# Statistical Methods for Analysing Multivariate Abundance Data

## Documentation for package ‘mvabund’ version 4.2.8

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

## Help Pages

mvabund-package | Statistical methods for analysing multivariate abundance data
anova.manyany | Analysis of Deviance for Many Univariate Models Fitted to Multivariate Abundance Data
anova.manyglm | Analysis of Deviance for Multivariate Generalized Linear Model Fits for Abundance Data
anova.manylm | ANOVA for Linear Model Fits for Multivariate Abundance Data
anova.traitglm | Testing for a environment-by-trait (fourth corner) interaction by analysis of deviance
antTraits | Ant data, with species traits
as.mvabund | Multivariate Abundance Data Objects
as.mvformula | Model Formulae for Multivariate Abundance Data
best.r.sq | Use R^2 to find the variables that best explain a multivariate response.
boxplot.mvabund | Boxplots for multivariate abundance Data
boxplot.mvformula | Boxplots for multivariate abundance Data
coefplot.manyglm | Plots the coefficients of the covariates of a manyglm object with confidence intervals.
cv.glm1path | Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the best model by corss-validation.
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) penalty, given a value of the penalty parameter.
glm1path | Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the model that minimises BIC.
is.mvabund | Multivariate Abundance Data Objects
is.mvformula | Model Formulae for Multivariate Abundance Data
logLik.manylm | Calculate the Log Likelihood
manyany | Fitting Many Univariate Models to Multivariate Abundance Data
manyglm | Fitting Generalized Linear Models for Multivariate Abundance Data
manylm | Fitting Linear Models for Multivariate Abundance Data
manylm.fit | workhose functions for fitting multivariate linear models
manylm.wfit | workhose functions for fitting multivariate linear models
meanvar.plot | Construct Mean-Variance plots for Multivariate Abundance Data
meanvar.plot-method | Construct Mean-Variance plots for Multivariate Abundance Data
meanvar.plot.mvabund | Construct Mean-Variance plots for Multivariate Abundance Data
meanvar.plot.mvformula | Construct Mean-Variance plots for Multivariate Abundance Data
mvabund | Multivariate Abundance Data Objects
mvabund-class | Multivariate Abundance Data Objects
mvformula | Model Formulae for Multivariate Abundance Data
mvformula-class | Model Formulae for Multivariate Abundance Data
plot.glm1path | Plot Diagnostics for a manyany or glm1path Object
plot.manyany | Plot Diagnostics for a manyany or glm1path Object
plot.manyglm | Plot Diagnostics for a manylm or a manyglm Object
plot.manylm | Plot Diagnostics for a manylm or a manyglm Object
plot.mvabund | Plot Multivariate Abundance Data and Formulae
plot.mvformula | 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
print.anova.manyany | Analysis of Deviance for Many Univariate Models Fitted to Multivariate Abundance Data
print.anova.manyglm | Analysis of Deviance for Multivariate Generalized Linear Model Fits for Abundance Data
print.anova.manylm | ANOVA for Linear Model Fits for Multivariate Abundance Data
print.manyany | Fitting Many Univariate Models to Multivariate Abundance Data
print.summary.manyglm | Summarizing Multivariate Generalized Linear Model Fits for Abundance Data
print.summary.manylm | Summarizing Linear Model Fits for Multivariate Abundance Data
residuals.glm1path | Residuals for MANYGLM, MANYANY, GLM1PATH Fits
residuals.manyany | Residuals for MANYGLM, MANYANY, GLM1PATH 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 Abundance Data
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 environmental variables and species traits.
unabund | Remove the mvabund Class Attribute