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Type 'q()' to quit R. > # # # 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