## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----run example model--------------------------------------------------------
library(rstan)
library(bennu)
library(bayesplot)
library(ggplot2)

rstan_options(auto_write = TRUE)
options(mc.cores = 2)

## basic example code
d <- generate_model_data()
# note iter should be at least 2000 to generate a reasonable posterior sample
fit <- est_naloxone(d, iter = 100)
mcmc_pairs(fit,
  pars = c("sigma", "mu0", "zeta"),
  off_diag_args = list(size = 1, alpha = 0.5)
)

## ----summarize draws----------------------------------------------------------
library(posterior)

summarise_draws(fit, default_summary_measures())

## ----plot draws---------------------------------------------------------------
plot_kit_use(model = fit, data = d)

## ----plot reported draws------------------------------------------------------
plot_kit_use(model = fit, reported = TRUE, data = d)

## ----plot draws filter regions------------------------------------------------
plot_kit_use(
  model = fit, data = d,
  regions_to_plot = c("2")
)

## ----run prior----------------------------------------------------------------
# note iter should be at least 2000 to generate a reasonable posterior sample
prior_fit <- est_naloxone(d,
  run_estimation = FALSE,
  iter = 100
)
mcmc_pairs(prior_fit,
  pars = c("sigma", "mu0", "zeta"),
  off_diag_args = list(size = 1, alpha = 0.5)
)

## ----plot compare prior posterior---------------------------------------------
plot_kit_use(prior = prior_fit, posterior = fit, data = d)

## ----nondefault prior---------------------------------------------------------
nondefault_priors <- list(
  c = list(mu = 0, sigma = 1),
  ct0 = list(mu = 0, sigma = 1),
  zeta = list(mu = 0, sigma = 0.01),
  mu0 = list(mu = 0, sigma = 1),
  sigma = list(mu = 0, sigma = 1)
)
nondefault_prior_fit <- est_naloxone(d, iter = 100, priors = nondefault_priors)

## ----plot compare prior posterior nondefault prior----------------------------
plot_kit_use(`Default prior` = fit,
             `Non-default prior` = nondefault_prior_fit, data = d)

## ----rw order 2 model---------------------------------------------------------
# note iter should be at least 2000 to generate a reasonable posterior sample
# note use `rw_type` to specify order of random walk
rw2_fit <- est_naloxone(d,
  rw_type = 2,
  iter = 100
)
mcmc_pairs(rw2_fit,
  pars = c("sigma", "mu0", "zeta"),
  off_diag_args = list(size = 1, alpha = 0.5)
)

## ----rw order 2 summary draws-------------------------------------------------
summarise_draws(rw2_fit, default_convergence_measures())

## ----plot draws comparison----------------------------------------------------
plot_kit_use(rw_1 = fit, rw_2 = rw2_fit, data = d)

## ----data generation lower frequency------------------------------------------
## basic example code
d_missing <- generate_model_data(reporting_freq = 3)
ggplot(aes(x = times, y = Reported_Used, color = as.factor(regions)),
  data = d_missing
) +
  geom_point()

## ----missing data inference---------------------------------------------------
missing_fit <- est_naloxone(d_missing,
  rw_type = 2,
  iter = 100
)
mcmc_pairs(missing_fit,
  pars = c("sigma", "mu0", "zeta"),
  off_diag_args = list(size = 1, alpha = 0.5)
)

## ----plot draws with missing data---------------------------------------------
plot_kit_use(model = missing_fit, data = d_missing)

## ----plot reported draws with missing data------------------------------------
plot_kit_use(model = missing_fit, data = d_missing, reported = TRUE)

## ----example change units of data, eval = FALSE-------------------------------
#  # monthly reporting delay distribution
#  psi_vec <- c(0.7, 0.2, 0.1)
#  # convert to weeks using interpolation
#  weekly_psi_vec <- rep(psi_vec, 4) / sum(psi_vec)
#  
#  # properties of order to distributed delay distribution in months
#  max_delays <- 3
#  delay_alpha <- 2
#  delay_beta <- 1
#  
#  # convert to weeks
#  weekly_max_delays <- max_delays * 4
#  weekly_delay_alpha <- delay_alpha
#  weekly_delay_beta <- 0.25 * delay_beta
#  
#  result <- est_naloxone(d,
#    psi_vec = weekly_psi_vec,
#    max_delays = weekly_max_delays,
#    delay_alpha = weekly_delay_alpha,
#    delay_beta = weekly_delay_beta
#  )