# mvabund v4.1.3

0

0th

Percentile

## 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.

## mvabund    =======

Statistical Methods for Analysing Multivariate Abundance Data

### Authors

Yi Wang, Ulrike Naumann, Stephen Wright, Dirk Eddelbuettel and David Warton

LGPL (>= 2.1)

## Functions in mvabund

 Name Description anova.manylm ANOVA for Linear Model Fits for Multivariate Abundance Data Tasmania Tasmania Dataset anova.manyglm Analysis of Deviance for Multivariate Generalized Linear Model Fits for Abundance Data anova.manyany Analysis of Deviance for Many Univariate Models Fitted to Multivariate Abundance Data boxplot.mvabund Boxplots for multivariate abundance Data anova.traitglm Testing for a environment-by-trait (fourth corner) interaction by analysis of deviance best.r.sq Use R^2 to find the variables that best explain a multivariate response. antTraits Ant data, with species traits cv.glm1path Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the best model by corss-validation. coefplot.manyglm Plots the coefficients of the covariates of a manyglm object with confidence intervals. extend.x.formula Extend a Formula to all of it's Terms manyany Fitting Many Univariate Models to Multivariate Abundance Data deviance.manylm Model Deviance glm1path Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the model that minimises BIC. plotMvaFactor Draw a Mvabund Object split into groups. manylm.fit workhose functions for fitting multivariate linear models glm1 Fits a Generalised Linear Models with a LASSO (or L1) penalty, given a value of the penalty parameter. manylm Fitting Linear Models for Multivariate Abundance Data formulaUnimva Create a List of Univariate Formulas logLik.manylm Calculate the Log Likelihood meanvar.plot Construct Mean-Variance plots for Multivariate Abundance Data mvformula Model Formulae for Multivariate Abundance Data manyglm Fitting Generalized Linear Models for Multivariate Abundance Data predict.manyglm Predict Method for MANYGLM Fits mvabund-package Statistical methods for analysing multivariate abundance data mvabund-internal Internal mvabund Objects shiftpoints Calculate a shift for plotting overlapping points solberg Solberg Data spider Spider data plot.mvabund Plot Multivariate Abundance Data and Formulae tikus Tikus Island Dataset mvabund Multivariate Abundance Data Objects plot.manylm Plot Diagnostics for a manylm or a manyglm Object summary.manylm Summarizing Linear Model Fits for Multivariate Abundance Data summary.manyglm Summarizing Multivariate Generalized Linear Model Fits for Abundance Data predict.manylm Model Predictions for Multivariate Linear Models plot.manyany Plot Diagnostics for a manyany or glm1path Object residuals.manyglm Residuals for MANYGLM, MANYANY, GLM1PATH Fits ridgeParamEst Estimation of the ridge parameter traitglm Fits a fourth corner model for abundance as a function of environmental variables and species traits. unabund Remove the mvabund Class Attribute predict.traitglm Predictions from fourth corner model fits No Results!