Introduction

Isoreader supports several dual inlet IRMS data formats. This vignette shows some of the functionality for dual inlet data files. For additional information on operations more generally (caching, combining read files, data export, etc.), please consult the operations vignette. For details on downstream data processing and visualization, see the isoprocessor package.

Note: this vignette is still a work in progress.

Reading files

Reading dual inlet files is as simple as passing one or multiple file or folder paths to the iso_read_dual_inlet() function. If folders are provided, any files that have a recognized continuous flow file extensions within those folders will be processed (e.g. all .did and .caf). Here we read several files that are bundled with the package as examples (and whose paths can be retrieved using the iso_get_reader_example() function).

File summary

The iso_files variable now contains a set of isoreader objects, one for each file. Take a look at what information was retrieved from the files using the iso_get_data_summary() function.

Problems

In case there was any trouble with reading any of the files, the following functions provide an overview summary as well as details of all errors and warnings, respectively. The examples here contain no errors but if you run into any unexpected file read problems, please file a bug report in the isoreader issue tracker.

File Information

Detailed file information can be aggregated for all isofiles using the iso_get_file_info() function which supports the full select syntax of the dplyr package to specify which fields are of interest (by default, all file information is retrieved). The following provides a few examples for how this can be used (the names of the interesting info columns may vary between different file formats):

Resistors

Additionally, some IRMS data files contain resistor information that are useful for downstream calculations (see e.g. section on signal conversion later in this vignette):

Reference values

As well as isotopic reference values for the different gases:

Raw Data

The raw data read from the IRMS files can be retrieved similarly using the iso_get_raw_data() function. Most data aggregation functions also allow for inclusion of file information using the include_file_info parameter, which functions identically to the select parameter of the iso_get_file_info function discussed earlier.

Data Processing

The isoreader package is intended to make raw stable isotope data easily accessible. However, as with most analytical data, there is significant downstream processing required to turn these raw signal intensities into properly referenced isotopic measurement. This and similar functionality as well as data visualization is part of the isoprocessor package which takes isotopic data through the various corrections in a transparent, efficient and reproducible manner.

That said, most vendor software also performs some of these calculations and it can be useful to be able to compare new data reduction procecures against those implemented in the vendor software. For this purpose, isoreader retrieves vendor computed data tables whenver possible, as illustrated below.

Vendor Data Table

As with most data retrieval funtions, the iso_get_vendor_data_table() function also allows specific column selection (by default, all columns are selected) and easy addition of file information via the include_file_info parameter (by default, none is included).

For expert users: retrieving all data

For users familiar with the nested data frames from the tidyverse (particularly tidyr’s nest and unnest), there is an easy way to retrieve all data from the iso file objects in a single nested data frame. Use the include_file_info, include_raw_data, and include_vendor_data_table parameters to specify which columns to include. By default, everything is included: