From 14a7c86797295c8068c737774eae69d7ea64d594 Mon Sep 17 00:00:00 2001
From: Adam Howes <xwg3@cdc.gov>
Date: Wed, 17 Jul 2024 22:14:29 +0100
Subject: [PATCH] Remove correct_primary_censoring_bias and call document
 (#168)

---
 NAMESPACE                             |  2 +-
 R/fitting-and-postprocessing.R        | 14 --------------
 R/globals.R                           | 23 +++++++++++++++++++++++
 man/add_natural_scale_mean_sd.Rd      |  1 -
 man/correct_primary_censoring_bias.Rd | 25 -------------------------
 man/draws_to_long.Rd                  |  1 -
 man/extract_lognormal_draws.Rd        |  1 -
 man/make_relative_to_truth.Rd         |  1 -
 man/sample_model.Rd                   |  1 -
 man/summarise_draws.Rd                |  1 -
 man/summarise_variable.Rd             |  1 -
 11 files changed, 24 insertions(+), 47 deletions(-)
 delete mode 100644 man/correct_primary_censoring_bias.Rd

diff --git a/NAMESPACE b/NAMESPACE
index c04f42354..d8c3ebd06 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -17,7 +17,6 @@ export(calculate_cohort_mean)
 export(calculate_truncated_means)
 export(combine_obs)
 export(construct_cases_by_obs_window)
-export(correct_primary_censoring_bias)
 export(draws_to_long)
 export(drop_zero)
 export(epidist)
@@ -63,6 +62,7 @@ importFrom(checkmate,assert_int)
 importFrom(checkmate,assert_names)
 importFrom(checkmate,assert_numeric)
 importFrom(posterior,as_draws_df)
+importFrom(rstan,lookup)
 importFrom(stats,as.formula)
 importFrom(stats,ecdf)
 importFrom(stats,integrate)
diff --git a/R/fitting-and-postprocessing.R b/R/fitting-and-postprocessing.R
index 0f8333a85..9ee948a24 100644
--- a/R/fitting-and-postprocessing.R
+++ b/R/fitting-and-postprocessing.R
@@ -112,20 +112,6 @@ extract_lognormal_draws <- function(data, id_vars, from_dt = FALSE) {
   return(draws[])
 }
 
-#' Primary event bias correction
-#'
-#' @param draws ...
-#' @family postprocess
-#' @export
-correct_primary_censoring_bias <- function(draws) {
-  draws <- data.table::copy(draws)
-  draws[, mean := mean - runif(.N, min = 0, max = 1)]
-  draws[, meanlog := log(mean^2 / sqrt(sd^2 + mean^2))]
-  draws[, sdlog := sqrt(log(1 + (sd^2 / mean^2)))]
-
-  return(draws[])
-}
-
 #' Convert posterior lognormal samples to long format
 #'
 #' @param draws ...
diff --git a/R/globals.R b/R/globals.R
index b4a8d25ba..88d1e6932 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -1,23 +1,30 @@
 # Generated by roxyglobals: do not edit by hand
 
 utils::globalVariables(c(
+  ":=", # <sample_model>
   "error", # <sample_model>
   "no_at_max_treedepth", # <sample_model>
   "max_treedepth", # <sample_model>
   "per_at_max_treedepth", # <sample_model>
   "run_time", # <sample_model>
+  ":=", # <add_natural_scale_mean_sd>
   "meanlog", # <add_natural_scale_mean_sd>
   "sdlog", # <add_natural_scale_mean_sd>
   "sd", # <add_natural_scale_mean_sd>
+  ":=", # <extract_lognormal_draws>
   "sdlog", # <extract_lognormal_draws>
   "sdlog_log", # <extract_lognormal_draws>
   "meanlog", # <extract_lognormal_draws>
   "id", # <extract_lognormal_draws>
+  ":=", # <make_relative_to_truth>
   "true_value", # <make_relative_to_truth>
   "value", # <make_relative_to_truth>
   "rel_value", # <make_relative_to_truth>
+  ":=", # <summarise_variable>
   "value", # <summarise_variable>
+  ":=", # <as_latent_individual.data.frame>
   "id", # <as_latent_individual.data.frame>
+  ".N", # <as_latent_individual.data.frame>
   "obs_t", # <as_latent_individual.data.frame>
   "obs_at", # <as_latent_individual.data.frame>
   "ptime_lwr", # <as_latent_individual.data.frame>
@@ -31,6 +38,7 @@ utils::globalVariables(c(
   "row_id", # <as_latent_individual.data.frame>
   "woverlap", # <epidist_stancode.epidist_latent_individual>
   "row_id", # <epidist_stancode.epidist_latent_individual>
+  ":=", # <observe_process>
   "ptime_daily", # <observe_process>
   "ptime", # <observe_process>
   "ptime_lwr", # <observe_process>
@@ -43,12 +51,14 @@ utils::globalVariables(c(
   "delay_lwr", # <observe_process>
   "delay_upr", # <observe_process>
   "obs_at", # <observe_process>
+  ":=", # <filter_obs_by_obs_time>
   "obs_at", # <filter_obs_by_obs_time>
   "ptime", # <filter_obs_by_obs_time>
   "censored_obs_time", # <filter_obs_by_obs_time>
   "ptime_lwr", # <filter_obs_by_obs_time>
   "censored", # <filter_obs_by_obs_time>
   "stime_upr", # <filter_obs_by_obs_time>
+  ":=", # <filter_obs_by_ptime>
   "censored", # <filter_obs_by_ptime>
   "ptime_upr", # <filter_obs_by_ptime>
   "stime_upr", # <filter_obs_by_ptime>
@@ -56,8 +66,10 @@ utils::globalVariables(c(
   "censored_obs_time", # <filter_obs_by_ptime>
   "ptime_lwr", # <filter_obs_by_ptime>
   "censored_obs_time", # <pad_zero>
+  ":=", # <pad_zero>
   "delay_lwr", # <pad_zero>
   "delay_daily", # <pad_zero>
+  ":=", # <plot_relative_recovery>
   "value", # <plot_relative_recovery>
   "rel_value", # <plot_relative_recovery>
   "case_type", # <plot_cases_by_obs_window>
@@ -73,15 +85,23 @@ utils::globalVariables(c(
   "ptime_daily", # <plot_mean_posterior_pred>
   "n", # <plot_mean_posterior_pred>
   "obs_horizon", # <plot_mean_posterior_pred>
+  ".data", # <plot_mean_posterior_pred>
+  ":=", # <linelist_to_counts>
   "time", # <linelist_to_counts>
+  ".N", # <linelist_to_counts>
+  ":=", # <linelist_to_cases>
   "primary", # <linelist_to_cases>
   "secondary", # <linelist_to_cases>
+  ":=", # <reverse_obs_at>
   "obs_at", # <reverse_obs_at>
   "stime", # <construct_cases_by_obs_window>
   "ptime", # <construct_cases_by_obs_window>
+  ":=", # <construct_cases_by_obs_window>
   "case_type", # <construct_cases_by_obs_window>
+  ":=", # <combine_obs>
   "obs_at", # <combine_obs>
   "stime_daily", # <combine_obs>
+  ":=", # <calculate_censor_delay>
   "ptime_delay", # <calculate_censor_delay>
   "ptime", # <calculate_censor_delay>
   "ptime_daily", # <calculate_censor_delay>
@@ -91,9 +111,12 @@ utils::globalVariables(c(
   "stime_delay", # <calculate_censor_delay>
   "stime", # <calculate_censor_delay>
   "stime_daily", # <calculate_censor_delay>
+  ".N", # <event_to_incidence>
   "ptime_daily", # <event_to_incidence>
   "rlnorm", # <simulate_secondary>
+  ":=", # <simulate_secondary>
   "delay", # <simulate_secondary>
+  ".N", # <simulate_secondary>
   "stime", # <simulate_secondary>
   "ptime", # <simulate_secondary>
   NULL
diff --git a/man/add_natural_scale_mean_sd.Rd b/man/add_natural_scale_mean_sd.Rd
index 269283932..3e54240d4 100644
--- a/man/add_natural_scale_mean_sd.Rd
+++ b/man/add_natural_scale_mean_sd.Rd
@@ -14,7 +14,6 @@ Add natural scale summary parameters for a lognormal distribution
 }
 \seealso{
 Other postprocess: 
-\code{\link{correct_primary_censoring_bias}()},
 \code{\link{draws_to_long}()},
 \code{\link{extract_lognormal_draws}()},
 \code{\link{make_relative_to_truth}()},
diff --git a/man/correct_primary_censoring_bias.Rd b/man/correct_primary_censoring_bias.Rd
deleted file mode 100644
index 1b167e343..000000000
--- a/man/correct_primary_censoring_bias.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fitting-and-postprocessing.R
-\name{correct_primary_censoring_bias}
-\alias{correct_primary_censoring_bias}
-\title{Primary event bias correction}
-\usage{
-correct_primary_censoring_bias(draws)
-}
-\arguments{
-\item{draws}{...}
-}
-\description{
-Primary event bias correction
-}
-\seealso{
-Other postprocess: 
-\code{\link{add_natural_scale_mean_sd}()},
-\code{\link{draws_to_long}()},
-\code{\link{extract_lognormal_draws}()},
-\code{\link{make_relative_to_truth}()},
-\code{\link{sample_model}()},
-\code{\link{summarise_draws}()},
-\code{\link{summarise_variable}()}
-}
-\concept{postprocess}
diff --git a/man/draws_to_long.Rd b/man/draws_to_long.Rd
index 0c64dfdaf..631e5adb6 100644
--- a/man/draws_to_long.Rd
+++ b/man/draws_to_long.Rd
@@ -15,7 +15,6 @@ Convert posterior lognormal samples to long format
 \seealso{
 Other postprocess: 
 \code{\link{add_natural_scale_mean_sd}()},
-\code{\link{correct_primary_censoring_bias}()},
 \code{\link{extract_lognormal_draws}()},
 \code{\link{make_relative_to_truth}()},
 \code{\link{sample_model}()},
diff --git a/man/extract_lognormal_draws.Rd b/man/extract_lognormal_draws.Rd
index d154b6abb..7b1a4c69f 100644
--- a/man/extract_lognormal_draws.Rd
+++ b/man/extract_lognormal_draws.Rd
@@ -19,7 +19,6 @@ Extract posterior samples for a lognormal brms model
 \seealso{
 Other postprocess: 
 \code{\link{add_natural_scale_mean_sd}()},
-\code{\link{correct_primary_censoring_bias}()},
 \code{\link{draws_to_long}()},
 \code{\link{make_relative_to_truth}()},
 \code{\link{sample_model}()},
diff --git a/man/make_relative_to_truth.Rd b/man/make_relative_to_truth.Rd
index 99573f12a..446bec6de 100644
--- a/man/make_relative_to_truth.Rd
+++ b/man/make_relative_to_truth.Rd
@@ -19,7 +19,6 @@ Make posterior lognormal samples relative to true values
 \seealso{
 Other postprocess: 
 \code{\link{add_natural_scale_mean_sd}()},
-\code{\link{correct_primary_censoring_bias}()},
 \code{\link{draws_to_long}()},
 \code{\link{extract_lognormal_draws}()},
 \code{\link{sample_model}()},
diff --git a/man/sample_model.Rd b/man/sample_model.Rd
index fbb6a5e40..22506ef23 100644
--- a/man/sample_model.Rd
+++ b/man/sample_model.Rd
@@ -29,7 +29,6 @@ Sample from the posterior of a model with additional diagnositics
 \seealso{
 Other postprocess: 
 \code{\link{add_natural_scale_mean_sd}()},
-\code{\link{correct_primary_censoring_bias}()},
 \code{\link{draws_to_long}()},
 \code{\link{extract_lognormal_draws}()},
 \code{\link{make_relative_to_truth}()},
diff --git a/man/summarise_draws.Rd b/man/summarise_draws.Rd
index 617082e01..96f5e5b5e 100644
--- a/man/summarise_draws.Rd
+++ b/man/summarise_draws.Rd
@@ -21,7 +21,6 @@ Summarise posterior draws
 \seealso{
 Other postprocess: 
 \code{\link{add_natural_scale_mean_sd}()},
-\code{\link{correct_primary_censoring_bias}()},
 \code{\link{draws_to_long}()},
 \code{\link{extract_lognormal_draws}()},
 \code{\link{make_relative_to_truth}()},
diff --git a/man/summarise_variable.Rd b/man/summarise_variable.Rd
index 955897398..048a7cbac 100644
--- a/man/summarise_variable.Rd
+++ b/man/summarise_variable.Rd
@@ -21,7 +21,6 @@ Summarise a variable
 \seealso{
 Other postprocess: 
 \code{\link{add_natural_scale_mean_sd}()},
-\code{\link{correct_primary_censoring_bias}()},
 \code{\link{draws_to_long}()},
 \code{\link{extract_lognormal_draws}()},
 \code{\link{make_relative_to_truth}()},