mvabund v3.13.1

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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.

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mvabund Build Status License CRAN Downloads

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Statistical Methods for Analysing Multivariate Abundance Data

Authors

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

License

LGPL (>= 2.1)

Functions in mvabund

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

Date 2018-01-18
LinkingTo Rcpp, RcppGSL
License LGPL (>= 2.1)
NeedsCompilation yes
Packaged 2018-01-19 10:31:46 UTC; David Warton
RoxygenNote 6.0.1
Repository CRAN
Date/Publication 2018-01-19 13:09:00 UTC

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