Nothing
## -----------------------------------------------------------------------------
## Load package
library(dalmatian)
## -----------------------------------------------------------------------------
## Load pied flycatcher data
data(pied_flycatchers_1)
## Create variables bounding the true load
pfdata$lower=ifelse(pfdata$load==0,log(.001),log(pfdata$load-.049))
pfdata$upper=log(pfdata$load+.05)
## -----------------------------------------------------------------------------
## Mean model
mymean <- list(fixed=list(name="alpha",
formula=~ log(IVI) + sex,
priors=list(c("dnorm",0,.001))))
## Dispersion model
mydisp=list(fixed=list(name="psi",
formula=~sex,
priors=list(c("dnorm",0,.001))),
link="log")
## Joint components
myjoint <- list(fixed = list(name = "gamma",
formula = ~-1 + broodsize,
priors = list(c("dnorm",0,.001))))
## ---- eval = FALSE------------------------------------------------------------
#
# ## Set working directory
# ## By default uses a system temp directory. You probably want to change this.
# workingDir <- tempdir()
#
# ## Define list of arguments for jags.model()
# jm.args <- list(file=file.path(workingDir,"pied_flycatcher_joint_1_jags.R"),n.adapt=1000)
#
# ## Define list of arguments for coda.samples()
# cs.args <- list(n.iter=5000,thin=20)
#
# ## Run the model using dalmatian
# pfmcmc4 <- dalmatian(df=pfdata,
# mean.model=mymean,
# dispersion.model=mydisp,
# joint.model=myjoint,
# jags.model.args=jm.args,
# coda.samples.args=cs.args,
# rounding=TRUE,
# lower="lower",
# upper="upper",
# residuals = FALSE,
# debug=FALSE)
## ---- echo = FALSE------------------------------------------------------------
load(system.file("pfresults4.RData",package="dalmatian"))
## ---- eval = FALSE------------------------------------------------------------
# ## Compute convergence diagnostics
# pfconvergence4 <- convergence(pfmcmc4)
#
## -----------------------------------------------------------------------------
## Gelman-Rubin diagnostics
pfconvergence4$gelman
## Raftery diagnostics
pfconvergence4$raftery
## Effective sample size
pfconvergence4$effectiveSize
## ---- eval = FALSE------------------------------------------------------------
# ## Generate traceplots
# pftraceplots4 <- traceplots(pfmcmc4,show=FALSE,nthin=10)
#
## ----fig.width=6,fig.align="center"-------------------------------------------
## Fixed effects for mean
pftraceplots4$meanFixed
## Fixed effects for dispersion
pftraceplots4$dispersionFixed
## ---- eval = FALSE------------------------------------------------------------
# ## Compute numerical summaries
# pfsummary4 <- summary(pfmcmc4)
## -----------------------------------------------------------------------------
## Print numerical summaries
pfsummary4
## ---- eval = FALSE------------------------------------------------------------
# ## Generate caterpillar
# pfcaterpillar4 <- caterpillar(pfmcmc4,show = FALSE)
#
## ----fig.width=6,fig.align="center"-------------------------------------------
## Fixed effects for mean
pfcaterpillar4$meanFixed
## Fixed effects for dispersion
pfcaterpillar4$dispersionFixed
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.