iso_reread_files: Re-read iso_files

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files from their original data files (e.g. after modifying raw data files in vendor software, or after upgrading to a newer version of the isoreader package that provides new functionality).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

isoreader documentation built on Nov. 19, 2021, 1:07 a.m.