R Under development (unstable) (2024-05-06 r86526 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. 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 = system.file("extdata", "banff_example.xlsx", package = "banffIT") > > banff_launcher( + input_file = input_file, + output_folder = 'tests', + language = 'label:en', + option_filter = adequacy == 1, + detail = TRUE) Welcome to the Banff diagnosis helper. Press [enter] to continue or [esc] to quit. [1/6] - Import data [2/6] - Evaluation of 'banff_example' [3/6] - Add diagnosis to each observation of'banff_example' [4/6] - Generate labels for each variable of 'banff_example' Processing of : patient_id Processing of : center Processing of : biopsy_id Processing of : sc_date_bx Processing of : date_tx Processing of : type_bx Processing of : adequacy Processing of : fixation_ff Processing of : fixation_paraffin Processing of : fixation_elec Processing of : fixation_rna Processing of : microscopy Processing of : c4d_if Processing of : c4d_ihc Processing of : dsa Processing of : hist_dsa Processing of : i_score Processing of : t_score Processing of : v_score Processing of : g_score Processing of : ptc_score Processing of : ti_score Processing of : cg_score Processing of : mm_score Processing of : cv_score Processing of : ci_score Processing of : ct_score Processing of : ah_score Processing of : glomeruli Processing of : arteries Processing of : bk Processing of : gs Processing of : i_ifta_score Processing of : atma Processing of : ctma Processing of : atn Processing of : agn Processing of : cgn Processing of : infec Processing of : cni Processing of : ain Processing of : ptld Processing of : sptcbmml Processing of : leuscint Processing of : monofibneoint Processing of : newaif Processing of : othi_ifta Processing of : genetx Processing of : hist_aamr Processing of : hist_camr Processing of : hist_tcmr Processing of : adequacy_calculated Processing of : c4d Processing of : nogn Processing of : ifta Processing of : aamr11.1 Processing of : aamr11.2 Processing of : aamr12 Processing of : aamr13 Processing of : aamr14 Processing of : aamr1 Processing of : aamr21 Processing of : aamr22.1 Processing of : aamr22.2 Processing of : aamr22.3 Processing of : aamr2 Processing of : aamr Processing of : susp_aamr Processing of : c4dneg_aamr Processing of : susp_c4dneg_aamr Processing of : dsaneg_aamr Processing of : susp_activeaamr Processing of : hist_dsa1 Processing of : hist_dsa2 Processing of : hist_dsa_calculated Processing of : hist_tcmr1 Processing of : hist_tcmr2 Processing of : hist_tcmr3 Processing of : hist_tcmr_calculated Processing of : camr11 Processing of : camr12 Processing of : camr13 Processing of : camr1 Processing of : activeabmr Processing of : camr Processing of : susp_camr Processing of : c4dneg_camr Processing of : susp_c4dneg_camr Processing of : dsaneg_camr Processing of : chractabmr Processing of : susp_chractabmr Processing of : hist_camr1 Processing of : hist_camr2 Processing of : hist_camr_calculated Processing of : hist_aamr1 Processing of : hist_aamr2 Processing of : hist_aamr_calculated Processing of : chrabmr3 Processing of : chrabmr Processing of : c4d_only Processing of : final_abmr Processing of : final_susp_abmr Processing of : final_abmr_verified Processing of : diag_code_1 Processing of : diag_code_2 Processing of : diag_code_2_final_abmr Processing of : diag_code_2_final_susp_abmr Processing of : diag_code_3 Processing of : diag_code_4_active Processing of : diag_code_4_chronic Processing of : diag_code_5 Processing of : diag_code_bk Processing of : diag_code_ptld Processing of : diag_code_cni Processing of : diag_code_atn Processing of : diag_code_cgn Processing of : diag_code_agn Processing of : diag_code_infec Processing of : diag_code_ain [5/6] - Assessment of the the annotated 'banff_example' - DATA DICTIONARY ASSESSMENT: data_dict -------------- Assess the standard adequacy of naming Assess the uniqueness of variable names Assess the presence of possible duplicated columns Assess the presence of empty rows in the data dictionary Assess the presence of empty columns in the data dictionary Assess the presence of categories not in the data dictionary Assess the completion of `label(:xx)` column in 'Variables' Assess the `valueType` column in 'Variables' Assess presence and completion of `label(:xx)` column in 'Categories' Assess the logical values of missing column in Categories Generate report The data dictionary contains no error/warning. - WARNING MESSAGES (if any): -------------------------------------------- - DATASET ASSESSMENT: banff_example -------------------------- Assess the standard adequacy of naming Assess the presence of variable names both in dataset and data dictionary Assess the presence of possible duplicated variable in the dataset Assess the presence of duplicated participants in the dataset Assess the presence of unique value columns in dataset Assess the presence of empty rows in the data dictionary Assess the presence all NA(s) of columns in the data dictionary Assess the presence of categories not in the data dictionary Generate report - WARNING MESSAGES (if any): ------------------------------------------------- - DATASET SUMMARIZE: banff_example -------------------------- Summarize the data type of each variable across the dataset Summarize information for all variables Summarize information for numerical variables Summarize information for text variables Summarize information for date variables Summarize information for datetime variables Summarize information for categorical variables Summarize global information (Overview) Generate report [6/6] - Export XLSX files in 'tests' The assessment and addition of diagnoses on your dataset is now finished. In the output folder, you will find an Excel file containing both labels and codes of your dataset and for each participant, additional variables corresponding to the diagnoses. An assessment and summary report has been generated in your output folder to help you assess and interpret your dataset. You can open it as an Excel file. For further information please refer to documentation. Export Banff diagnoses Excel files in 'tests/banff_example-2024-05-07-180040-diagnoses.xlsx' Export Banff report Excel files in 'tests/banff_example-2024-05-07-180040-report.xlsx' Export Banff dictionary Excel files in 'tests/banff_dictionary.xlsx' > > > > > proc.time() user system elapsed 69.65 1.09 70.73