mvabund: Statistical Methods for Analysing Multivariate Abundance Data

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.

Install the latest version of this package by entering the following in R:
install.packages("mvabund")
AuthorYi Wang, Ulrike Naumann, Stephen Wright, Dirk Eddelbuettel and David Warton
Date of publication2017-04-27 23:27:39 UTC
MaintainerDavid Warton <David.Warton@unsw.edu.au>
LicenseLGPL (>= 2.1)
Version3.12.3

View on CRAN

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

absspp Man page
anova.manyany Man page
anova.manyglm Man page
anova.manyglmlist Man page
anova.manylm Man page
anova.manylmlist Man page
anova.traitglm Man page
antTraits Man page
as.data.frame.mvabund Man page
as.matrix.mvabund Man page
as.mvabund Man page
as.mvformula Man page
best.r.sq Man page
betaest Man page
betaphiest Man page
boxplot.mvabund Man page
boxplot.mvformula Man page
case.names.manyglm Man page
case.names.manylm Man page
cbind.mvabund Man page
covratio Man page
cv.glm1path Man page
deviance.manylm Man page
dffits Man page
effic.make.link Man page
extend.x.formula Man page
formulaMva Man page
formulaUnimva Man page
geecalc Man page
geecalcI Man page
geecalcLR Man page
geecalcsumm Man page
geecalcsummI Man page
geecalcsummLR Man page
geeSummaryTest Man page
geeTest Man page
get.colors Man page
glm1 Man page
glm1path Man page
influence.measures Man page
is.formulaUnimva Man page
is.mvabund Man page
is.mvformula Man page
LLCalc Man page
LLSolve Man page
logLik.manylm Man page
makePlot Man page
manyany Man page
manyglm Man page
manylm Man page
manylm.fit Man page
manylm.multiwfit Man page
manylm.wfit Man page
meanvar.plot Man page
meanvar.plot,data.frame-method Man page
meanvar.plot,formula-method Man page
meanvar.plot,matrix-method Man page
meanvar.plot.mvabund Man page
meanvar.plot,mvabund-method Man page
meanvar.plot.mvformula Man page
meanvar.plot,mvformula-method Man page
mvabund Man page
[.mvabund Man page
mvabund-class Man page
mvabund-package Man page
mvformula Man page
mvformula-class Man page
nbinall Man page
nbinall2 Man page
nbinfit Man page
plot Man page
plotFormulafeature Man page
plot.glm1path Man page
plot.manyany Man page
plot.manyglm Man page
plot.manylm Man page
plot.mvabund Man page
plotMvaFactor Man page
plot.mvformula Man page
predict.manyglm Man page
predict.manylm Man page
predict.traitglm Man page
print.anova.manyany Man page
print.anova.manyglm Man page
print.anova.manyglm Man page
print.anova.manylm Man page
print.manyany Man page
print.manyglm Man page
print.manylm Man page
print.mvabund Man page
print.mvformula Man page
print.summary.manyglm Man page
print.summary.manylm Man page
rbind.mvabund Man page
rcalc Man page
RcppVersion Man page
residuals.glm1path Man page
residuals.manyany Man page
residuals.manyglm Man page
ridgeParamEst Man page
shiftpoints Man page
shiftpoints Man page
solberg Man page
spider Man page
summary.manyglm Man page
summary.manylm Man page
Tasmania Man page
tikus Man page
traitglm Man page
transAxis Man page
unabund Man page
variable.names.manyglm Man page
weighted.residuals Man page
weights.manyglm Man page

Files

src
src/Makevars
src/Rinterface.cpp
src/rnd.cpp
src/anova.cpp
src/simutility.cpp
src/summary.cpp
src/calctest.cpp
src/mvabund_init.c
src/io.cpp
src/resampTest.h
src/glm.cpp
src/mvabund_types.h
src/Makevars.win
src/RcppExports.cpp
src/rmv.h
src/glmtest.cpp
NAMESPACE
data
data/antTraits.RData
data/solberg.RData
data/spider.RData
data/tikus.RData
data/Tasmania.RData
R
R/mvabund.object.R R/cv.glm1path.R R/make.vslink.R R/manylm.R R/quasiloglik.R R/residuals.glm1path.R R/glm1.R R/effic.make.link.R R/anova.manyglm.R R/transAxis.SW.R R/weighted.residuals.manylm.R R/plot.mvabund.R R/rstandard.manylm.R R/absspp.R R/default.boxplot.mvabund.R R/default.print.summary.manyglm.R R/print.mvformula.R R/default.print.anova.manyglm.R R/manyany.R R/default.plot.mvabund.R R/variable.names.manyglm.R R/print.anova.manylm.R R/print.summary.manylm.R R/shiftpoints.R R/extract.mvabund.R R/residuals.manyglm.R R/AllClass.R R/rstudent.manylm.R R/default.plotMvaFactor.R R/plot.mvformula.R R/cooks.distance.manylm.R R/predict.manylm.R R/dffits.manylm.R R/print.manyglm.R R/formulaUnimva.R R/summary.manylm.R R/anova.manylm.R R/as.data.frame.mvabund.R R/deviance.manylm.R R/is.wholenumber.R R/boxplot.mvformula.R R/mvformula.R R/quasipoisson.R R/default.plot.manyglm.R R/binstruc.R R/default.plot.mvformula.R R/dfbeta.manylm.R R/default.plot.manylm.R R/logLik.manylm.R R/hatvalues.manylm.R R/covratio.manylm.R R/manylm.influence.R R/RcppExports.R R/betaest.R R/plot.manylm.R R/predict.traitglm.R R/manylm.influence.measures.R R/boxplot.mvabund.R R/manyglm.R R/best.r.sq.R R/as.matrix.mvabund.R R/plot.manyglm.R R/meanvar.plot.R R/plotFormulafeature.R R/logLik.manyglm.R R/nobs.manyglm.R R/RcppVersion.R R/predict.manyglm.R R/weights.manyglm.R R/print.anova.manyglm.R R/RidgeParamEst.R R/cbind.mvabund.R R/quasibinomialMany.R R/anova.traitglm.R R/unabund.R R/case.names.manylm.R R/summary.manyglm.R R/influence.manylm.R R/print.summary.manyglm.R R/print.infl.mvabund.R R/plotMvaFactor.R R/glm1path.R R/anova.manyany.R R/rbind.mvabund.R R/rcalc.R R/traitglm.R R/dfbetas.manylm.R R/extend.x.formula.R R/default.meanvar.plot.R R/qordinal.R R/extractAIC.manyglm.R R/default.boxplot.mvformula.R R/manylm.multiwfit.R
MD5
DESCRIPTION
man
man/anova.traitglm.Rd man/plotMvaFactor.Rd man/mvformula.Rd man/predict.traitglm.Rd man/extend.x.formula.Rd man/manyglm.Rd man/antTraits.Rd man/manyany.Rd man/summary.manylm.Rd man/summary.manyglm.Rd man/plot.manyany.Rd man/mvabund-internal.Rd man/predict.manyglm.Rd man/plot.mvabund.Rd man/tikus.Rd man/cv.glm1path.Rd man/manylm.Rd man/mvabund-package.Rd man/spider.Rd man/residuals.manyglm.Rd man/predict.manylm.Rd man/glm1path.Rd man/mvabund.Rd man/shiftpoints.Rd man/boxplot.mvabund.Rd man/meanvar.plot.Rd man/formulaUnimva.Rd man/ridgeParamEst.Rd man/plot.manylm.Rd man/traitglm.Rd man/manylm.fit.Rd man/unabund.Rd man/deviance.manylm.Rd man/logLik.manylm.Rd man/anova.manyglm.Rd man/best.r.sq.Rd man/solberg.Rd man/anova.manyany.Rd man/glm1.Rd man/Tasmania.Rd man/anova.manylm.Rd
cleanup

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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