Update to local script to show the range in which failing variables lie

valid_variables_script2.R

@@ -16,7 +16,7 @@ source("necessary_functions_connection.R")
 dep_list = c("jsonlite", "stringr","DSI","DSOpal","DSLite", "fields", "metafor", "ggplot2", "gridExtra", "data.table", "dsBaseClient", "openxlsx")
 install_dependencies(dep_list)
 
-codebook_file <- "20220315_Data Harmonisation.xlsb.xlsx"
+codebook_file <- "20220315_Data_Harmonisation.xlsb.xlsx"
 
 codebook_demo <- read.xlsx(codebook_file , sheet = 2 )
 codebook_com_and_rf <- read.xlsx(codebook_file , sheet = 3 ) 

valid_variables_script_local.R

@@ -2,6 +2,7 @@ rm(list=ls())
 
 dir_name <- readline("Introduce the name of the directory please: ")
 # C:\Users\guill\Documents\harmonize_scripts
+# /Users/gnl/Documents/CTB UPM/UNCOVER/uncover_harmonization
 
 setwd(dir_name)
 
@@ -11,7 +12,7 @@ source("dependency_installer.R")
 dep_list = c("jsonlite", "stringr","DSI","DSOpal","DSLite", "fields", "metafor", "ggplot2", "gridExtra", "data.table", "dsBaseClient", "openxlsx")
 install_dependencies(dep_list)
 
-codebook_file <- "20220315_Data Harmonisation.xlsb.xlsx"
+codebook_file <- "20220315_Data_Harmonisation.xlsb.xlsx"
 
 codebook_demo <- read.xlsx(codebook_file , sheet = 2 )
 codebook_com_and_rf <- read.xlsx(codebook_file , sheet = 3 ) 
@@ -101,11 +102,13 @@ check_valid_name <- function(col_name){
 }
 
  check_valid_values_continuous <- function(colname , codebook_param , column){
+   
 
    column <- as.numeric(column[column != "."])
    possible_values_format <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == colname]
-
+   
    value_format <- strsplit(possible_values_format, " / ")[[1]]
+
    min_value <- str_trim(gsub(",", ".", (sub("-.*", "", value_format[1]))))
    max_value <- str_trim(gsub(",", ".", (sub(".*-", "", value_format[1]))))
    if(min_value == ""){
@@ -114,9 +117,6 @@ check_valid_name <- function(col_name){
    }
    min_value <- as.double(min_value)
    max_value <- as.double(max_value)
-   print(colname)
-   print(min_value)
-   print(max_value)
 
    failing_values <- column[column < min_value | column > max_value]
    number_of_failing_values <- length(failing_values[!is.na(failing_values)])
@@ -128,15 +128,36 @@ check_valid_name <- function(col_name){
      failing_values <- failing_values[!is.na(failing_values)]
      failing_value_counts <- table(failing_values)
 
-     str_res <- paste(colname, "has failing values:")
-
-     for (i in seq_along(failing_value_counts)) {
-       value <- names(failing_value_counts)[i]
-       count <- failing_value_counts[i]
-       str_res <- paste(str_res, paste(value, "(", count, "times)", collapse = " "), sep = " ")
-     }
-
-     str_res <- paste(str_res, "should be in range", value_format, "(continuous)", sep = " ")
+     str_res <- paste(colname, "has wrong values:")
+     
+     str_res <- paste(str_res, paste(number_of_failing_values, ",", sep = ""))
+     
+     str_res <- paste(str_res, "should be in the range:", paste(min_value, max_value, sep = "-"), "(continuous),", sep = " ")
+     
+     first <- names(failing_value_counts)[1]
+     
+     last <- names(failing_value_counts)[length(failing_value_counts)]
+     
+     print(colname)
+     print("first")
+     print(first)
+     print("last")
+     print(last)
+     
+     str_res <- paste(str_res, "Values lie in the range:", paste("[", first, " - ",last, "]", sep = "" ))
+     
+     
+     # if(number_of_failing_values < 30) {
+     #   # list_values <- paste( failing_values , collapse = " ")
+     #   str_res <- paste(str_res, "Wrong values:")
+     #  
+     #   for (i in seq_along(failing_value_counts)) {
+     #     value <- names(failing_value_counts)[i]
+     #     count <- failing_value_counts[i]
+     #     str_res <- paste(str_res, paste(value, paste("(", count, ")", sep = ""), collapse = " "), sep = " ")
+     #   }
+     # }
+     
    }
 
    return(str_res)
@@ -324,6 +345,13 @@ check_valid_values <- function(valid_colnames, codebook_param){
       next
     }
     
+    if(is.na(codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == name])){
+      variable <- paste("Variable ", name, " with no value format", sep = " ")
+      res <- paste(res,  variable , sep="\n")
+      next
+    }
+    
+    
     result = switch(  
       column_type,  
       "Continuous"= check_valid_values_continuous(name , codebook_param , column),