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mvabund (version 3.12.3)

Statistical Methods for Analysing Multivariate Abundance Data

Description

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.

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Version

Install

install.packages('mvabund')

Monthly Downloads

1,379

Version

3.12.3

License

LGPL (>= 2.1)

Maintainer

David Warton

Last Published

April 27th, 2017

Functions in mvabund (3.12.3)

Tasmania Dataset

Analysis of Deviance for Many Univariate Models Fitted to Multivariate Abundance Data

Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the best model by corss-validation.

deviance.manylm

Use R^2 to find the variables that best explain a multivariate response.

ANOVA for Linear Model Fits for Multivariate Abundance Data

Testing for a environment-by-trait (fourth corner) interaction by analysis of deviance

Ant data, with species traits

boxplot.mvabund

Boxplots for multivariate abundance Data

Fits a Generalised Linear Models with a LASSO (or L1) penalty, given a value of the penalty parameter.

Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the model that minimises BIC.

Analysis of Deviance for Multivariate Generalized Linear Model Fits for Abundance Data

workhose functions for fitting multivariate linear models

Construct Mean-Variance plots for Multivariate Abundance Data

Plot Diagnostics for a manyany or glm1path Object

Plot Diagnostics for a manylm or a manyglm Object

Plot Multivariate Abundance Data and Formulae

Draw a Mvabund Object split into groups.

Calculate the Log Likelihood

Fitting Many Univariate Models to Multivariate Abundance Data

Multivariate Abundance Data Objects

Model Formulae for Multivariate Abundance Data

extend.x.formula

Extend a Formula to all of it's Terms

Create a List of Univariate Formulas

mvabund-internal

Internal mvabund Objects

mvabund-package

Statistical methods for analysing multivariate abundance data

predict.traitglm

Predictions from fourth corner model fits

residuals.manyglm

Residuals for MANYGLM, MANYANY, GLM1PATH Fits

Fitting Generalized Linear Models for Multivariate Abundance Data

Fitting Linear Models for Multivariate Abundance Data

predict.manyglm

Predict Method for MANYGLM Fits

Tikus Island Dataset

Fits a fourth corner model for abundance as a function of environmental variables and species traits.

Remove the mvabund Class Attribute

summary.manyglm

Summarizing Multivariate Generalized Linear Model Fits for Abundance Data

Summarizing Linear Model Fits for Multivariate Abundance Data

Model Predictions for Multivariate Linear Models

Estimation of the ridge parameter

Calculate a shift for plotting overlapping points