changed df to adults df to extract relevant info

read_data.R

@@ -26,9 +26,16 @@ all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_
                    , fileEncoding = 'latin1') 
 
 # meta data columns                   
-meta_data_cols = c("mosaic", "gender", "age", "adult", "flustat", "type"
-                   , "obesity", "obese2", "height", "height_unit", "weight"
-                   , "weight_unit", "visual_est_bmi", "bmi_rating")
+meta_data_cols = c("mosaic", "gender", "age"
+                   , "adult"
+                   , "flustat", "type"
+                   , "obesity"
+                   , "obese2"
+                   , "height", "height_unit"
+                   , "weight", "weight_unit"
+                   , "ia_height_ftin", "ia_height_m", "ia_weight"
+                   , "visual_est_bmi", "bmi_rating"
+                   )
 
 # check if these columns to select are present in the data
 meta_data_cols%in%colnames(all_df)
@@ -36,6 +43,19 @@ all(meta_data_cols%in%colnames(all_df))
 
 metadata_all = all_df[, meta_data_cols]
 
+
+#==============
+# adult patients
+#==============
+
+adult_df = all_df[all_df$age>=18,]
+
+if (table(adult_df$adult == 1)[[1]] == nrow(adult_df) ){
+  cat ("PASS: adult df extracted successfully")
+} else{
+  cat ("FAIL: adult df number mismatch!")
+}
+
 #============
 # hc
 #============