fix: update create duplicates

R/create_duplicates.R

@@ -23,7 +23,7 @@
 #'
 #' @export
 create_duplicates <- function(conc_data,
-                                      groups = c("USUBJID", "ANALYTE", "PCSPEC"),
+                                      groups = slopes_groups(),
                                       dosno = "DOSNO",
                                       arrlt = "ARRLT",
                                       afrlt = "AFRLT",
@@ -37,59 +37,62 @@ create_duplicates <- function(conc_data,
 
   # Step 1: Identify the dosing times (ARRLT == 0)
   dose_times <- conc_data %>%
-    mutate(dose_time = .data[[afrlt]] - .data[[arrlt]]) %>%
-    select(all_of(groups), .data[[dosno]], dose_time) %>%
-    group_keys(c(groups, dosno)) %>%
-    summarize(dose_time = first(dose_time), .groups = "drop")
+    mutate(dose_time = .data[[afrlt]] - .data[[arrlt]],
+           nom_dose_time = .data[[nfrlt]] - .data[[nrrlt]]) %>%
+    select(all_of(groups), dose_time, nom_dose_time) %>%
+    group_keys(c(groups)) %>%
+    summarize(dose_time = first(dose_time),
+              nom_dose_time = first(nom_dose_time),
+                                    .groups = "drop")
 
   # Step 2: Calculate dosing intervals
   dosing_intervals <- dose_times %>%
     group_keys(groups) %>%
     mutate(
-      interval_next = lead(dose_time) - dose_time,
       interval_prev = dose_time - lag(dose_time),
-      interval_next = replace_na(interval_next, 0),
       interval_prev = replace_na(interval_prev, 0),
-      next_dose = interval_next + dose_time
+      nom_interval_prev = nom_dose_time - lag(nom_dose_time),
+      nom_interval_prev = replace_na(nom_interval_prev, 0),
     ) %>%
     ungroup()
 
-  # Step 3: Duplicate predose values for the previous dose
+
+  # Step 3: Duplicate predose values to be clast for the previous dose
   predose_duplicates <- conc_data %>%
     filter(.data[[arrlt]] <= 0, .data[[dosno]] > 1) %>%
-    left_join(dosing_intervals, by = c(dosno, groups)) %>%
+    left_join(dosing_intervals, by = c(groups)) %>%
     mutate(
       !!dosno := .data[[dosno]] - 1,
       !!arrlt := .data[[arrlt]] + interval_prev,
-      !!nrrlt := .data[[nfrlt]] - interval_prev
+      !!nrrlt := .data[[nrrlt]] + nom_interval_prev
     ) %>%
-    select(-interval_next, -interval_prev)
+    select(-interval_prev, -nom_interval_prev)
 
   # Step 4: Identify missing predose values for the next dose
   missing_predose <- dose_times %>%
     anti_join(
       conc_data %>% filter(.data[[arrlt]] < 0),
-      by = c(groups, dosno)
+      by = c(groups)
     )
 
-  # Step 5: Duplicate last value of the previous dose
+  # Step 5: Duplicate last value of the previous dose to become predose of next
   last_values <- conc_data %>%
-    semi_join(missing_predose, by = c(groups, dosno)) %>%
-    group_keys(c(groups, dosno)) %>%
+    semi_join(missing_predose, by = c(groups)) %>%
+    group_keys(c(groups)) %>%
     slice_tail(n = 1) %>%
     ungroup() %>%
-    left_join(dosing_intervals, by = c(groups, dosno)) %>%
+    left_join(dosing_intervals, by = c(groups)) %>%
     mutate(
       !!dosno := .data[[dosno]] + 1,
       !!arrlt := .data[[arrlt]] - interval_prev,
-      !!nrrlt := .data[[nrrlt]] + interval_prev
+      !!nrrlt := .data[[nrrlt]] - nom_interval_prev
     ) %>%
-    select(-interval_next, -interval_prev)
+    select(-interval_prev, -nom_interval_prev)
 
   # Step 6: Combine all data
   conc_data <- conc_data %>%
     bind_rows(predose_duplicates, last_values) %>%
-    arrange(across(all_of(c(groups, dosno, arrlt))))
+    arrange(across(all_of(c(groups, arrlt))))
 
   return(conc_data)
 }

R/lambda_slope_plot.R

@@ -57,7 +57,7 @@ lambda_slope_plot <- function(
 ) {
 
   #Create duplicates for predose and last dose points per profile
-  conc_pknca_df <- create_duplicates(conc_pknca_df)
+  conc_pknca_df <- create_duplicates(conc_pknca_df, column_names)
 
   #Obtain values for slopes selection
   lambda_res <- res_pknca_df %>%