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mvabund (version 3.11.4)

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

1,713

Version

3.11.4

License

LGPL (>= 2.1)

Maintainer

David Warton

Last Published

October 22nd, 2015

Functions in mvabund (3.11.4)

ANOVA for Linear Model Fits for Multivariate Abundance Data

Tasmania Dataset

Calculate the Log Likelihood

Multivariate Abundance Data Objects

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

Remove the mvabund Class Attribute

Summarizing Linear Model Fits for Multivariate Abundance Data

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

Plot Diagnostics for a manylm or a manyglm Object

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

extend.x.formula

Extend a Formula to all of it's Terms

boxplot.mvabund

Boxplots for multivariate abundance Data

Draw a Mvabund Object split into groups.

Ant data, with species traits

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

Construct Mean-Variance plots for Multivariate Abundance Data

Model Predictions for Multivariate Linear Models

residuals.manyglm

Residuals for MANYGLM, MANYANY, GLM1PATH Fits

summary.manyglm

Summarizing Multivariate Generalized Linear Model Fits for Abundance Data

workhose functions for fitting multivariate linear models

predict.traitglm

Predictions from fourth corner model fits

Fitting Many Univariate Models to Multivariate Abundance Data

Create a List of Univariate Formulas

deviance.manylm

mvabund-package

Statistical methods for analysing multivariate abundance data

Calculate a shift for plotting overlapping points

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

mvabund-internal

Internal mvabund Objects

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

Tikus Island Dataset

Fitting Generalized Linear Models for Multivariate Abundance Data

Plot Multivariate Abundance Data and Formulae

Model Formulae for Multivariate Abundance Data

Estimation of the ridge parameter

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

predict.manyglm

Predict Method for MANYGLM Fits

Fitting Linear Models for Multivariate Abundance Data

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

Plot Diagnostics for a manyany or glm1path Object