Nothing
## ---- eval=TRUE, echo=FALSE---------------------------------------------------
library(adnuts)
## -----------------------------------------------------------------------------
fit <- readRDS('fit.RDS')
print(fit)
summary(fit$monitor$n_eff)
summary(fit$monitor$Rhat)
## -----------------------------------------------------------------------------
post <- extract_samples(fit)
str(post[,1:5])
sp <- extract_sampler_params(fit)
str(sp)
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# post <- extract_samples(fit, as.list=TRUE)
# postlist <- coda::mcmc.list(lapply(post, coda::mcmc))
# coda::traceplot(postlist)
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# library(bayesplot)
# library(dplyr)
# library(tidyr)
# library(ggplot2)
# color_scheme_set("red")
# np <- extract_sampler_params(fit) %>%
# pivot_longer(-c(chain, iteration), names_to='Parameter', values_to='Value') %>%
# select(Iteration=iteration, Parameter, Value, Chain=chain) %>%
# mutate(Parameter=factor(Parameter),
# Iteration=as.integer(Iteration),
# Chain=as.integer(Chain)) %>% as.data.frame()
# mcmc_nuts_energy(np) + ggtitle("NUTS Energy Diagnostic") + theme_minimal()
## ----fig1, fig.width=6, fig.height=4.5----------------------------------------
plot_marginals(fit, pars=1:9)
## ----fig2, fig.width=6, fig.height=4.5----------------------------------------
pairs_admb(fit, pars=1:3, order='slow')
pairs_admb(fit, pars=c('sigmaphi', 'sigmap', 'sigmayearphi'))
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