Remove correct_primary_censoring_bias and call document (#168)

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)

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 ...

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>
@@ -43,21 +51,25 @@ 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>
   "ptime", # <filter_obs_by_ptime>
   "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