Load continuous flow data

iso_read_continuous_flow(..., root = ".",
  read_raw_data = default(read_raw_data),
  read_file_info = default(read_file_info),
  read_method_info = default(read_method_info),
  read_vendor_data_table = default(read_vendor_data_table),
  discard_duplicates = TRUE, parallel = FALSE,
  parallel_plan = future::multiprocess, cache = default(cache),
  cache_files_with_errors = TRUE, read_cache = default(cache),
  quiet = default(quiet))

Arguments

...

one or multiple file/folder paths. All files must have a supported file extension. All folders are expanded and searched for files with supported file extensions (which are then included in the read).

root

root for relative paths. Can be relative to the current working directory (e.g. "data") or an absolute path on the file system (e.g. "/Users/..." or "C:/Data/.."). The default is the current working directory ("."). Can be supplied as a vector of same length as the provided paths if the paths have different roots.

read_raw_data

whether to read the raw mass/ion data from the file

read_file_info

whether to read auxiliary file information (file id, sequence information, etc.)

read_method_info

whether to read methods information (standards, processing info)

read_vendor_data_table

whether to read the vendor computed data table

discard_duplicates

whether to automatically discard files with duplicate file IDs (i.e. duplicate file names). If TRUE (the default), only the first files are kept and any files with the same file ID are discarded. If FALSE, all duplicate files are kept but their file IDs are appended with suffix #1, #2, etc.

parallel

whether to process in parallel based on the number of available CPU cores. This may yield performance increases for files that are slow to parse such as continuous flow isodat files but usually provides little benefit for efficient data formats such as reading from R Data Archives.

parallel_plan

which parallel processing strategy to use, see plan, typically future::multiprocess (the default, uses multicore if supported by the operating system, otherwise multisession), future::multisession or future::multicore.

cache

whether to cache iso_files. Note that previously exported R Data Archives (di.rda, cf.rda) are never cached since they are already essentially in cached form.

cache_files_with_errors

whether to cache files that had errors during reading

read_cache

whether to reload from cache if a cached version exists. Note that it will only read from cache if the file was previously read with the exact same isoreader version and read options and has not been modified since.

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_message_on and iso_turn_info_message_off

See also

Other isoread functions for different types of IRMS data: iso_read_dual_inlet