boral: Bayesian Ordination and Regression AnaLysis

Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.

Author
Francis K.C. Hui
Date of publication
2016-10-10 13:51:41
Maintainer
Francis Hui <fhui28@gmail.com>
License
GPL-2
Version
1.1.1

View on CRAN

Man pages

boral
Fitting boral (Bayesian Ordination and Regression AnaLysis)...
boral-package
Bayesian Ordination and Regression AnaLysis (boral)
calc.condlogLik
Conditional log-likelihood for an boral model
calc.logLik.lv0
Log-likelihood for a boral model with no latent variables
calc.marglogLik
Marginal log-likelihood for an boral model
coefsplot
Caterpillar plots of the regression coefficients from a boral...
create.life
Simulate a Multivariate Response Matrix
ds.residuals
Dunn-Smyth Residuals for a boral model
fitted.boral
Extract Model Fitted Values for an boral object
get.dic
Extract Deviance Information Criterion for boral model
get.enviro.cor
Extract covariances and correlations due to shared...
get.hpdintervals
Highest posterior density intervals for an boral model
get.measures
Information Criteria for boral models
get.more.measures
Additional Information Criteria for boral models
get.residual.cor
Extract residual correlations from boral models
lvsplot
Plot the latent variables from an boral model
make.jagsboralmodel
Write a text file containing an boral model for use into JAGS
make.jagsboralnullmodel
Write a text file containing an boral model for use into JAGS
plot.boral
Plots of a fitted boral object
summary.boral
Summary of fitted boral object

Files in this package

boral
boral/inst
boral/inst/NEWS.Rd
boral/NAMESPACE
boral/R
boral/R/auxilaryfunctions.R
boral/R/unseenfunctions.R
boral/R/makejagsscriptfunctions.R
boral/R/boral.jags.R
boral/MD5
boral/DESCRIPTION
boral/man
boral/man/make.jagsboralnullmodel.Rd
boral/man/boral.Rd
boral/man/get.hpdintervals.Rd
boral/man/create.life.Rd
boral/man/calc.marglogLik.Rd
boral/man/get.enviro.cor.Rd
boral/man/make.jagsboralmodel.Rd
boral/man/coefsplot.Rd
boral/man/fitted.boral.Rd
boral/man/get.measures.Rd
boral/man/ds.residuals.Rd
boral/man/plot.boral.Rd
boral/man/summary.boral.Rd
boral/man/lvsplot.Rd
boral/man/calc.condlogLik.Rd
boral/man/get.residual.cor.Rd
boral/man/calc.logLik.lv0.Rd
boral/man/boral-package.Rd
boral/man/get.more.measures.Rd
boral/man/get.dic.Rd