Statistical Methods for Analysing Multivariate Abundance Data

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Documentation for package ‘mvabund’ version 4.2.1

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