MCMC Diagnostics

Code

library(plotly)
library(gganimate)
library(knitr)
library(kableExtra)
library(tidybayes)
library(posterior)
library(bayesplot)
library(cmdstanr)
library(tidyverse)

Code

register_knitr_engine(override = TRUE)
theme_set(theme_bw(base_size = 14, base_line_size = 1))

set_cmdstan_path("~/Torsten/cmdstan")

1 Introduction

We need to do some MCMC diagnostics to make sure our fit is valid.

2 Read in the fit

We read in the CmdStanMCMC object that we fit in Fitting a Model

Code

fit <- read_rds(here::here("Stan/Fits/depot_1cmt_ppa_covariates.rds"))