Sometimes it is useful to reload isotope files from their original data files (e.g. after modifying raw data files in vendor software, or after upgrading to a newer version of the isoreader package that provides new functionality). The functions described below are intended to make this very easy. However, re-reading files from disc is only possible if file paths still point to the original raw data files. If they have moved, please use
iso_set_file_root first to change the root directory of your
iso_reread_files(iso_files, ...) iso_reread_all_files( iso_files, ..., stop_if_missing = FALSE, quiet = default(quiet) ) iso_reread_changed_files( iso_files, ..., stop_if_missing = FALSE, quiet = default(quiet) ) iso_reread_outdated_files( iso_files, ..., stop_if_missing = FALSE, quiet = default(quiet) ) iso_reread_problem_files( iso_files, ..., stop_if_missing = FALSE, reread_files_with_errors = TRUE, reread_files_with_warnings = FALSE, quiet = default(quiet) ) iso_reread_storage(...) iso_reread_archive(...)
collection of iso_files
additional read parameters that should be used for re-reading the iso_files, see
iso_read_scan for details (except
read_cache which is always set to
FALSE to force re-reads).
whether to stop re-reading if any of the original data files are missing (if FALSE, will warn about the missing files adding a warning to them, but also re-read those that do exist)
whether to display (quiet=FALSE) or silence (quiet = TRUE) information messages. Set parameter to overwrite global defaults for this function or set global defaults with calls to iso_turn_info_messages_on and iso_turn_info_messages_off
whether to re-read files that had read in with errors the last time (default TRUE)
whether to re-read files that had read in with warnings the last time (default TRUE)
To re-read files that have been modified on disc, please use
iso_reread_changed_files(). To re-read files because of an isoreader version upgrade, please use
iso_reread_outdated_files(). To try re-reading files that previously had warnings and/or errors, please use
iso_reread_all_files re-reads all files in the collection.
iso_reread_changed_files re-reads all files that have been modified (e.g. in the vendor software) since they were last read by isoreader.
iso_reread_outdated_files re-reads all files that were read with an outdated version of isoreader.
iso_reread_problem_files re-reads all files that have had errors the last time they were read by isoreader (set
reread_files_with_warnings = TRUE to also re-read those that have warnings).
iso_reread_storage is deprecated.
iso_reread_archive is deprecated.
# example for re-reading a saved isofile collection iso_turn_reader_caching_off() #> Info: caching turned off saved_files_path <- "saved_isofile.scan.rds" # create saved collection iso_get_reader_examples_folder() %>% iso_read_scan() %>% iso_save(saved_files_path) #> Info: preparing to read 4 data files... #> Info: reading file 'background_scan_example.scn' with '.scn' reader... #> Info: reading file 'full_scan_example.scn' with '.scn' reader... #> Info: reading file 'peak_shape_scan_example.scn' with '.scn' reader... #> Info: reading file 'time_scan_example.scn' with '.scn' reader... #> Info: finished reading 4 files in 2.94 secs #> Info: exporting data from 4 iso_files into R Data Storage 'saved_isofile.scan.rds' # load collection iso_read_scan(saved_files_path) %>% # reread outdated files (alternatively "_all_" or "_changed_") iso_reread_outdated_files() %>% # re-save collection to its original location iso_save(saved_files_path) #> Info: preparing to read 1 data files... #> Info: reading file 'saved_isofile.scan.rds' with '.scan.rds' reader... #> Info: loaded 4 data files from R Data Storage #> Info: finished reading 1 files in 0.16 secs #> Info: found 0 outdated data file(s), re-reading 0/4. #> Info: exporting data from 4 iso_files into R Data Storage 'saved_isofile.scan.rds' # cleanup unlink(saved_files_path)