write_csv_and_db

This helper function writes data to CSV files and/or database based on the
configuration. Useful for large-scale cloud compute where CSV files may be
unnecessary when using database storage.

internal

Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the Stanford Wu Tsai Human Performance Alliance, Stanford Ric Weiland Graduate Fellowship, Stanford Center for Mind, Brain, Computation and Technology, NIH National Institute on Aging Grants (R01-AG065255, R01-AG079345), NSF GRFP (DGE-2146755), McKnight Brain Research Foundation Clinical Translational Research Scholarship in Cognitive Aging and Age-Related Memory Loss, American Brain Foundation, and the American Academy of Neurology.

Shawn Schwartz

eyeris

Flexible, Extensible, & Reproducible Pupillometry Preprocessing

write_csv_and_db function

<dl><dt>data</dt>
<dd>Data frame to write</dd>
<dt>csv_path</dt>
<dd>Full path where CSV file should be written (ignored if csv_enabled = FALSE)</dd>
<dt>csv_enabled</dt>
<dd>Whether to write CSV files (defaults to TRUE for backward compatibility)</dd>
<dt>db_con</dt>
<dd>Database connection (NULL if not enabled)</dd>
<dt>data_type</dt>
<dd>Type of data ("timeseries", "epochs", "epoch_timeseries", "epoch_summary", "events", "blinks", "confounds")</dd>
<dt>sub</dt>
<dd>Subject ID</dd>
<dt>ses</dt>
<dd>Session ID</dd>
<dt>task</dt>
<dd>Task name</dd>
<dt>run</dt>
<dd>Run number (optional)</dd>
<dt>eye_suffix</dt>
<dd>Eye suffix for binocular data (optional)</dd>
<dt>epoch_label</dt>
<dd>Epoch label for epoched data (optional, used in table naming)</dd>
<dt>verbose</dt>
<dd>Whether to print verbose output</dd></dl>

Arguments

Write data to CSV and/or database (helper function) — write_csv_and_db

<dl>

<dt>data</dt>
<dd>Data frame to write</dd>


<dt>csv_path</dt>
<dd>Full path where CSV file should be written (ignored if csv_enabled = FALSE)</dd>


<dt>csv_enabled</dt>
<dd>Whether to write CSV files (defaults to TRUE for backward compatibility)</dd>


<dt>db_con</dt>
<dd>Database connection (NULL if not enabled)</dd>


<dt>data_type</dt>
<dd>Type of data ("timeseries", "epochs", "epoch_timeseries", "epoch_summary", "events", "blinks", "confounds")</dd>


<dt>sub</dt>
<dd>Subject ID</dd>


<dt>ses</dt>
<dd>Session ID</dd>


<dt>task</dt>
<dd>Task name</dd>


<dt>run</dt>
<dd>Run number (optional)</dd>


<dt>eye_suffix</dt>
<dd>Eye suffix for binocular data (optional)</dd>


<dt>epoch_label</dt>
<dd>Epoch label for epoched data (optional, used in table naming)</dd>


<dt>verbose</dt>
<dd>Whether to print verbose output</dd>

</dl>

write_csv_and_db: Write data to CSV and/or database (helper function)

Description

Usage

Value

Arguments