Quick Start Guide

2021-10-15

Introduction

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.

# load isoreader package
library(isoreader)

Data files

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

Dual Inlet Files

# 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 2.46 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_to_excel(di_files, filepath = "di_export")

Continuous Flow Files

# 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: processing config 'N2' (332628-345196)
#> Info: processing config 'CO2' (345196-369809)
#> Info: processing data for 'N2' (128025-158837)
#> Info: processing data for 'CO2' (158931-196381)
#> Info: reading file 'continuous_flow_example.iarc' with '.iarc' reader...
#>       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'
#> DEBUG: species configurations:
#> Beam3, Beam1, 30   , 28   
#> Beam2, Beam1, 66 ...
#>       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 3.67 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_to_excel(cf_files, filepath = "cf_export")

Scan Files

# 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 0.56 secs
# 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_to_excel(scan_files, filepath = "scan_export")