Simplify the logic in slope plots, add order option & allow download in ZIP

NAMESPACE

@@ -21,15 +21,13 @@ export(apply_mapping)
 export(calculate_f)
 export(calculate_ratios)
 export(calculate_summary_stats)
-export(check_slope_rule_overlap)
 export(convert_volume_units)
 export(create_metabfl)
 export(create_start_impute)
 export(detect_study_types)
 export(dose_profile_duplicates)
 export(export_cdisc)
 export(filter_breaks)
-export(filter_slopes)
 export(flexible_violinboxplot)
 export(format_pkncaconc_data)
 export(format_pkncadata_intervals)
@@ -45,7 +43,6 @@ export(get_label)
 export(interval_add_impute)
 export(interval_remove_impute)
 export(l_pkcl01)
-export(lambda_slope_plot)
 export(multiple_matrix_ratios)
 export(parse_annotation)
 export(pivot_wider_pknca_results)
@@ -70,11 +67,11 @@ import(rlistings)
 import(tidyr)
 importFrom(PKNCA,exclude)
 importFrom(PKNCA,pk.calc.c0)
+importFrom(PKNCA,pk.nca)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,`%>%`)
 importFrom(dplyr,across)
 importFrom(dplyr,add_count)
-importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
@@ -83,6 +80,7 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,group_split)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
@@ -97,10 +95,17 @@ importFrom(dplyr,where)
 importFrom(flextable,flextable)
 importFrom(formatters,var_labels)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggplot_build)
 importFrom(ggplot2,ggplot_gtable)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_alpha_manual)
+importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_shape_manual)
 importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,theme_bw)
 importFrom(grid,convertUnit)
 importFrom(magrittr,`%>%`)
 importFrom(methods,is)
@@ -114,23 +119,24 @@ importFrom(officer,ph_location_type)
 importFrom(officer,ph_slidelink)
 importFrom(officer,ph_with)
 importFrom(officer,read_pptx)
+importFrom(plotly,add_lines)
 importFrom(plotly,add_trace)
-importFrom(plotly,config)
 importFrom(plotly,ggplotly)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
-importFrom(plotly,style)
+importFrom(plotly,plotly_build)
 importFrom(purrr,imap)
 importFrom(purrr,pmap)
 importFrom(purrr,pmap_chr)
 importFrom(purrr,reduce)
 importFrom(rlang,expr)
-importFrom(rlang,set_names)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
 importFrom(stats,as.formula)
+importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,na.omit)
+importFrom(stats,predict)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stringr,str_glue)

R/PKNCA.R

@@ -117,7 +117,7 @@ PKNCA_create_data_object <- function(adnca_data, nca_exclude_reason_columns = NU
   # Set default settings
   df_conc$is.excluded.hl <- FALSE
   df_conc$is.included.hl <- FALSE
-  df_conc$REASON <- NA
+  df_conc$REASON <- ""
   df_conc$exclude_half.life <- FALSE
 
   # Create PKNCA conc object
@@ -197,6 +197,8 @@ PKNCA_create_data_object <- function(adnca_data, nca_exclude_reason_columns = NU
 #'
 #' Step 5: Impute start values if requested
 #'
+#' Step 6: Indicate points excluded / selected manually for half-life
+#'
 #' Note*: The function assumes that the `adnca_data` object has been
 #' created using the `PKNCA_create_data_object()` function.
 #'
@@ -205,6 +207,9 @@ PKNCA_create_data_object <- function(adnca_data, nca_exclude_reason_columns = NU
 #' @param selected_analytes User selected analytes
 #' @param selected_profile User selected dose numbers/profiles
 #' @param selected_pcspec User selected specimen
+#' @param hl_adj_rules A data frame containing half-life adjustment rules. It must
+#' contain group columns and rule specification columns;
+#' TYPE: (Inclusion, Exclusion), RANGE: (start-end).
 #' @param should_impute_c0 Logical indicating whether to impute start concentration values
 #' @param exclusion_list List of exclusion reasons and row indices to apply to the
 #' concentration data. Each item in the list should have:
@@ -226,6 +231,7 @@ PKNCA_update_data_object <- function( # nolint: object_name_linter
   selected_profile,
   selected_pcspec,
   should_impute_c0 = TRUE,
+  hl_adj_rules = NULL,
   exclusion_list = NULL
 ) {
 
@@ -269,6 +275,10 @@ PKNCA_update_data_object <- function( # nolint: object_name_linter
       PCSPEC %in% selected_pcspec
     )
 
+  # Update concentration data to indicate points excluded / selected manually for half-life
+  if (!is.null(hl_adj_rules)) {
+    data <- update_pknca_with_rules(data, hl_adj_rules)
+  }
   data
 }
 
@@ -650,6 +660,53 @@ PKNCA_hl_rules_exclusion <- function(res, rules) { # nolint
   res
 }
 
+
+#' Checks Before Running NCA
+#'
+#' This function checks that:
+#' 1) exclusions_have_reasons: all manually excluded half-life points in the concentration data
+#' have a non-empty reason provided. If any exclusions are missing a reason, it stops with an error
+#' and prints the affected rows (group columns and time column).
+#'
+#' @param processed_pknca_data A processed PKNCA data object.
+#' @param exclusions_have_reasons Logical; Check that all exclusions have a reason (default: TRUE).
+#'
+#' @return The processed_pknca_data object (input), if checks are successful.
+#'
+#' @details
+#' - If any excluded half-life points are missing a reason, an error is thrown.
+#' - If no exclusions or all have reasons, the function returns the input object.
+#' - Used to enforce good practice/documentation before NCA calculation.
+#'
+#' @examples
+#' # Suppose processed_pknca_data is a valid PKNCA data object
+#' # check_valid_pknca_data(processed_pknca_data)
+check_valid_pknca_data <- function(processed_pknca_data, exclusions_have_reasons = TRUE) {
+  if (exclusions_have_reasons) {
+    excl_hl_col <- processed_pknca_data$conc$columns$exclude_half.life
+
+    if (!is.null(excl_hl_col)) {
+      data_conc <- processed_pknca_data$conc$data
+      conc_groups <- group_vars(processed_pknca_data$conc)
+      time_col <- processed_pknca_data$conc$columns$time
+
+      missing_reasons <- data_conc[[excl_hl_col]] & nchar(data_conc[["REASON"]]) == 0
+      missing_reasons_rows <- data_conc[missing_reasons, ] %>%
+        select(any_of(c(conc_groups, time_col)))
+
+      if (nrow(missing_reasons_rows) > 0) {
+        stop(
+          "No reason provided for the following half-life exclusions:\n",
+          "\n",
+          paste(capture.output(print(missing_reasons_rows)), collapse = "\n"),
+          "\n",
+          "Please go to `Slope Selection` table and include it"
+        )
+      }
+    }
+  }
+  processed_pknca_data
+}
 #' Add Exclusion Reasons to PKNCAdata Object
 #'
 #' This function adds exclusion reasons to the `exclude` column of the concentration object

R/g_pkcg.R

@@ -49,14 +49,15 @@ g_pkcg01_log <- function(data, ...) {
 #' @importFrom ggplot2 aes scale_x_continuous labs
 #' @importFrom tern g_ipp
 #' @importFrom stats setNames
+#' @importFrom plotly ggplotly layout
 #'
 #' @examples
 #' adnca <- read.csv(system.file("shiny/data/example-ADNCA.csv", package = "aNCA"))
 #' adnca <- subset(adnca, adnca$USUBJID %in% unique(adnca$USUBJID)[c(1, 2)])
 #' attr(adnca[["AFRLT"]], "label") <- "Actual time from first dose"
 #' attr(adnca[["AVAL"]], "label") <- "Analysis val"
 #'
-#' plots_lin <- pkcg01(adnca = adnca, xmax = 1)
+#' plots_lin <- pkcg01(adnca = adnca, xmax = 1, scale = "LIN")
 #'
 #' @export
 #' @author Gerardo Rodriguez