model Fits for Multivariate Abundance Data
anova.traitglm: Testing for a environment-by-trait (fourth corner)...
antTraits: Ant data, with species traits
best.r.sq: Use R^2 to find the variables that best explain a...
boxplot.mvabund: Boxplots for multivariate abundance Data
cv.glm1path: Fits a path of Generalised Linear Models with LASSO (or L1)...
deviance.manylm: Model Deviance
extend.x.formula: Extend a Formula to all of it's Terms
formulaUnimva: Create a List of Univariate Formulas
glm1: Fits a Generalised Linear Models with a LASSO (or L1)...
glm1path: Fits a path of Generalised Linear Models with LASSO (or L1)...
logLik.manylm: Calculate the Log Likelihood
manyany: Fitting Many Univariate Models to Multivariate Abundance Data
manyglm: Fitting Generalized Linear Models for Multivariate Abundance...
manylm: Fitting Linear Models for Multivariate Abundance Data
manylm.fit: workhose functions for fitting multivariate linear models
meanvar.plot: Construct Mean-Variance plots for Multivariate Abundance Data
mvabund: Multivariate Abundance Data Objects
mvabund-internal: Internal mvabund Objects
mvabund-package: Statistical methods for analysing multivariate abundance data
mvformula: Model Formulae for Multivariate Abundance Data
plot.manyany: Plot Diagnostics for a manyany or glm1path Object
plot.manylm: Plot Diagnostics for a manylm or a manyglm Object
plot.mvabund: Plot Multivariate Abundance Data and Formulae
plotMvaFactor: Draw a Mvabund Object split into groups.
predict.manyglm: Predict Method for MANYGLM Fits
predict.manylm: Model Predictions for Multivariate Linear Models
predict.traitglm: Predictions from fourth corner model fits
residuals.manyglm: Residuals for MANYGLM, MANYANY, GLM1PATH Fits
ridgeParamEst: Estimation of the ridge parameter
shiftpoints: Calculate a shift for plotting overlapping points
solberg: Solberg Data
spider: Spider data
summary.manyglm: Summarizing Multivariate Generalized Linear Model Fits for...
summary.manylm: Summarizing Linear Model Fits for Multivariate Abundance Data
Tasmania: Tasmania Dataset
tikus: Tikus Island Dataset
traitglm: Fits a fourth corner model for abundance as a function of...
unabund: Remove the mvabund Class Attribute

Functions

LLCalc Man page Source code
LLSolve Man page Source code
RcppVersion Man page Source code
Tasmania Man page
[.mvabund Man page
absspp Man page Source code
anova.manyany Man page Source code
anova.manyglm Man page Source code
anova.manyglmlist Man page
anova.manylm Man page Source code
anova.manylmlist Man page
anova.traitglm Man page Source code
antTraits Man page
as.data.frame.mvabund Man page Source code
as.matrix.mvabund Man page Source code
as.mvabund Man page Source code
as.mvformula Man page Source code
axisTicks Source code
best.r.sq Man page Source code
betaest Man page Source code
betaphiest Man page
binstruc Source code
bootAnova Source code
boxplot.mvabund Man page Source code
boxplot.mvformula Man page Source code
case.names.manyglm Man page
case.names.manylm Man page
cbind.mvabund Man page Source code
coef.manyany Source code
cooks.distance.manylm Source code
covratio Man page
covratio.manylm Source code
cv.glm1path Man page Source code
default.boxplot.mvabund Source code
default.boxplot.mvformula Source code
default.meanvar.plot.mvabund Source code
default.meanvar.plot.mvformula Source code
default.plot.manyglm Source code
default.plot.manylm Source code
default.plot.mvabund Source code
default.plot.mvformula Source code
default.plotMvaFactor Source code
default.print.anova.manyglm Source code
default.print.summary.manyglm Source code
deviance.manylm Man page Source code
dfbetas.manylm Source code
dffits Man page
dffits.manylm Source code
effic.make.link Man page Source code
extend.x.formula Man page Source code
extractAIC.manyglm Source code
formulaMva Man page Source code
formulaUnimva Man page Source code
geeSummaryTest Man page
geeTest Man page
geecalc Man page
geecalcI Man page
geecalcLR Man page
geecalcsumm Man page
geecalcsummI Man page
geecalcsummLR Man page
get.colors Man page
get.design Source code
get.polys Source code
glm1 Man page Source code
glm1path Man page Source code
hatvalues.manylm Source code
influence.manylm Source code
influence.measures Man page
is.formulaUnimva Man page Source code
is.mvabund Man page Source code
is.mvformula Man page Source code
is.wholenumber Source code Source code
logLik.manyany Source code
logLik.manyglm Source code
logLik.manylm Man page Source code
make.vslink Source code
makePlot Man page Source code
manyany Man page Source code
manyglm Man page Source code
manylm Man page Source code
manylm.fit Man page Source code
manylm.influence Source code
manylm.influence.measures Source code
manylm.multiwfit Man page Source code Source code
manylm.wfit Man page Source code
meanvar.plot Man page Source code
meanvar.plot,data.frame-method Man page
meanvar.plot,formula-method Man page
meanvar.plot,matrix-method Man page
meanvar.plot,mvabund-method Man page
meanvar.plot,mvformula-method Man page
meanvar.plot.mvabund Man page Source code
meanvar.plot.mvformula Man page Source code
mu.update Source code
mvabund Man page Source code
mvabund-class Man page
mvabund-package Man page
mvformula Man page Source code
mvformula-class Man page
nbinall Man page
nbinall2 Man page
nbinfit Man page
nobs.manyglm Source code
plot Man page
plot.glm1path Man page Source code
plot.manyany Man page Source code
plot.manyglm Man page Source code
plot.manylm Man page Source code
plot.mvabund Man page Source code
plot.mvformula Man page Source code
plotFormulafeature Man page Source code
plotMvaFactor Man page Source code
predict.manyglm Man page Source code
predict.manylm Man page Source code
predict.traitglm Man page Source code
print.anova.manyany Man page Source code
print.anova.manyglm Man page Man page Source code
print.anova.manylm Man page Source code
print.infl.mvabund Source code
print.manyany Source code
print.manyglm Man page Source code
print.manylm Man page Source code
print.mvabund Man page Source code
print.mvformula Man page Source code
print.summary.manyglm Man page Source code
print.summary.manylm Man page Source code
qordinal Source code
quasibinomialMany Source code
quasiloglik Source code
quasipoisson Source code
rbind.mvabund Man page Source code
rcalc Man page Source code
residuals.glm1path Man page Source code
residuals.manyany Man page Source code
residuals.manyglm Man page Source code
ridgeParamEst Man page Source code
rstandard.manylm Source code
rstudent.manylm Source code
shiftpoints Man page Man page Source code
solberg Man page
spider Man page
summary.manyglm Man page Source code
summary.manylm Man page Source code
tikus Man page
traitglm Man page Source code
transAxis Man page Source code
unabund Man page Source code
variable.names.manyglm Man page Source code
weighted.residuals Man page
weighted.residuals.manylm Source code
weights.manyglm Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClass.R
R/RcppVersion.R
R/RidgeParamEst.R
R/absspp.R
R/anova.manyany.R
R/anova.manyglm.R
R/anova.manylm.R
R/anova.traitglm.R
R/as.data.frame.mvabund.R
R/as.matrix.mvabund.R
R/best.r.sq.R
R/betaest.R
R/binstruc.R
R/boxplot.mvabund.R
R/boxplot.mvformula.R
R/case.names.manylm.R
R/cbind.mvabund.R
R/cooks.distance.manylm.R
R/covratio.manylm.R
R/cv.glm1path.R
R/default.boxplot.mvabund.R
R/default.boxplot.mvformula.R
R/default.meanvar.plot.R
R/default.plot.manyglm.R
R/default.plot.manylm.R
R/default.plot.mvabund.R
R/default.plot.mvformula.R
R/default.plotMvaFactor.R
R/default.print.anova.manyglm.R
R/default.print.summary.manyglm.R
R/deviance.manylm.R
R/dfbeta.manylm.R
R/dfbetas.manylm.R
R/dffits.manylm.R
R/effic.make.link.R
R/extend.x.formula.R
R/extract.mvabund.R
R/extractAIC.manyglm.R
R/formulaUnimva.R
R/glm1.R
R/glm1path.R
R/hatvalues.manylm.R
R/influence.manylm.R
R/is.wholenumber.R
R/logLik.manyglm.R
R/logLik.manylm.R
R/make.vslink.R
R/manyany.R
R/manyglm.R
R/manylm.R
R/manylm.influence.R
R/manylm.influence.measures.R
R/manylm.multiwfit.R
R/meanvar.plot.R
R/mvabund.object.R
R/mvformula.R
R/nobs.manyglm.R
R/plot.manyglm.R
R/plot.manylm.R
R/plot.mvabund.R
R/plot.mvformula.R
R/plotFormulafeature.R
R/plotMvaFactor.R
R/predict.manyglm.R
R/predict.manylm.R
R/predict.traitglm.R
R/print.anova.manyglm.R
R/print.anova.manylm.R
R/print.infl.mvabund.R
R/print.manyglm.R
R/print.mvformula.R
R/print.summary.manyglm.R
R/print.summary.manylm.R
R/qordinal.R
R/quasibinomialMany.R
R/quasiloglik.R
R/quasipoisson.R
R/rbind.mvabund.R
R/rcalc.R
R/residuals.glm1path.R
R/residuals.manyglm.R
R/rstandard.manylm.R
R/rstudent.manylm.R
R/shiftpoints.R
R/summary.manyglm.R
R/summary.manylm.R
R/traitglm.R
R/transAxis.SW.R
R/unabund.R
R/variable.names.manyglm.R
R/weighted.residuals.manylm.R
R/weights.manyglm.R
cleanup
configure
configure.ac
data
data/Tasmania.RData
data/antTraits.RData
data/solberg.RData
data/spider.RData
data/tikus.RData
man
man/Tasmania.Rd
man/anova.manyany.Rd
man/anova.manyglm.Rd
man/anova.manylm.Rd
man/anova.traitglm.Rd
man/antTraits.Rd
man/best.r.sq.Rd
man/boxplot.mvabund.Rd
man/cv.glm1path.Rd
man/deviance.manylm.Rd
man/extend.x.formula.Rd
man/formulaUnimva.Rd
man/glm1.Rd
man/glm1path.Rd
man/logLik.manylm.Rd
man/manyany.Rd
man/manyglm.Rd
man/manylm.Rd
man/manylm.fit.Rd
man/meanvar.plot.Rd
man/mvabund-internal.Rd
man/mvabund-package.Rd
man/mvabund.Rd
man/mvformula.Rd
man/plot.manyany.Rd
man/plot.manylm.Rd
man/plot.mvabund.Rd
man/plotMvaFactor.Rd
man/predict.manyglm.Rd
man/predict.manylm.Rd
man/predict.traitglm.Rd
man/residuals.manyglm.Rd
man/ridgeParamEst.Rd
man/shiftpoints.Rd
man/solberg.Rd
man/spider.Rd
man/summary.manyglm.Rd
man/summary.manylm.Rd
man/tikus.Rd
man/traitglm.Rd
man/unabund.Rd
src
src/Makevars.in
src/Makevars.win
src/RtoAnovaCpp.cpp
src/RtoGlm.cpp
src/RtoGlmAnova.cpp
src/RtoGlmSmry.cpp
src/RtoSmryCpp.cpp
src/anova.cpp
src/calctest.cpp
src/glm.cpp
src/glmtest.cpp
src/io.cpp
src/resampTest.h
src/rmv.h
src/rnd.cpp
src/simutility.cpp
src/summary.cpp
mvabund documentation built on May 21, 2017, 3:42 a.m.