mvabund: Statistical Methods for Analysing Multivariate Abundance Data

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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.

Author
Yi Wang, Ulrike Naumann, Stephen Wright, Dirk Eddelbuettel and David Warton
Date of publication
2016-04-29 12:11:50
Maintainer
David Warton <David.Warton@unsw.edu.au>
License
LGPL (>= 2.1)
Version
3.11.9

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

Files in this package

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