Reading IRMS data files

These functions provide the core functionality for the package. They parse the raw isotope ratio mass spectrometry data files.

iso_read_continuous_flow()

Load continuous flow data

iso_read_dual_inlet()

Load dual inlet data

iso_read_scan()

Load scan data

iso_reread_files() iso_reread_storage() iso_reread_archive()

Re-read iso_files

Data wrangeling

These functions provide tools to easily filter read files and update file information (in the works). The package also provides a few functions that expand on useful text processing provided by the readr package (summarized in extract_data).

iso_filter_files()

Filter iso_files

extract_data

Overview of text data extraction functions

extract_substring()

Extract a substring from text

extract_word()

Extract words from text

Aggregating the data

These functions aggregate the data collected from one or many IRMS data files.

iso_get_data_summary()

Get data summary

iso_get_data()

Aggregate all isofiles data

iso_get_file_info()

Aggregate file info

iso_get_raw_data()

Aggregate raw data

iso_get_bgrd_data()

Aggregate background data

iso_get_vendor_data_table()

Aggregate vendor computed table data

iso_get_resistors_info()

Aggregate resistors from methods info

iso_get_standards_info()

Aggregate standards from methods info

Exporting/saving data: Feather, Excel, and R Data Archives

These functions provide tools to save the data to specific file formats.

iso_save()

Save data to R Data Storage (.rds)

iso_export_to_excel()

Export data to Excel

iso_export_to_feather()

Export to feather

Package information and default parameters

These functions provide information about the package capabilities, easy access to example files, and ways to set default parameters across the package.

iso_get_supported_file_types()

Supported file types

iso_get_reader_example() iso_get_reader_examples()

Example files

iso_turn_reader_caching_on() iso_turn_reader_caching_off()

Turn caching on/off

iso_cleanup_reader_cache()

Cleanup old cached files

iso_turn_info_messages_on() iso_turn_info_messages_off()

Turn information messages on/off

iso_set_default_read_parameters()

Set default read options

iso_get_default_reader_parameters()

Get the current default parameters

iso_show_default_reader_parameters()

Show the current default parameters

Dealing with read problems

iso_problem_functions

Problem Functions Overview

iso_has_problems()

Check for parsing problems

iso_get_problems_summary()

Retrieve a summary of the problems

iso_get_problems()

Retrieve parsing problems

iso_omit_files_with_problems()

Remove problematic files

File system functions

Functions to find IRMS data files and root file paths.

iso_expand_paths()

Expand file paths

iso_root_paths()

Root paths

iso_find_absolute_path_roots()

Find roots for absolute paths

iso_shorten_relative_paths()

Shorten relative paths

Low-level IO, debugging, and development tools

See the advanced vignette for details.

iso_read_files()

Core function to read isotope data files

iso_register_dual_inlet_file_reader() iso_register_continuous_flow_file_reader()

Register file readers

iso_is_file() iso_is_file_list() iso_is_object() iso_is_dual_inlet() iso_is_continuous_flow() iso_as_file_list()

Isoreader data structure functions

iso_turn_debug_on() iso_turn_debug_off() set_read_file_event_expr() set_finish_file_event_expr()

Debugging functions

print(<binary_structure_map>)

Print binary structure map

print(<iso_file_list>) print(<iso_file>) print(<dual_inlet>) print(<continuous_flow>)

Isofile printing

Moved to isoprocessor or deprecated

iso_calculate_ratios()

moved to isoprocessor

iso_convert_signals()

moved to isoprocessor

iso_convert_time()

moved to isoprocessor

iso_plot_continuous_flow_data()

moved to isoprocessor

iso_plot_dual_inlet_data()

moved to isoprocessor

iso_plot_raw_data()

moved to isoprocessor

iso_export_to_rda()

Export data to R Data Archive (.rda) (deprecated)

isoread()

Read isotope data file