finish over-reporting

R/S3_simaerep.R

@@ -58,7 +58,6 @@ validate_simaerep <- function(x) {
 #'  Default: list(method = "med75_adj", min_pat_pool = 0.2)
 #'@param param_sim_sites list of parameters passed to [sim_sites()][sim_sites],
 #'  Default: list(r = 1000, poisson_test = FALSE, prob_lower = TRUE)
-#'@param under_only compute under-reporting probabilities only, default = TRUE
 #'@param param_eval_sites list of parameters passed to
 #'  [eval_sites()][eval_sites], Default: list(method = "BH")
 #'@param progress logical, display progress bar, Default = TRUE
@@ -67,6 +66,9 @@ validate_simaerep <- function(x) {
 #'  sets. Default: TRUE
 #'@param env optional, provide environment of original visit data, Default:
 #'  parent.frame()
+#'@param under_only, logical compute under-reporting probabilities only,
+#'  superseeds under_only parameter passed to [eval_sites()][eval_sites] and
+#'  [sim_sites()][sim_sites], Default: TRUE
 #'@return simaerep object
 #'@details executes [site_aggr()][site_aggr], [sim_sites()][sim_sites] and
 #'  [eval_sites()][eval_sites] on original visit data and stores all
@@ -90,7 +92,8 @@ validate_simaerep <- function(x) {
 #' str(aerep)
 #'
 #'@seealso [site_aggr()][site_aggr], [sim_sites()][sim_sites],
-#'  [eval_sites()][eval_sites], [orivisit()][orivisit], [plot.simaerep()][plot.simaerep]
+#'  [eval_sites()][eval_sites], [orivisit()][orivisit],
+#'  [plot.simaerep()][plot.simaerep]
 #'@rdname simaerep
 #'@export
 simaerep <- function(df_visit,
@@ -101,15 +104,15 @@ simaerep <- function(df_visit,
                      param_sim_sites = list(
                        r = 1000,
                        poisson_test = FALSE,
-                       prob_lower = TRUE,
-                       under_only = TRUE
+                       prob_lower = TRUE
                      ),
                      param_eval_sites = list(
                        method = "BH"
                      ),
                      progress = TRUE,
                      check = TRUE,
-                     env = parent.frame()) {
+                     env = parent.frame(),
+                     under_only = TRUE) {
 
   call <- rlang::enexpr(df_visit)
 
@@ -119,6 +122,9 @@ simaerep <- function(df_visit,
     df_visit <- check_df_visit(df_visit)
   }
 
+  param_sim_sites$under_only <- under_only
+  param_eval_sites$under_only <- under_only
+
   df_site <- do.call(
     site_aggr,
     c(

R/simaerep.R

@@ -309,6 +309,7 @@ get_visit_med75 <- function(df_pat,
 #' @param df_sim_sites dataframe generated by \code{\link[simaerep]{sim_sites}}
 #' @param method character, passed to stats::p.adjust(), if NULL
 #' eval_sites_deprecated() is used instead, Default = "BH"
+#' @inheritParams sim_sites
 #' @param ... use to pass r_sim_sites parameter to eval_sites_deprecated()
 #' @return dataframe with the following columns:
 #' \describe{
@@ -410,7 +411,7 @@ eval_sites <- function(df_sim_sites,
 
     if (! under_only) {
       df_out <- df_out %>%
-        mutate(prob_high = 1 - prob_low) %>%
+        mutate(prob_high = 1 - .data$prob_low) %>%
         arrange(.data$study_id, .data$prob_high) %>%
         mutate(
           prob_high_adj = p.adjust(.data$prob_high, method = method),

R/simaerep_plot.R

@@ -406,6 +406,7 @@ get_legend <- function(p) {
 #' @param study study
 #' @param n_sites integer number of most at risk sites, Default: 16
 #' @param pval logical show p-value, Default:FALSE
+#' @param prob_col character, denotes probability column, Default: "prob_low_prob_ur"
 #' @return ggplot
 #' @details Left panel shows mean AE reporting per site (lightblue and darkblue
 #'   lines) against mean AE reporting of the entire study (golden line). Single

R/simulate_test_data.R

@@ -1,12 +1,14 @@
 #' @title simulate study test data
 #' @description evenly distributes a number of given patients across a number of
 #'   given sites. Then simulates ae development of each patient reducing the
-#'   number of reported AEs for patients distributed to AE-under-reporting sites.
+#'   number of reported AEs for patients distributed to AE-under-reporting
+#'   sites.
 #' @param n_pat integer, number of patients, Default: 1000
 #' @param n_sites integer, number of sites, Default: 20
 #' @param frac_site_with_ur fraction of AE under-reporting sites, Default: 0
 #' @param ur_rate AE under-reporting rate, will lower mean ae per visit used to
-#'   simulate patients at sites flagged as AE-under-reporting., Default: 0
+#'   simulate patients at sites flagged as AE-under-reporting. Negative Values
+#'   will simulate over-reporting., Default: 0
 #' @param max_visit_mean mean of the maximum number of visits of each patient,
 #'   Default: 20
 #' @param max_visit_sd standard deviation of maximum number of visits of each

_pkgdown.yml

@@ -37,6 +37,7 @@ articles:
   - check_poisson
   - visits_or_days
   - gsm_perf
+  - over
 
 reference:
 - title: S3 Interface

data-raw/generate_test_data.R

@@ -25,7 +25,7 @@ df_visit_test <- dplyr::bind_rows(df_visit1, df_visit2)
 
 df_site_test <- site_aggr(df_visit_test)
 
-df_sim_sites_test <- sim_sites(df_site_test, df_visit, r = 100)
+df_sim_sites_test <- sim_sites(df_site_test, df_visit_test, r = 100)
 
 df_eval_test <- eval_sites(df_sim_sites_test)
 
@@ -35,7 +35,7 @@ visit_test <- orivisit(df_visit_test)
 
 # portfolio performance
 
-df_site_max_test <- df_visit %>%
+df_site_max_test <- df_visit_test %>%
   group_by(study_id, site_number, patnum) %>%
   summarise(max_visit = max(visit),
             max_ae = max(n_ae),