mvabund

v. 
by David Warton
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Date 2016-04-29
LinkingTo Rcpp, RcppGSL
License LGPL (>= 2.1)
NeedsCompilation yes
Packaged 2016-04-29 05:07:43 UTC; z3103495
Repository CRAN
Date/Publication 2016-04-29 12:11:50

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.
Full Readme

Functions in mvabund

Name Description
glm1path Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the model that minimises BIC.
deviance.manylm Model Deviance
anova.traitglm Testing for a environment-by-trait (fourth corner) interaction by analysis of deviance
Tasmania Tasmania Dataset
manyany Fitting Many Univariate Models to Multivariate Abundance Data
boxplot.mvabund Boxplots for multivariate abundance Data
logLik.manylm Calculate the Log Likelihood
mvabund-package Statistical methods for analysing multivariate abundance data
glm1 Fits a Generalised Linear Models with a LASSO (or L1) penalty, given a value of the penalty parameter.
plot.manyany Plot Diagnostics for a manyany or glm1path Object
meanvar.plot Construct Mean-Variance plots for Multivariate Abundance Data
solberg Solberg Data
spider Spider data
mvformula Model Formulae for Multivariate Abundance Data
residuals.manyglm Residuals for MANYGLM, MANYANY, GLM1PATH Fits
manylm.fit workhose functions for fitting multivariate linear models
anova.manyany Analysis of Deviance for Many Univariate Models Fitted to Multivariate Abundance Data
unabund Remove the mvabund Class Attribute
summary.manyglm Summarizing Multivariate Generalized Linear Model Fits for Abundance Data
plotMvaFactor Draw a Mvabund Object split into groups.
summary.manylm Summarizing Linear Model Fits for Multivariate Abundance Data
mvabund Multivariate Abundance Data Objects
mvabund-internal Internal mvabund Objects
plot.manylm Plot Diagnostics for a manylm or a manyglm Object
anova.manylm ANOVA for Linear Model Fits for Multivariate Abundance Data
shiftpoints Calculate a shift for plotting overlapping points
anova.manyglm Analysis of Deviance for Multivariate Generalized Linear Model Fits for Abundance Data
cv.glm1path Fits a path of Generalised Linear Models with LASSO (or L1) penalties, and finds the best model by corss-validation.
plot.mvabund Plot Multivariate Abundance Data and Formulae
predict.manylm Model Predictions for Multivariate Linear Models
traitglm Fits a fourth corner model for abundance as a function of environmental variables and species traits.
manyglm Fitting Generalized Linear Models for Multivariate Abundance Data
extend.x.formula Extend a Formula to all of it's Terms
formulaUnimva Create a List of Univariate Formulas
tikus Tikus Island Dataset
ridgeParamEst Estimation of the ridge parameter
predict.manyglm Predict Method for MANYGLM Fits
predict.traitglm Predictions from fourth corner model fits
best.r.sq Use R^2 to find the variables that best explain a multivariate response.
manylm Fitting Linear Models for Multivariate Abundance Data
antTraits Ant data, with species traits
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