Introduction

Isoreader supports several dual inlet IRMS data formats. This vignette shows some of the functionality for scan 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 scan files is as simple as passing one or multiple file or folder paths to the iso_read_scan() function. If folders are provided, any files that have a recognized scan file extensions within those folders will be processed (e.g. all .scn). 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 scan_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 columns are of interest (by default, all file information is retrieved).

Select/Rename

File information can also be modified across an entire collection of isofiles using the iso_select_file_info() and iso_rename_file_info() functions:

Filter

Any collection of isofiles can also be filtered based on the available file information using the function iso_filter_files. This function can operate on any column available in the file information and supports full dplyr syntax.

Mutate

The file information in any collection of isofiles can also be mutated using the function iso_mutate_file_info. This function can introduce new columns and operate on any existing columns available in the file information (even if it does not exist in all files) and supports full dplyr syntax.

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):

Raw Data

The raw data read from the scan 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.

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: