change to

NAMESPACE

@@ -5,8 +5,8 @@ export(combine_plots)
 export(gen_data_le)
 export(gen_data_mean)
 export(gen_data_mean_weighted_burden_wide)
-export(gen_data_mean_weighted_inc_wide)
 export(gen_data_weighted)
+export(gen_data_weighted_ds)
 export(gen_data_weighted_rf)
 export(hgps_theme)
 export(inc_cum)

R/data-process.R

@@ -168,45 +168,63 @@ gen_data_weighted_rf <- function(data_weighted) {
 #'
 #' This function calculates the differences between intervention and baseline values for incidences.
 #'
-#' @param data_mean_weighted A data frame containing weighted mean values for various metrics.
+#' @param data_weighted A data frame containing weighted mean values for various metrics.
 #' @return A data frame with differences between intervention and baseline values for incidences.
 #' @export
-gen_data_mean_weighted_inc_wide <- function(data_mean_weighted) {
-  data_mean_weighted_inc <- dplyr::select(data_mean_weighted,
-                                          data_mean_weighted$source,
-                                          data_mean_weighted$timediff,
-                                          data_mean_weighted$totalcase_ihd,
-                                          data_mean_weighted$totalcase_diabetes,
-                                          data_mean_weighted$totalcase_stroke,
-                                          data_mean_weighted$totalcase_asthma,
-                                          #data_mean_weighted$totalcase_stomachcancer,
-                                          data_mean_weighted$totalcase_ckd)
+gen_data_weighted_ds <- function(data_weighted) {
+  data_weighted_ds <- dplyr::select(data_weighted,
+                                          data_weighted$source,
+                                          data_weighted$time,
+                                          data_weighted$simID,
+                                          data_weighted$totalcase_ihd,
+                                          data_weighted$totalcase_diabetes,
+                                          data_weighted$totalcase_stroke,
+                                          data_weighted$totalcase_asthma,
+                                          data_weighted$totalcase_ckd)
+
+  data_weighted_ds_wide <- tidyr::pivot_wider(data_weighted_ds,
+                                             names_from = data_weighted_ds$source,
+                                             id_cols = c(data_weighted_ds$time, data_weighted_ds$simID),
+                                             values_from = c(data_weighted_ds$totalcase_ihd,
+                                                             data_weighted_ds$totalcase_diabetes,
+                                                             data_weighted_ds$totalcase_stroke,
+                                                             data_weighted_ds$totalcase_asthma,
+                                                             data_weighted_ds$totalcase_ckd))
 
-  data_mean_weighted_inc_wide <- tidyr::pivot_wider(data_mean_weighted_inc,
-                                             names_from = data_mean_weighted_inc$source,
-                                             id_cols = data_mean_weighted_inc$timediff,
-                                             values_from = c(data_mean_weighted_inc$totalcase_ihd,
-                                                             data_mean_weighted_inc$totalcase_diabetes,
-                                                             data_mean_weighted_inc$totalcase_stroke,
-                                                             data_mean_weighted_inc$totalcase_asthma,
-                                                             #data_mean_weighted_inc$totalcase_stomachcancer,
-                                                             data_mean_weighted_inc$totalcase_ckd))
+  data_weighted_ds_wide <- data_weighted_ds_wide |>
+    dplyr::mutate(data_weighted_ds_wide$diff_inc_ihd <- 100*(data_weighted_ds_wide$totalcase_ihd_intervention - data_weighted_ds_wide$totalcase_ihd_baseline),
+                  data_weighted_ds_wide$diff_inc_db <- 100*(data_weighted_ds_wide$totalcase_diabetes_intervention - data_weighted_ds_wide$totalcase_diabetes_baseline),
+                  data_weighted_ds_wide$diff_inc_stroke <- 100*(data_weighted_ds_wide$totalcase_stroke_intervention - data_weighted_ds_wide$totalcase_stroke_baseline),
+                  data_weighted_ds_wide$diff_inc_asthma <- 100*(data_weighted_ds_wide$totalcase_asthma_intervention - data_weighted_ds_wide$totalcase_asthma_baseline),
+                  data_weighted_ds_wide$diff_inc_ckd <- 100*(data_weighted_ds_wide$totalcase_ckd_intervention - data_weighted_ds_wide$totalcase_ckd_baseline))
 
-  data_mean_weighted_inc_wide$diff_ihd <- 100*(data_mean_weighted_inc_wide$totalcase_ihd_intervention - data_mean_weighted_inc_wide$totalcase_ihd_baseline)
-  data_mean_weighted_inc_wide$diff_diabetes <- 100*(data_mean_weighted_inc_wide$totalcase_diabetes_intervention - data_mean_weighted_inc_wide$totalcase_diabetes_baseline)
-  data_mean_weighted_inc_wide$diff_stroke <- 100*(data_mean_weighted_inc_wide$totalcase_stroke_intervention - data_mean_weighted_inc_wide$totalcase_stroke_baseline)
-  data_mean_weighted_inc_wide$diff_asthma <- 100*(data_mean_weighted_inc_wide$totalcase_asthma_intervention - data_mean_weighted_inc_wide$totalcase_asthma_baseline)
-  #data_mean_weighted_inc_wide$diff_stomachcancer <- 100*(data_mean_weighted_inc_wide$totalcase_stomachcancer_intervention - data_mean_weighted_inc_wide$totalcase_stomachcancer_baseline)
-  data_mean_weighted_inc_wide$diff_ckd <- 100*(data_mean_weighted_inc_wide$totalcase_ckd_intervention - data_mean_weighted_inc_wide$totalcase_ckd_baseline)
+  data_weighted_ds_wide <- data_weighted_ds_wide |>
+    dplyr::group_by(data_weighted_ds_wide$simID) |>
+    dplyr::mutate(data_weighted_ds_wide$cumdiff_inc_ihd <- cumsum(data_weighted_ds_wide$diff_inc_ihd),
+                  data_weighted_ds_wide$cumdiff_inc_db <- cumsum(data_weighted_ds_wide$diff_inc_db),
+                  data_weighted_ds_wide$cumdiff_inc_stroke <- cumsum(data_weighted_ds_wide$diff_inc_stroke),
+                  data_weighted_ds_wide$cumdiff_inc_asthma <- cumsum(data_weighted_ds_wide$diff_inc_asthma),
+                  data_weighted_ds_wide$cumdiff_inc_ckd <- cumsum(data_weighted_ds_wide$diff_inc_ckd))
 
-  data_mean_weighted_inc_wide$cumdiff_ihd <- cumsum(data_mean_weighted_inc_wide$diff_ihd)
-  data_mean_weighted_inc_wide$cumdiff_diabetes <- cumsum(data_mean_weighted_inc_wide$diff_diabetes)
-  data_mean_weighted_inc_wide$cumdiff_stroke <- cumsum(data_mean_weighted_inc_wide$diff_stroke)
-  data_mean_weighted_inc_wide$cumdiff_asthma <- cumsum(data_mean_weighted_inc_wide$diff_asthma)
-  #data_mean_weighted_inc_wide$cumdiff_stomachcancer <- cumsum(data_mean_weighted_inc_wide$diff_stomachcancer)
-  data_mean_weighted_inc_wide$cumdiff_ckd <- cumsum(data_mean_weighted_inc_wide$diff_ckd)
+  data_weighted_ds_wide_collapse <- data_weighted_ds_wide |>
+    dplyr::group_by(data_weighted_ds_wide$time) |>
+    dplyr::summarise(data_weighted_ds_wide$diff_inc_ihd_mean <- mean(data_weighted_ds_wide$cumdiff_inc_ihd),
+                     data_weighted_ds_wide$diff_inc_ihd_min <- min(data_weighted_ds_wide$cumdiff_inc_ihd),
+                     data_weighted_ds_wide$diff_inc_ihd_max <- max(data_weighted_ds_wide$cumdiff_inc_ihd),
+                     data_weighted_ds_wide$diff_inc_db_mean <- mean(data_weighted_ds_wide$cumdiff_inc_db),
+                     data_weighted_ds_wide$diff_inc_db_min <- min(data_weighted_ds_wide$cumdiff_inc_db),
+                     data_weighted_ds_wide$diff_inc_db_max <- max(data_weighted_ds_wide$cumdiff_inc_db),
+                     data_weighted_ds_wide$diff_inc_stroke_mean <- mean(data_weighted_ds_wide$cumdiff_inc_stroke),
+                     data_weighted_ds_wide$diff_inc_stroke_min <- min(data_weighted_ds_wide$cumdiff_inc_stroke),
+                     data_weighted_ds_wide$diff_inc_stroke_max <- max(data_weighted_ds_wide$cumdiff_inc_stroke),
+                     data_weighted_ds_wide$diff_inc_asthma_mean <- mean(data_weighted_ds_wide$cumdiff_inc_asthma),
+                     data_weighted_ds_wide$diff_inc_asthma_min <- min(data_weighted_ds_wide$cumdiff_inc_asthma),
+                     data_weighted_ds_wide$diff_inc_asthma_max <- max(data_weighted_ds_wide$cumdiff_inc_asthma),
+                     data_weighted_ds_wide$diff_inc_ckd_mean <- mean(data_weighted_ds_wide$cumdiff_inc_ckd),
+                     data_weighted_ds_wide$diff_inc_ckd_min <- min(data_weighted_ds_wide$cumdiff_inc_ckd),
+                     data_weighted_ds_wide$diff_inc_ckd_max <- max(data_weighted_ds_wide$cumdiff_inc_ckd))
 
-  return(data_mean_weighted_inc_wide)
+  return(data_weighted_ds_wide_collapse)
 }
 
 #' Calculate Differences for Burden of Disease