Prerelease clean up

R/create_nepexplorer_app.R

@@ -41,7 +41,7 @@ if (is.null(mapping)) {
                                "visit_col" = "VISIT",
                                "visitn_col" = "VISITN",
                                "baseline_flag" = "BLFL",
-                               "baseline_values" = "Y",
+                               "baseline_values" = list("Y" = "Y"),
                                "normal_col_high" = "STNRHI",
                                "id_col" = "USUBJID",
                                "age_col" = "AGE",

R/creatinine_data_fcn.R

@@ -15,10 +15,9 @@ creatinine_data_fcn <- function(df, settings) {
            .data[[settings$measure_col]],
            .data[[settings$value_col]], .data[[settings$baseline_flag]])
 
-
   #get baseline creatinine levels for each subject for hover text
   baseline_creat <- creatinine_data %>%
-    filter(.data[[settings$baseline_flag]] == settings$baseline_values) %>%
+    filter(.data[[settings$baseline_flag]] == settings$baseline_values$Y) %>%
     select(.data[[settings$id_col]], BASELINE = .data[[settings$value_col]])
 
 

R/init_nepExplorer.R

@@ -11,27 +11,48 @@
 #' @export
 
 init_nepExplorer <- function(data, settings) {
+
+  # check for any missing required settings and warn user
+  missing_settings <- check_required_settings(expected_settings, settings)
+
+  if (length(missing_settings) > 0) {
+    warning(paste("The following required nepExplorer settings were not detected:",
+                  paste(names(missing_settings), collapse = ", ")))
+  }
+
+  # check for any missing columns that are specified in settings
+  missing_cols_results <- lapply(c("labs", "vitals", "dm"),
+                                 function(domain) check_expected_cols(domain, settings, data))
+
+  missing_cols_msgs <- Filter(Negate(is.null), missing_cols_results)
+
+  if (length(missing_cols_msgs) > 0) {
+    warning(paste(missing_cols_msgs, collapse = "\n"))
+  }
+
+  # subset vital signs dataset to blood pressure tests
   vs_sub <-
     data$vitals %>%
     filter(.data[[settings[["vitals"]]$measure_col]] %in%
              c(
                settings[["vitals"]]$measure_values$DIABP,
                settings[["vitals"]]$measure_values$SYSBP
              ))
-
+
+  # stack labs and vitals
   vs_labs <- data$labs %>% bind_rows(vs_sub)
-
+
+  #subset dm dataset to usable columns
   dm_sub <- data$dm %>%
     dplyr::select(any_of(c(settings[["dm"]][["id_col"]],
-                  settings[["dm"]][["treatment_col"]],
-                  settings[["dm"]][["race_col"]],
-                  settings[["dm"]][["age_col"]])))
-
-  # left join to keep all rows in dm
+                           settings[["dm"]][["treatment_col"]],
+                           settings[["dm"]][["race_col"]],
+                           settings[["dm"]][["age_col"]])))
+  
+  # left join labs/vitals to keep all rows in dm
   anly <- dm_sub %>%
     dplyr::left_join(vs_labs,
-                     by = c(settings[["labs"]][["id_col"]],
-                            settings[["labs"]][["treatment_col"]]))
-
+                     by = setNames(settings[["dm"]][["id_col"]], settings[["labs"]][["id_col"]]))
+
   list(data = anly, settings = settings)
 }

R/nepexplorerMod.R

@@ -118,10 +118,9 @@ nepexplorer_server <- function(input, output, session, params) {
                                       measure_values[grep("nepFC", names(measure_values))])
 
     # update selectize to reflect what's specific in metadata
-
     shinyWidgets::updatePickerInput(session,
                          "measures",
-                         choices = measures,
+                         choices = measures[!is.na(measures)],
                          selected = fold_change_measures
     )
   })

R/validation_checks_util.R

@@ -0,0 +1,102 @@
+#' Expected Settings List
+#'
+#' This list defines the expected settings for different data domains.
+#' Each domain contains specific columns and values that are required for data processing.
+#'
+#' @format A list with the following structure:
+#' \describe{
+#'   \item{labs}{A list containing the expected settings for laboratory data:
+#'     \describe{
+#'       \item{id_col}{Column name for the subject identifier (e.g., "USUBJID").}
+#'       \item{measure_col}{Column name for the measure parameter (e.g., "PARAM").}
+#'       \item{measure_values}{A list of measure values and their corresponding descriptions
+#'       (e.g., list("CREAT" = "Creatinine")).}
+#'       \item{value_col}{Column name for the measurement value (e.g., "STRESN").}
+#'       \item{unit_col}{Column name for the measurement unit (e.g., "STRESU").}
+#'       \item{studyday_col}{Column name for the study day (e.g., "DY").}
+#'       \item{visit_col}{Column name for the visit description (e.g., "VISIT").}
+#'       \item{visitn_col}{Column name for the visit number (e.g., "VISITN").}
+#'       \item{baseline_flag}{Column name for the baseline flag (e.g., "BLFL").}
+#'       \item{baseline_values}{Value indicating baseline (e.g., "Y").}
+#'       \item{normal_col_high}{Column name for the upper limit of normal range
+#'       (e.g., "STNRHI").}
+#'     }
+#'   }
+#'   \item{dm}{A list containing the expected settings for demographic data:
+#'     \describe{
+#'       \item{id_col}{Column name for the subject identifier (e.g., "USUBJID").}
+#'     }
+#'   }
+#'   \item{vitals}{A list containing the expected settings for vital signs data:
+#'     \describe{
+#'       \item{id_col}{Column name for the subject identifier (e.g., "USUBJID").}
+#'       \item{measure_col}{Column name for the measure parameter (e.g., "PARAM").}
+#'     }
+#'   }
+#' }
+expected_settings <-  list(labs = list("id_col" = "USUBJID", "measure_col" = "PARAM",
+                                       "measure_values" = list("CREAT" = "Creatinine"),
+                                       "value_col" = "STRESN",
+                                       "unit_col" = "STRESU",
+                                       "studyday_col" = "DY",
+                                       "visit_col" = "VISIT",
+                                       "visitn_col" = "VISITN",
+                                       "baseline_flag" = "BLFL",
+                                       "baseline_values" = list("Y" = "Y"),
+                                       "normal_col_high" = "STNRHI"),
+                           dm = list("id_col" = "USUBJID"),
+                           vitals = list("id_col" = "USUBJID", "measure_col" = "PARAM"))
+
+#' Check Required Settings in a List
+#'
+#' This function checks if a given list contains all the required elements specified in another list.
+#' It allows for additional elements at any nesting level and prints out a message listing the missing settings, if any.
+#'
+#' @param required_list A list specifying the required elements.
+#' @param actual_list A list to be checked against the required elements.
+#' @param parent_key (Optional) A string used internally to track the full key path during recursion.
+#'  Default is an empty string.
+#' @return A list of missing elements, if any.
+check_required_settings <- function(required_list, actual_list, parent_key = "") {
+  missing_elements <- list()
+
+  for (name in names(required_list)) {
+    full_key <- if (parent_key == "") name else paste(parent_key, name, sep = "$")
+
+    if (!name %in% names(actual_list)) {
+      missing_elements[[full_key]] <- required_list[[name]]
+    } else if (is.list(required_list[[name]])) {
+      if (!is.list(actual_list[[name]])) {
+        missing_elements[[full_key]] <- required_list[[name]]
+      } else {
+        nested_missing <- check_required_settings(required_list[[name]], actual_list[[name]], full_key)
+        missing_elements <- c(missing_elements, nested_missing)
+      }
+    }
+  }
+
+  return(missing_elements)
+}
+
+#' Check for Missing Columns in Data
+#'
+#' This function checks for any columns specified in the settings object that are not present in the data.
+#' It returns a message listing the missing columns, if any.
+#'
+#' @param data_domain A string specifying the data domain to check (e.g., "labs", "vitals", "dm").
+#' @param settings_list A list containing the settings for each data domain.
+#' @param data_list A list containing the data for each domain.
+#' @return A string message listing the missing columns, or NULL if all expected columns are present.
+check_expected_cols <- function(data_domain, settings_list, data_list) {
+
+  expected_cols <- settings_list[[data_domain]][!grepl("_values$", names(settings_list[[data_domain]]))] %>%  unlist()
+
+  missing_cols <- setdiff(expected_cols, colnames(data_list[[data_domain]]))
+
+  if (length(missing_cols) > 0) {
+    paste("The following columns were specified in", data_domain, "settings but not found in the",
+                 data_domain, "dataset: ", paste(missing_cols, collapse = ", "))
+  } else {
+    NULL
+  }
+}

data-raw/meta_nepExplorer.csv

@@ -1,28 +1,28 @@
-text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm
-id_col,vitals,id_col,,column,ID column,Unique subject identifier variable name.,FALSE,USUBJID,USUBJID
-value_col,vitals,value_col,,column,Value column,Vitals result variable name.,FALSE,AVAL,VSSTRESN
-measure_col,vitals,measure_col,,column,Measure column,Vitals measure variable name,FALSE,PARAM,VSTEST
-studyday_col,vitals,studyday_col,,column,Study Day column,Visit day variable name,FALSE,ADY,VSDY
-visit_col,vitals,visit_col,,column,Visit column,Visit variable name,FALSE,AVISIT,VISIT
-visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable name,FALSE,AVISITN,VISITNUM
-measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure 
-measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic  Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
-unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name,FALSE,,VSSTRESU
-vs_baseline_flag,vitals,vs_baseline_flag,,column,Vital Signs Baseline Flag,Column for assigning VS baseline visits,FALSE,ABLFL,
-vs_baseline_values--Y,vitals,vs_baseline_flag,Y,field,Vital Signs Baseline Flag value,Value used for VS Baseline in the specified baseline column,FALSE,Y,
-measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (mg/dL),Albumin
-measure_values--ALB/CREAT,labs,measure_col,ALB/CREAT,field,Albumin/Creatinine Ratio value,Value used for Albumin/Creatinine ratio in the specified measure column,FALSE,Albumin/Creatinine,
-measure_values--BUN/CREAT,labs,measure_col,BUN/CREAT,field,Blood Urea Nitrogen/Creatinine Ratio value,Value used for Blood Urea Nitrogen/Creatinine ratio in the specified measure column,FALSE,Blood Urea Nitrogen/Creatinine,
-measure_values--nepFC_BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate
-measure_values--nepFC_BUN,labs,measure_col,BUN,field,Blood Urea Nitrogen value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen
-measure_values--nepFC_CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium
-measure_values--nepFC_CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride
-measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (mg/dL),Creatinine
-measure_values--CYSTC,labs,measure_col,CYSTC,field,Cystatin C value,Value used for Cystatin C in the specified measure column,FALSE,Cystatin C (umol/L),Cystatin C
-measure_values--eGFR,labs,measure_col,eGFR,field,eGFR value,Value used for the Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFR (mL/min),eGFR
-measure_values--eGFRcys,labs,measure_col,eGFRcys,field,eGFRcys value,Value used for the Cystatic C-based Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFRcys (mL/min),eGFRcys
-measure_values--nepFC_PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate
-measure_values--nepFC_K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium
-measure_values--nepFC_SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium
-baseline_flag,labs,baseline_flag,,column,Baseline Flag column,Column for assigning baseline visits,FALSE,ABLFL,LBBLFL
-baseline_values--Y,labs,baseline_flag,Y,field,Baseline Flag value,Value used for Baseline in the specified baseline column,FALSE,Y,Y
+text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm
+id_col,vitals,id_col,,column,ID column,Unique subject identifier variable name.,FALSE,USUBJID,USUBJID
+value_col,vitals,value_col,,column,Value column,Vitals result variable name.,FALSE,AVAL,VSSTRESN
+measure_col,vitals,measure_col,,column,Measure column,Vitals measure variable name,FALSE,PARAM,VSTEST
+studyday_col,vitals,studyday_col,,column,Study Day column,Visit day variable name,FALSE,ADY,VSDY
+visit_col,vitals,visit_col,,column,Visit column,Visit variable name,FALSE,AVISIT,VISIT
+visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable name,FALSE,AVISITN,VISITNUM
+measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure 
+measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic  Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
+unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name,FALSE,,VSSTRESU
+baseline_flag,vitals,vs_baseline_flag,,column,Vital Signs Baseline Flag,Column for assigning VS baseline visits,FALSE,ABLFL,
+baseline_values--Y,vitals,vs_baseline_flag,Y,field,Vital Signs Baseline Flag value,Value used for VS Baseline in the specified baseline column,FALSE,Y,
+measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (mg/dL),Albumin
+measure_values--ALB/CREAT,labs,measure_col,ALB/CREAT,field,Albumin/Creatinine Ratio value,Value used for Albumin/Creatinine ratio in the specified measure column,FALSE,Albumin/Creatinine,
+measure_values--BUN/CREAT,labs,measure_col,BUN/CREAT,field,Blood Urea Nitrogen/Creatinine Ratio value,Value used for Blood Urea Nitrogen/Creatinine ratio in the specified measure column,FALSE,Blood Urea Nitrogen/Creatinine,
+measure_values--nepFC_BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate
+measure_values--nepFC_BUN,labs,measure_col,BUN,field,Blood Urea Nitrogen value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen
+measure_values--nepFC_CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium
+measure_values--nepFC_CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride
+measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (mg/dL),Creatinine
+measure_values--CYSTC,labs,measure_col,CYSTC,field,Cystatin C value,Value used for Cystatin C in the specified measure column,FALSE,Cystatin C (umol/L),Cystatin C
+measure_values--eGFR,labs,measure_col,eGFR,field,eGFR value,Value used for the Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFR (mL/min),eGFR
+measure_values--eGFRcys,labs,measure_col,eGFRcys,field,eGFRcys value,Value used for the Cystatic C-based Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFRcys (mL/min),eGFRcys
+measure_values--nepFC_PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate
+measure_values--nepFC_K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium
+measure_values--nepFC_SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium
+baseline_flag,labs,baseline_flag,,column,Baseline Flag column,Column for assigning baseline visits,FALSE,ABLFL,LBBLFL
+baseline_values--Y,labs,baseline_flag,Y,field,Baseline Flag value,Value used for Baseline in the specified baseline column,FALSE,Y,Y

data-raw/meta_nepExplorer2.csv

@@ -8,8 +8,8 @@ visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable n
 measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure 
 measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic  Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
 unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name for Blood Pressure,FALSE,STRESU,VSSTRESU
-vs_baseline_flag_col,vitals,vs_baseline_flag,,column,VS Baseline Flag,Column for assigning baseline visits for Blood Pressure,FALSE,ABLFL,
-vs_baseline_values--POS,vitals,vs_baseline_flag_col,POS,field,VS Baseline Flag value,Value used for Baseline in the specified baseline column  for Blood Pressure,FALSE,Y,Y
+baseline_flag_col,vitals,vs_baseline_flag,,column,VS Baseline Flag,Column for assigning baseline visits for Blood Pressure,FALSE,ABLFL,
+baseline_values--Y,vitals,vs_baseline_flag_col,Y,field,VS Baseline Flag value,Value used for Baseline in the specified baseline column  for Blood Pressure,FALSE,Y,Y
 lab_unit_col,labs,lab_unit_col,,column,Unit column,Unit of measure variable name,FALSE,STRESU,STRESU
 measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (g/L),Albumin
 measure_values--BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate