R Under development (unstable) (2025-07-03 r88378 ucrt) -- "Unsuffered Consequences"
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> # # # loading dataset
> # library(banffIT)
> # library(fs)
> # library(dplyr)
> # library(rlang)
> # library(tools)
> # # library(readr)
> # library(stringr)
> # library(lubridate)
> # library(tidyr)
> # library(fabR)
> # library(madshapR)
> # library(crayon)
> # # library(Rmonize)
> # # library(janitor)
> # #
> # # input_file = "tests/CHUQ_for_test_3.csv"
> # # output_folder = 'tests'
> # # language = 'label:en'
> # # option_filter = quote(adequacy == 1)
> # # detail = TRUE
> # # include_banff_dictionary = TRUE
> #
> # library(banffIT)
> #
> # input_file = '../../example_errors.csv'
> #
> # # banff_launcher(
> # #   input_file = 'inst/extdata/2022/banff_example.xlsx',
> # #   output_folder = 'tests',
> # #   version = 2022)
> # #
> # # banff_launcher(
> # #   input_file = 'inst/extdata/2017/banff_example.xlsx',
> # #   output_folder = 'tests',
> # #   version = 2017)
> #
> #
> #
> # patch_banffIT <- function(input_file){
> #
> #   library(fs)
> #   library(fabR)
> #   library(tidyr)
> #   library(stringr)
> #
> #   path_file <- input_file
> #   if(path_ext(path_file) == 'xlsx') file <- read_excel_allsheets(path_file)
> #   if(path_ext(path_file) == 'csv')  file <- read_csv_any_formats(path_file)
> #
> #   if(sum(c('sc_date_bx','date_tx') %in% names(file)) != 2)
> #     stop(
> # '`sc_date_bx` and/or `date_tx` is missing in your dataset. Please refer to online documentation')
> #
> #   if(sum(is.na(silently_run(as_any_date(file$sc_date_bx)))) >
> #      sum(is.na(file$sc_date_bx)) |
> #      sum(is.na(silently_run(as_any_date(file$date_tx)))) >
> #      sum(is.na(file$date_tx))) stop(
> # '\n\n
> # In `sc_date_bx` and/or `date_tx` : Some values in your file cannot be coerced in
> # dates. Open your file and check in these columns which values are not
> # compatible with date formats. Please refer to online documentation')
> #
> #   file_corrected            <- file
> #   file_corrected$sc_date_bx <- as_any_date(file_corrected$sc_date_bx)
> #   file_corrected$date_tx    <- as_any_date(file_corrected$date_tx)
> #
> #   new_name <-
> #     str_replace(path_file,
> #                 basename(path_file),paste0('Copy - ',
> #                 file_path_sans_ext(basename(path_file)),'.xlsx'))
> #
> #   write_excel_allsheets(file_corrected, new_name)
> #
> #   message(
> # "
> # A new file has been created in the same folder of the original file.
> # Use this file path instead of your original file, or replace your
> # dates columns with the one provided (All of the other columns are unchanged)
> #
> # input_file <- '", new_name,"'")
> #
> # }
> #
> # # patch_banffIT(input_file)
> #
> # input_file = 'inst/extdata/2022/banff_example.xlsx'
> #
> # differential_diagnoses <- function(input_file, between = NULL, and = NULL){
> #
> #   between <- suppressMessages(get_banff_version(between))
> #   and <- suppressMessages(get_banff_version(and))
> #
> #   if(between == and){
> #     return('Versions are identical')
> #   }
> #   input <- read_excel_allsheets(input_file)
> #   banff_data_dict_1 <- suppressMessages(get_banff_dictionary(version = between,which = "output"))
> #   banff_data_dict_2 <- suppressMessages(get_banff_dictionary(version = and,which = "output"))
> #
> #   diag_1 <- try(suppressMessages(add_diagnoses(input,version = between)),silent = TRUE)
> #   if(class(diag_1)[1] == 'try-error') add_diagnoses(input,version = between)
> #
> #   diag_2 <- try(suppressMessages(add_diagnoses(input,version = and)),silent = TRUE)
> #   if(class(diag_2)[1] == 'try-error') add_diagnoses(input,version = and)
> #
> #   diag_1 <-
> #     diag_1 %>%
> #     select(patient_id,starts_with('diag')) %>%
> #     data_dict_match_dataset(banff_data_dict_1,output = 'dataset')
> #
> #   diag_2 <-
> #     diag_2 %>%
> #     select(patient_id,starts_with('diag')) %>%
> #     data_dict_match_dataset(banff_data_dict_2,output = 'dataset')
> #
> #   message(paste0("\nVersion "),between,"\n")
> #   diag_1 <- dataset_cat_as_labels(diag_1,banff_data_dict_1) %>% pivot_longer(cols=starts_with("diag"))
> #
> #   message(paste0("\nVersion "),and,"\n")
> #   diag_2 <- dataset_cat_as_labels(diag_2,banff_data_dict_2) %>% pivot_longer(cols=starts_with("diag"))
> #
> #   diff <-
> #     bind_cols(diag_1,value_2 =diag_2$value) %>%
> #     # mutate(
> #     #   value = str_squish(str_remove(value, "^[^:]+:")),
> #     #   value_2 = str_squish(str_remove(value_2, "^[^:]+:"))) %>%
> #     filter(value != value_2) %>%
> #     rename_with(.cols = c("value","value_2"),~c(toString(between),toString(and)))
> #
> #   return(diff)
> # }
> # differential_diagnoses(input_file,between = 2017,and = 2022)
> 
> proc.time()
   user  system elapsed 
   0.12    0.03    0.14