Isoreader supports various dual inlet, continuous flow, and scan file formats. This vignette shows how to get started reading these raw IRMS data files and exporting the information to Excel. For more details on isoreader functionality and each file type, please read the Full Examples vignettes. For more information on downstream processing with isoverse, check out the isoprocessor package.
For demonstration purposes, this vignette simply reads all supported dual inlet, continuous flow, and scan files that are bundled with the isoreader package. For a more detailed introduction to each file type, check out the specific vignettes for each:
# all available examples
iso_get_reader_examples() |> knitr::kable()| filename | type | software | description |
|---|---|---|---|
| continuous_flow_example.cf | continuous flow | Isodat | Continuous Flow file format (older) |
| continuous_flow_example.dxf | continuous flow | Isodat | Continuous Flow file format (newer) |
| continuous_flow_example.iarc | continuous flow | ionOS | Continuous Flow data archive |
| dual_inlet_example.caf | dual inlet | Isodat | Dual Inlet file format (older) |
| dual_inlet_example.did | dual inlet | Isodat | Dual Inlet file format (newer) |
| dual_inlet_nu_example.txt | dual inlet | Nu | Dual Inlet file format |
| background_scan_example.scn | scan | Isodat | Scan file format |
| full_scan_example.scn | scan | Isodat | Scan file format |
| peak_shape_scan_example.scn | scan | Isodat | Scan file format |
| time_scan_example.scn | scan | Isodat | Scan file format |
# read all available examples
di_files <- iso_read_dual_inlet(iso_get_reader_examples_folder())
#> Info: preparing to read 3 data files...
#> Info: reading file 'dual_inlet_example.caf' with '.caf' reader...
#> Info: reading file 'dual_inlet_example.did' with '.did' reader...
#> Info: reading file 'dual_inlet_nu_example.txt' with '.txt' reader...
#> Warning: found 6 channels but 0 masses were specified - the raw data will b...
#> Info: finished reading 3 files in 8.15 secs
#> Warning: encountered 1 problem.
#> # | FILE | PROBLEM | OCCURRED IN | DETAILS
#> 1 | dual_inlet_nu_example.txt | warning | iso_read_nu | found 6 channels but ...
#> Use iso_get_problems(...) for more details.
# save as r data storage (read back in with iso_read_dual_inlet)
iso_save(di_files, filepath = "di_save")
#> Info: exporting data from 3 iso_files into R Data Storage 'di_save.di.rds'
# export to excel
iso_export_files_to_excel(di_files, filepath = "di_export")
# read all available examples
cf_files <- iso_read_continuous_flow(iso_get_reader_examples_folder())
#> Info: preparing to read 3 data files...
#> Info: reading file 'continuous_flow_example.cf' with '.cf' reader...
#> Info: reading file 'continuous_flow_example.dxf' with '.dxf' reader...
#> Info: reading file 'continuous_flow_example.iarc' with '.iarc' reader...
#> unpacking isoprime archive file...
#> found 1 processing list(s) in .iarc: 'ProcessingList_1'
#> found 2 method(s) in .iarc: 'Method_320', 'Method_77'
#> found 4 sample(s) in .iarc
#> searching processing list 'ProcessingList_1' for gas configurations...
#> found configurations for 'CO', 'SO2', 'CO2', 'H2', 'N2'
#> processing sample '6632_WSL-2 wood' (IRMS data '133.hdf5', '135.hdf5')
#> processing sample '6605_USGS41' (IRMS data '40.hdf5', '43.hdf5')
#> processing sample '6617_IAEA600' (IRMS data '80.hdf5', '82.hdf5')
#> processing sample '6630_GlutamicAcid04' (IRMS data '124.hdf5', '126.h...
#> Info: finished reading 3 files in 5.65 secs
# save as r data storage (read back in with iso_read_continuous_flow)
iso_save(cf_files, filepath = "cf_save")
#> Info: exporting data from 6 iso_files into R Data Storage 'cf_save.cf.rds'
# export to excel
iso_export_files_to_excel(cf_files, filepath = "cf_export")
# read all available examples
scan_files <- iso_read_scan(iso_get_reader_examples_folder())
#> 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 1.03 secs
#> Warning: file creation date could not be accessed for all files because this
#> information is not available on some Linux systems, reporting last modified
#> time for file_datetime instead. To turn these warnings off, call
#> iso_turn_datetime_warnings_off() and reread these files with
#> iso_reread_all_files().
#> Warning: encountered 4 problems.
#> # | FILE | PROBLEM | OCCURRED IN ...
#> 1 | background_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 2 | full_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 3 | peak_shape_scan_example.scn | warning | extract_os_file_creation_datetime...
#> 4 | time_scan_example.scn | warning | extract_os_file_creation_datetime...
#> Use iso_get_problems(...) for more details.
# save as r data storage (read back in with iso_read_scan)
iso_save(scan_files, filepath = "scan_save")
#> Info: exporting data from 4 iso_files into R Data Storage 'scan_save.scan.rds'
# export to excel
iso_export_files_to_excel(scan_files, filepath = "scan_export")