bw score part is being tested

aminuldu07 · Oct 9, 2024 · 1c18e1e · 1c18e1e
1 parent a5c8295
commit 1c18e1e
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Showing 2 changed files with 60 additions and 50 deletions.
diff --git a/R/get_bw_score.R b/R/get_bw_score.R
@@ -32,7 +32,7 @@ get_bw_score <- function(studyid = NULL,
                          use_xpt_file = FALSE,
                          master_compiledata = NULL,
                          return_individual_scores = FALSE) {
-
+browser()
   studyid <- as.character(studyid)
   path <- path_db
 
@@ -79,6 +79,21 @@ get_bw_score <- function(studyid = NULL,
 
   }
 
+  # Ensuring "BWSTRESN", "VISITDY", "BWDY" columns are numeric
+  bw$BWSTRESN <- as.numeric(bw$BWSTRESN)
+  bw$VISITDY <- as.numeric(bw$VISITDY)
+  bw$BWDY <- as.numeric(bw$BWDY)
+
+  #check for NAs introduced by the conversion
+  if (any(is.na(bw$BWSTRESN))) {
+    warning("Non-numeric values in BWSTRESN were coerced to NA")
+  }
+  if (any(is.na(bw$VISITDY))) {
+    warning("Non-numeric values in VISITDY were coerced to NA")
+  }
+  if (any(is.na(bw$BWDY))) {
+    warning("Non-numeric values in BWDY were coerced to NA")
+  }
 
   #.................. "BodyWeight_zScore" .....calculation........
   #................... Initial BW weight calculation..............
@@ -138,7 +153,7 @@ get_bw_score <- function(studyid = NULL,
             # Set BWSTRESN to 0 for the rows that meet the condition
             null_visitdy_large_bw$BWSTRESN <- 0
 
-            # Choose the row with the minimum BWDY value greater than 5
+            # Choose the row with the minimum VISITDY value greater than 5
             closest_row_null_visitdy <- which.min(null_visitdy_large_bw$VISITDY)
             SubjectInitialWeight <- null_visitdy_large_bw[closest_row_null_visitdy, c("STUDYID", "USUBJID", "BWSTRESN", "VISITDY")]
           }
@@ -179,7 +194,7 @@ get_bw_score <- function(studyid = NULL,
     # only the first occurrence of each unique USUBJID will be kept, and subsequent duplicates will be removed
     StudyInitialWeights <- StudyInitialWeights[!duplicated(StudyInitialWeights$USUBJID), ]
 
-
+browser()
     #.......................................................................
     # ..........Final day "StudyBodyWeights" calculation.....................
 
@@ -212,7 +227,7 @@ get_bw_score <- function(studyid = NULL,
 
         # 1. Check if BWTESTCD == TERMBW is present
         SubjectBodyWeight <- subj_bw_data[subj_bw_data$BWTESTCD == "TERMBW",
-                                          c("STUDYID", "USUBJID", "BWTESTCD","BWSTRESN", "VISITDY")] #,"BWNOMDY","BWNOMLBL","BWBLFL")]
+                                          c("STUDYID", "USUBJID", "BWTESTCD","BWSTRESN", "VISITDY")]
 
         # If BWTESTCD == TERMBW not present,
         # 2. If no  BWTESTCD == TERMBW,try  VISITDY > 5"

diff --git a/inst/testing_rscript.R b/inst/testing_rscript.R
@@ -461,49 +461,44 @@ predicted_rf <- predicted_random_forest_model(dbPath_liver, dbPath_not_liver)
 # print(time_taken)
 # #####
 #
-# ####bw##score testing
-# ######
-# rm(list = ls())
-# devtools::load_all(".")
-#
-# path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/all_fakedata_liver_/FAKE10663'
-# #
-# # fake_xpt_compiltdata <- get_compile_data(studyid = NULL,
-# #                                                 path_db,
-# #                                                 fake_study = TRUE,
-# #                                                 use_xpt_file = TRUE)
-# #
-# #
-# # studyid = '10663'
-# # path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/liver_1.db'
-# # fake_compiledata <- get_compile_data(studyid,
-# #                                                  path_db,
-# #                                                  fake_study = TRUE,
-# #                                                  use_xpt_file = FALSE)
-#
-#
-#
-#
-#
-#
-# fake_bw_xpt <- get_bw_score(studyid = NULL,
-#                         path_db,
-#                         fake_study = TRUE,
-#                         master_compiledata = NULL,
-#                         return_individual_scores = FALSE,
-#                         use_xpt_file = TRUE)
-#
-#
-#
-#
-#
-#
-#
-#
-#
-#
-#
-#
-#
-#
-# https://aminuldu07.github.io/SENDQSAR/
+####bw##score testing
+######
+rm(list = ls())
+devtools::load_all(".")
+
+path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/all_fakedata_liver_/FAKE10663'
+path_db = "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/all_fakedata_liver_/FAKE11094"
+
+fake_bw_xpt <- get_bw_score(studyid = NULL,
+                        path_db,
+                        fake_study = TRUE,
+                        master_compiledata = NULL,
+                        return_individual_scores = FALSE,
+                        use_xpt_file = TRUE)
+
+# for multiple folders
+
+rm(list = ls())
+devtools::load_all(".")
+
+# Set the main directory
+main_dir <- "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/all_fakedata_liver_/"
+
+# List all subdirectories
+subdirs <- list.dirs(main_dir, full.names = TRUE, recursive = FALSE)
+
+fake_xpt_results <- list()
+
+# Loop through each subdirectory and process it
+for (subdir in subdirs) {
+  # Assuming your function works with each subdirectory
+  fake_bw_xpt <- get_bw_score(studyid = NULL,
+                              path_db = subdir,
+                              fake_study = TRUE,
+                              master_compiledata = NULL,
+                              return_individual_scores = FALSE,
+                              use_xpt_file = TRUE)
+
+  # Do something with the result, e.g., store it in a list
+  fake_xpt_results <- append(fake_xpt_results, list(fake_bw_xpt))
+}