before-chapter.R

# LIBRARY CONFIGURATION

library(arm)
library(bayesplot)
  # theme_set(bayesplot::theme_default())
library(dplyr)
library(ggplot2)
library(knitr)
  knitr::opts_chunk$set(
    cache = TRUE,
    collapse = TRUE,
    comment = NA,
    dev = "png",
    dpi = 150,
    echo = FALSE,
    fig.align = "center",
    fig.width = 6,
    fig.asp = 0.618,  # 1 / phi
    fig.show = "hold",
    include = TRUE,
    message = FALSE,
    out.width = "70%",
    tidy = FALSE,
    warning = FALSE
  )
library(lubridate)
library(rstan)
  rstan_options(auto_write = FALSE)
  options(mc.cores = 1)


# UTILITY FUNCTIONS

printf <- function(pattern, ...) {
  cat(sprintf(pattern, ...))
}

print_file <- function(file) {
  cat(paste(readLines(file), "\n", sep=""), sep="")
}

extract_one_draw <- function(stanfit, chain = 1, iter = 1) {
  x <- get_inits(stanfit, iter = iter)
  x[[chain]]
}

# GENERAL R CONFIGURATION

options(digits = 2)
options(htmltools.dir.version = FALSE)


set.seed(1123)