Bug: AUC start 0 (which also needs Feature: C0 imputation)

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: aNCA
-Title: (Pre-)clinical NCA in a dynamic shiny app
+Title: (Pre-)Clinical NCA in a Dynamic Shiny App
 Version: 0.0.0.9000
 Authors@R: c(
     person("Ercan", "Suekuer", , "[email protected]", role = c("aut", "cre"),
@@ -55,7 +55,8 @@ Imports:
     tidyr,
     tools,
     utils,
-    zip
+    zip,
+    rlang
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

NAMESPACE

@@ -1,14 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
+export(PKNCA_impute_method_start_c1)
+export(PKNCA_impute_method_start_logslope)
 export(anonymize_pk_data)
 export(apply_filters)
 export(as_factor_preserve_label)
 export(calculate_summary_stats)
 export(create_conc)
 export(create_dose)
+export(create_dose_intervals)
+export(create_start_impute)
 export(filter_breaks)
 export(flexible_violinboxplot)
-export(format_data)
 export(general_lineplot)
 export(general_meanplot)
 export(geometric_mean)
@@ -36,6 +39,7 @@ importFrom(PKNCA,PKNCA.options)
 importFrom(PKNCA,PKNCAconc)
 importFrom(PKNCA,PKNCAdata)
 importFrom(PKNCA,PKNCAdose)
+importFrom(PKNCA,pk.calc.c0)
 importFrom(PKNCA,pk.nca)
 importFrom(PKNCA,pknca_units_table)
 importFrom(dplyr,across)
@@ -84,6 +88,7 @@ importFrom(reactable,renderReactable)
 importFrom(reactable.extras,dropdown_extra)
 importFrom(reactable.extras,text_extra)
 importFrom(rio,export_list)
+importFrom(rlang,sym)
 importFrom(rmarkdown,render)
 importFrom(shinyBS,bsModal)
 importFrom(shinyFiles,shinyDirChoose)

R/PKNCA_impute_method_additions.R

@@ -0,0 +1,75 @@
+#' This function imputes the start concentration using the log slope method.
+#'
+#' @param conc Numeric vector of concentrations.
+#' @param time Numeric vector of times corresponding to the concentrations.
+#' @param start Numeric value indicating the start/dose time.
+#' @param end Numeric value indicating the end time.
+#' @param ... Additional arguments (currently not used).
+#' @param options List of options (currently not used).
+#'
+#' @return A data frame with imputed start concentration.
+#' @details
+#' This function adheres to the structure required by the `PKNCA` package to work with its
+#' functionalities. For more information, see the
+#' [PKNCA Data Imputation Vignette](https://cran.r-project.org/web/packages/PKNCA/vignettes).
+#' @export
+#'
+#' @examples
+#' conc <- c(5, 4, 3, 2, 1)
+#' time <- c(1, 2, 3, 4, 5)
+#' start <- 0
+#' end <- 4
+#' PKNCA_impute_method_start_logslope(conc, time, start, end)
+
+PKNCA_impute_method_start_logslope <- function(conc, time, start, end, ..., options = list()) { # nolint
+
+  d_conc_time <- data.frame(conc = conc, time = time)
+  if (!any(time == start)) {
+    all_concs <- conc[time >= start  &  time <= end]
+    all_times <- time[time >= start  &  time <= end]
+    if (!all(is.na(all_concs))) {
+      c0 <- PKNCA::pk.calc.c0(all_concs, all_times, method = "logslope")
+      if (!is.na(c0)) {
+        d_conc_time <- rbind(d_conc_time, data.frame(time = start, conc = c0))
+        d_conc_time <- d_conc_time[order(d_conc_time$time), ]
+      }
+    }
+  }
+  d_conc_time
+}
+
+#' This function imputes the start concentration using the first concentration after dose
+#'
+#' @param conc Numeric vector of concentrations.
+#' @param time Numeric vector of times corresponding to the concentrations.
+#' @param start Numeric value indicating the start/dose time.
+#' @param end Numeric value indicating the end time.
+#' @param ... Additional arguments (currently not used).
+#' @param options List of options (currently not used).
+#'
+#' @return A data frame with imputed start concentration.
+#' @details
+#' This function adheres to the structure required by the `PKNCA` package to work with its
+#' functionalities.For more information, see the
+#' [PKNCA Data Imputation Vignette](https://cran.r-project.org/web/packages/PKNCA/vignettes).
+#' @export
+#'
+#' @examples
+#' conc <- c(1, 2, 3, 4, 5)
+#' time <- c(1, 2, 3, 4, 5)
+#' start <- 0
+#' end <- 4
+#' PKNCA_impute_method_start_c1(conc, time, start, end)
+PKNCA_impute_method_start_c1 <- function(conc, time, start, end, ..., options = list()) { # nolint
+  d_conc_time <- data.frame(conc = conc, time = time)
+  if (!any(time == start)) {
+    all_concs <- conc[time >= start  &  time <= end]
+    all_times <- time[time >= start  &  time <= end]
+    if (!all(is.na(all_concs))) {
+      c1 <- all_concs[which.min(all_times)]
+      d_conc_time <- rbind(d_conc_time, data.frame(time = start, conc = c1))
+      d_conc_time <- d_conc_time[order(d_conc_time$time), ]
+    }
+  }
+  d_conc_time
+}

R/create_start_impute.R

@@ -0,0 +1,102 @@
+#' Create C0 Impute Column
+#'
+#' Defines an impute column in the intervals of the PKNCAdata object based on data
+#'
+#' @param mydata A PKNCAdata object containing concentration and dose data.
+#' @return A PKNCAdata object with updated intervals table including start imputation strategies.
+#' @import dplyr
+#' @importFrom rlang sym
+#' @importFrom PKNCA pk.calc.c0
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' mydata <- create_start_impute(mydata)
+#' }
+create_start_impute <- function(mydata) {
+
+  # Define columns
+  conc_column <- mydata$conc$columns$conc
+  time_column <- mydata$conc$columns$time
+  analyte_column <- mydata$conc$columns$groups$group_analyte
+  route_column <- mydata$dose$columns$route
+  duration_column <- mydata$dose$columns$duration
+  drug_column <- "DRUG"  # At some point should be added at least manually in PKNCA mydata object
+  conc_group_columns <- unname(unlist(mydata$conc$columns$groups))
+  dose_group_columns <- unname(unlist(mydata$dose$columns$groups))
+  group_columns <- unique(c(conc_group_columns, dose_group_columns))
+
+  # Define dose number (DOSNO) if not present in dose data
+  if (!"DOSNO" %in% mydata$dose$data) {
+    mydata$dose$data <- mydata$dose$data %>%
+      group_by(across(all_of(c(unname(unlist(mydata$dose$columns$groups)))))) %>%
+      mutate(DOSNO = row_number()) %>%
+      ungroup()
+  }
+
+  mydata_with_int <- merge(
+    x = mydata$conc$data %>%
+      dplyr::select(any_of(c(conc_group_columns, conc_column, time_column))),
+    y = mydata$dose$data %>%
+      dplyr::select(any_of(c(dose_group_columns, route_column,
+                             duration_column, "DOSNO", "DRUG")))
+  ) %>%
+    merge(mydata$intervals)
+
+  # Define dosing drug as analyte if not present
+  if (!"DRUG" %in% colnames(mydata_with_int)) {
+    if (length(analyte_column) == 1) {
+      mydata_with_int <- mydata_with_int %>%
+        mutate(DRUG = !!sym(analyte_column))
+      drug_column <- "DRUG"
+    } else {
+      mydata_with_int <- mydata_with_int %>%
+        mutate(DRUG = "A", ANALYTE = "A")
+      drug_column <- "DRUG"
+      analyte_column <- "ANALYTE"
+    }
+  }
+
+  # Process imputation strategy based on each interval
+  new_intervals <- mydata_with_int %>%
+    group_by(across(all_of(c(group_columns, "DOSNO", "start", "end")))) %>%
+    arrange(across(all_of(c(group_columns, time_column)))) %>%
+    dplyr::mutate(
+      vr_avals = paste0("c(", paste0(!!sym(conc_column), collapse = ","), ")"),
+      vr_times = paste0("c(", paste0(!!sym(time_column), collapse = ","), ")")
+    ) %>%
+    arrange((!!sym(time_column) - start) < 0,
+            (!!sym(time_column) - start)) %>%
+    slice(1) %>%
+    ungroup() %>%
+    rowwise() %>%
+    mutate(
+      impute = case_when(
+        !!sym(time_column) == start & !is.na(!!sym(conc_column)) ~ NA,
+        DOSNO == 1 &
+          (tolower(!!sym(route_column)) == "extravascular" |
+             !!sym(duration_column) > 0 |
+             !!sym(analyte_column) != !!sym(drug_column)) ~ "start_conc0",
+        DOSNO > 1 &
+          (tolower(!!sym(route_column)) == "extravascular" |
+             !!sym(duration_column) > 0 |
+             !!sym(analyte_column) != !!sym(drug_column)) ~ "start_predose",
+        tolower(!!sym(route_column)) == "intravascular" &
+          !!sym(duration_column) == 0 &
+          !!sym(analyte_column) == !!sym(drug_column) &
+          !is.na(PKNCA::pk.calc.c0(conc = eval(parse(text = vr_avals)),
+                                   time = eval(parse(text = vr_times)),
+                                   time.dose = start,
+                                   method = "logslope")) ~ "start_logslope",
+        tolower(!!sym(route_column)) == "intravascular" &
+          !!sym(duration_column) == 0 &
+          !!sym(analyte_column) == !!sym(drug_column) ~ "start_c1"
+      )
+    ) %>%
+    # Select only the columns of interest
+    select(any_of(c(names(mydata$intervals), "impute")))
+
+  mydata$intervals <- new_intervals
+
+  return(mydata)
+}