iso_reread_files: Re-read iso_files

In KopfLab/isoreader: Read Stable Isotope Data Files

Re-read iso_files

Description

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files from their original data files (e.g. after modifying raw data files in vendor software, or after upgrading to a newer version of the isoreader package that provides new functionality).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_files.

Usage

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(...)

Arguments

iso_files	collection of iso_files
...	additional read parameters that should be used for re-reading the iso_files, see iso_read_dual_inlet, iso_read_continuous_flow and iso_read_scan for details (except read_cache which is always set to FALSE to force re-reads).
stop_if_missing	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)
quiet	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
reread_files_with_errors	whether to re-read files that had read in with errors the last time (default TRUE)
reread_files_with_warnings	whether to re-read files that had read in with warnings the last time (default TRUE)

Details

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_problem_files().

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.

Examples

# example for re-reading a saved isofile collection
iso_turn_reader_caching_off()
saved_files_path <- "saved_isofile.scan.rds"

# create saved collection
iso_get_reader_examples_folder() |> 
 iso_read_scan() |>
 iso_save(saved_files_path)
 
# 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)

# cleanup
unlink(saved_files_path)

KopfLab/isoreader documentation built on Aug. 6, 2023, 9:22 p.m.