convert_external_format {allMT} | R Documentation |
Get standard data structure
Description
Convert a maintenance therapy excel sheet created by user into a standard format for analysis
Usage
convert_external_format(
inputpath_to_excelfolder,
exportpath_to_csvfolder,
pat_data_file_path,
daily_mp_dose = 60,
weekly_mtx_dose = 20
)
Arguments
inputpath_to_excelfolder |
Path to folder containing input excel files (in quotes) |
exportpath_to_csvfolder |
Path to folder in which to save final output csv files (in quotes) |
pat_data_file_path |
Path to excel file with patient IDs and corresponding BSA (body surface area) values. Column names - "ID", "BSA". |
daily_mp_dose |
numeric value of DAILY 6-Mercaptopurine dose per |
weekly_mtx_dose |
numeric value of WEEKLY absolute Methotrexate dose per |
Value
Folder with converted csv files
Note
If MT excel files are missing in the input folder for any patient IDs provided in the pat_data_file ID column, the function will show a message of missing IDs but will continue to convert the available files.
See Also
Examples
# As per ICiCLe-ALL-14 protocol (Reference PMID - 35101099):
path_to_excel = paste0(system.file("extdata/external_data/", package = "allMT"), "/")
save_path = paste0(tempdir(),"/")
path_to_bsa = system.file("extdata/external_data/", "BSA.xlsx", package = "allMT")
convert_external_format(inputpath_to_excelfolder = path_to_excel,
exportpath_to_csvfolder = save_path,
pat_data_file_path = path_to_bsa,
daily_mp_dose = 60,
weekly_mtx_dose = 20)
# As per ICiCLe-ALL-14 protocol (Reference PMID - 35101099):
convert_external_format(inputpath_to_excelfolder = "../csv_trial/",
exportpath_to_csvfolder = save_path,
pat_data_file_path = "BSAFile.xlsx")
# As per BFM protocol (Reference PMID - 15902295):
convert_external_format(inputpath_to_excelfolder = "../csv_trial/",
exportpath_to_csvfolder = save_path,
pat_data_file_path = "BSAFile.xlsx",
daily_mp_dose = 50,
weekly_mtx_dose = 20)
# As per St Jude protocol (Reference PMID - 15902295):
convert_external_format(inputpath_to_excelfolder = "../csv_trial/",
exportpath_to_csvfolder = save_path,
pat_data_file_path = "BSAFile.xlsx",
daily_mp_dose = 75,
weekly_mtx_dose = 40)