lbommi score list updated

aminuldu07 · Dec 14, 2024 · dda9e82 · dda9e82
1 parent c419c91
commit dda9e82
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Showing 10 changed files with 211 additions and 450 deletions.
diff --git a/R/get_lb_score.R b/R/get_lb_score.R
@@ -154,8 +154,9 @@ get_lb_score <- function(studyid = NULL,
 
     # # Filtering the tk animals and the recovery animals
     # # Remove the TK animals and Recovery animals
-    # LB_tk_recovery_filtered <- max_visitdy_df %>%
-    #   dplyr::filter(USUBJID %in% master_compiledata$USUBJID)
+
+    LB_tk_recovery_filtered <- max_visitdy_df %>%
+      dplyr::filter(USUBJID %in% master_compiledata$USUBJID)
 
     # Perform a left join to match USUBJID and get ARMCD ## 020924
     #-inner_join() used instead of left_join()#199

diff --git a/R/get_liver_om_lb_mi_tox_score_list.R b/R/get_liver_om_lb_mi_tox_score_list.R
@@ -1,3 +1,5 @@
+
+
 #' @title get_liver_om_lb_mi_tox_score_list
 #' @param selected_studies Mandatory, character \cr
 #'   Studyid number
@@ -107,14 +109,17 @@ if(output_individual_scores ) {
                                 stringsAsFactors = FALSE)
 }
 
+  #---------------------------------------------------------------------------
+  #---------------------------------------------------------------------------
+
   # iterate over studyid or each xpt folder
 for (studyid in selected_studies){
 
   print(studyid)
 
   if( multiple_xpt_folder == TRUE) {
 
-    path_db <- studyid
+    path_db <- studyid # giving the path of the xpt folder
 
     print(path_db)
    }
@@ -630,6 +635,9 @@ for (studyid in selected_studies){
 
 }
 
+  #---------------------------------------------------------------------------
+  #---------------------------------------------------------------------------
+
   if (output_individual_scores) {
 
     # Perform the merge using full_join to keep all rows from each data frame

diff --git a/R/get_repeat_dose_parallel_studyids.R b/R/get_repeat_dose_parallel_studyids.R
@@ -0,0 +1,50 @@
+
+get_repeat_dose_parallel_studyids <- function (databasetype = NULL ) {
+
+
+# #Database Load
+# dbtoken <- sendigR::initEnvironment(dbType = 'sqlite',
+#                                     dbPath = "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/TestDB.db",
+#                                     dbCreate = FALSE)
+#
+# parallel_StudyID <- sendigR::getStudiesSDESIGN(dbtoken, studyDesignFilter = "PARALLEL")
+#
+#
+# # Filtering the Repeat dose Studies
+# repeat_dose_STUDYIDs <- sendigR::genericQuery(dbtoken, queryString = "SELECT DISTINCT STUDYID
+#                              FROM ts
+#                              WHERE TSPARMCD = 'SSTYP'
+#                              AND TSVAL IN ('REPEAT DOSE TOXICITY', 'REPEAT-DOSE TOXICITY', 'Repeat-Dose Toxicity', 'Repeat Dose Toxicity')",
+#                                               queryParams = NULL)
+#
+# # COMMON STUDYIDs from PARALLEL STUDYIDs and repeat_dose_STUDYIDs.....
+# parallel_repeat_dose_intersect <- intersect(parallel_StudyID$STUDYID,repeat_dose_STUDYIDs$STUDYID)
+#
+# # converting "parallel_repeat_dose_intersect" to a data frame
+# parallel_repeat_dose_intersec_df <- data.frame(STUDYID = parallel_repeat_dose_intersect)
+#
+# # convert to a vector( selected_studies should be always vector)
+# #selected_studies <- as.vector(parallel_repeat_dose_intersec_df$STUDYID)
+#
+# # get the studies for the rat only species
+# rat_STUDYID_ts_species <- sendigR::genericQuery(dbtoken, queryString = "SELECT STUDYID, TSPARMCD, TSVAL
+#                              FROM ts
+#                              WHERE TSPARMCD = 'SPECIES' AND UPPER(TSVAL) LIKE '%RAT%'", queryParams = NULL)
+#
+# selected_studies <- as.vector(rat_STUDYID_ts_species$STUDYID)
+# #selected_studies <- c("2170016", "1021-9743")
+# #selected_studies <- c("2170016")
+# #selected_studies  <- c("8514252")
+#
+# path_db='C:/Users/mdaminulisla.prodhan/OneDrive - FDA/TestDB.db'
+# start_time <- Sys.time()
+# allscore <- get_liver_om_lb_mi_tox_score_list(selected_studies,
+#                                               path_db,
+#                                               fake_study = FALSE,
+#                                               output_individual_scores = TRUE)
+# end_time <- Sys.time()
+# time_taken <- end_time - start_time
+# print(time_taken)
+# #####
+#
+}
diff --git a/inst/test_get_liver_om_lb_mi_score_list.R b/inst/test_get_liver_om_lb_mi_score_list.R
@@ -0,0 +1,52 @@
+rm(list = ls())
+devtools::load_all(".")
+
+# #Database Load
+# dbtoken <- sendigR::initEnvironment(dbType = 'sqlite',
+#                                     dbPath = "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/TestDB.db",
+#                                     dbCreate = FALSE)
+
+
+path_db='C:/Users/MdAminulIsla.Prodhan/OneDrive - FDA/Documents/DATABASES/TestDB.db'
+
+#selected_studies <- c("2170016")
+
+
+
+R_SQL_om_lb_mi_CD <- get_liver_om_lb_mi_tox_score_list  (selected_studies = selected_studies,
+                                               path_db = path_db,
+                                               fake_study = FALSE,
+                                               use_xpt_file = FALSE,
+                                               multiple_xpt_folder = FALSE,
+                                               output_individual_scores = FALSE,
+                                               output_zscore_by_USUBJID = FALSE)
+
+# For multiple xpt folder
+
+selected_studies <- list.dirs(path_db , full.names = TRUE, recursive = FALSE)
+
+R_XPT_om_lb_mi_CD <- get_liver_om_lb_mi_tox_score_list  (selected_studies = selected_studies,
+                                                         path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/real_xpt_dir/IND051292_1017-3581',
+                                                         fake_study = FALSE,
+                                                         use_xpt_file = FALSE,
+                                                         multiple_xpt_folder = FALSE,
+                                                         output_individual_scores = FALSE,
+                                                         output_zscore_by_USUBJID = FALSE)
+
+
+selected_studies <- c("10663")
+fake_SQL_om_lb_mi_CD <- get_liver_om_lb_mi_tox_score_list  (selected_studies = selected_studies,
+                                                         path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/liver_1.db',
+                                                         fake_study = FALSE,
+                                                         use_xpt_file = FALSE,
+                                                         multiple_xpt_folder = FALSE,
+                                                         output_individual_scores = FALSE,
+                                                         output_zscore_by_USUBJID = FALSE)
+
+fake_XPT_om_lb_mi_CD <- get_liver_om_lb_mi_tox_score_list  (selected_studies = NULL,
+                                                         path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/all_fakedata_liver_/FAKE10663',
+                                                         fake_study = FALSE,
+                                                         use_xpt_file = FALSE,
+                                                         multiple_xpt_folder = FALSE,
+                                                         output_individual_scores = FALSE,
+                                                         output_zscore_by_USUBJID = FALSE)
diff --git a/inst/test_get_mi_score.R b/inst/test_get_mi_score.R
@@ -46,5 +46,39 @@ reat_XPT_mi_score <- get_mi_score(studyid=NULL,
 
 
 
-
+# #####----mi-score--calculation-------------------------
+#
+# rm(list = ls())
+# devtools::load_all(".")
+# mi_R_SQL_mi_zscore <- get_mi_score(studyid='A2018086-T002-01',
+#                                    path_db='C:/Users/mdaminulisla.prodhan/OneDrive - FDA/TestDB.db',
+#                                    fake_study = FALSE,
+#                                    use_xpt_file = FALSE,
+#                                    master_compiledata = NULL,
+#                                    return_individual_scores = TRUE)
+#
+#
+# mi_R_XPT_mi_zscore <- get_mi_score (studyid= NULL,
+#                                     path_db='C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/real_xpt_dir/IND051292_1017-3581',
+#                                     fake_study = FALSE,
+#                                     use_xpt_file = TRUE,
+#                                     master_compiledata = NULL,
+#                                     return_individual_scores = TRUE)
+#
+#
+# mi_fake_SQL_mi_zscore <- get_mi_score (studyid = '10663',
+#                                        path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/liver_1.db',
+#                                        fake_study = TRUE,
+#                                        use_xpt_file = FALSE,
+#                                        master_compiledata = NULL,
+#                                        return_individual_scores = TRUE)
+#
+#
+# mi_fake_XPT_mi_zscore <- get_mi_score (studyid = NULL,
+#                                        path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/all_fakedata_liver_/FAKE10663',
+#                                        fake_study = TRUE,
+#                                        use_xpt_file = TRUE,
+#                                        master_compiledata = NULL,
+#                                        return_individual_scores = TRUE)
+#
 
diff --git a/inst/test_random_forest_model.R b/inst/test_random_forest_model.R
@@ -0,0 +1,62 @@
+
+
+### ###########################-randomforestmodel-#############################
+# rm(list = ls())
+# devtools::load_all(".")
+#
+# # #Database Load
+# dbtoken_liver <- sendigR::initEnvironment(dbType = 'sqlite',
+#                                     #dbPath = "/opt/rstudio/users/MdAminulIslam.Prodhan/DataCentral.db",
+#                                     dbPath = "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/liver_1.db",
+#                                     dbCreate = FALSE)
+# # get the studies for the rat only species
+# STUDYID_liver <- sendigR::genericQuery(dbtoken_liver, queryString = "SELECT DISTINCT STUDYID, DOMAIN
+#                              FROM bw ", queryParams = NULL)
+#
+# selected_studies_liver <- as.vector(STUDYID_liver$STUDYID)
+#
+#
+#
+# Liver_get_liver_om_lb_mi_tox_score_list <- get_liver_om_lb_mi_tox_score_list  (selected_studies = selected_studies_liver,
+#                                                                                path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/liver_1.db',
+#                                                                                fake_study = TRUE,
+#                                                                                use_xpt_file = FALSE,
+#                                                                                output_individual_scores = TRUE)
+#
+#
+#
+# dbtoken_not_liver <- sendigR::initEnvironment(dbType = 'sqlite',
+#                                           #dbPath = "/opt/rstudio/users/MdAminulIslam.Prodhan/DataCentral.db",
+#                                           dbPath = "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/fake_not_liver_update.db",
+#                                           dbCreate = FALSE)
+#
+# # get the studies for the rat only species
+# STUDYID_not_liver <- sendigR::genericQuery(dbtoken_not_liver, queryString = "SELECT DISTINCT STUDYID, DOMAIN
+#                              FROM bw ", queryParams = NULL)
+#
+# selected_studies_not_liver <- as.vector(STUDYID_not_liver$STUDYID)
+#
+#
+# not_Liver_get_liver_om_lb_mi_tox_score_list <- get_liver_om_lb_mi_tox_score_list  (selected_studies = selected_studies_not_liver,
+#                                                             path_db = 'C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/fake_not_liver_update.db',
+#                                                             fake_study = TRUE,
+#                                                             use_xpt_file = FALSE,
+#                                                             output_individual_scores = TRUE)
+#
+#
+#
+# amin_get_random_forest_model <- get_random_forest_model(Liver_get_liver_om_lb_mi_tox_score_list,
+#                                                         not_Liver_get_liver_om_lb_mi_tox_score_list)
+#
+#
+
+
+#
+dbPath_liver = "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/liver_1.db"
+dbPath_not_liver = "C:/Users/mdaminulisla.prodhan/OneDrive - FDA/2023-2024_projects/FAKE_DATABASES/fake_not_liver_update.db"
+
+predicted_rf <- predicted_random_forest_model(dbPath_liver, dbPath_not_liver)
+
+
+
+