eyeris3.0.1 package

Add unique event identifiers to handle duplicate event messages

Add unique identifiers to a single events data frame

Save out pupil time series data in a BIDS-like structure

Bin pupil data into specified time bins

Bin pupil time series by averaging within time bins

Calculate Euclidean distance between points

Calculate confounds for epoched data

Check and create directory if it doesn't exist

Check for Arrow availability

Check baseline and epoch counts match

Check baseline input arguments

Check if baseline mean is zero

Check if column exists in data frame

Check if object is of class eyeris

Check for DuckDB availability

Check epoch input for plotting

Check epoch manual input data structure

Check epoch manual input data frame format

Check epoch message values against available events

Check if input argument is provided

Check limits in wildcard mode

Check if pupil_raw column exists

Check start and end timestamps are balanced

Check time series monotonicity

Clean string by removing non-alphanumeric characters

Clean up individual image files in run directories after HTML generati...

Clean up source figures after report generation

Cleanup temporary database

Compute baseline correction for epoch data

Create or connect to eyeris project database

Convert nested data.table objects to tibbles

Count epochs and validate data is epoched

Create a counter progress bar

Create zip file from epoch images

Create table name for eyeris data

Create temporary database for parallel processing

Internal function to remove blink artifacts from pupil data

NA-pad blink events / missing data

Internal function to remove transient artifacts from pupil data

Remove pupil samples that are physiologically unlikely

Internal function to detrend pupil data

Detrend the pupil time series

Disconnect from eyeris database

Internal function to downsample pupil data

Downsample pupil time series with anti-aliasing filtering

Draw vertical lines at NA positions

Draw random epochs for plotting

Block-by-block epoch and baseline handler

Manually epoch using provided start/end data frames of timestamps

Epoch based on a single event message (without explicit limits)

Main epoching and baselining logic

Epoch using a start and an end message (explicit timestamps)

Epoch using a start message with fixed limits around it

Epoch (and baseline) pupil data based on custom event message structur...

Handle errors with custom error classes

Evaluate pipeline step parameters

Export confounds data to CSV files and/or database

Extract baseline epochs from time series data

Extract event identifiers from event messages

Access example EyeLink .asc binocular mock dataset file provided by th...

Access example EyeLink .asc demo dataset file provided by the eyeris p...

Run eyeris commands with automatic logging of R console's stdout and...

Default color palette for eyeris plotting functions

Extract and aggregate eyeris data across subjects from database

Connect to eyeris project database (user-facing)

Disconnect from eyeris database (user-facing)

List available tables in eyeris database

Read eyeris data from database

Reconstruct eyerisdb from chunked files

Split eyerisdb for data sharing and distribution

Get summary statistics for eyeris database

Export eyeris database to chunked files

Split eyeris database into N parquet files by data type

eyeris: Flexible, Extensible, & Reproducible Pupillometry Preprocessin...

Filter epoch names from eyeris object

Find baseline structure name for a given epoch

Format call stack information for display

Extract block numbers from eyeris object or character vector

Calculate confounds for a single pupil data step

Get formatted timestamp for logging

Obtain timestamps from events data

Internal glassbox function for processing individual eyes

The opinionated "glass box" eyeris pipeline

Index metadata from data frame

Interpolate missing pupil data using linear interpolation

Interpolate missing pupil samples

Check if object is a binocular eyeris object

Load and parse SR Research EyeLink .asc files

Log an error message and abort

Log an informational message

Core logging function with timestamp and glue support

Log a success message

Log a warning message

Standardized logging functions for eyeris

Internal function to lowpass filter pupil data

Lowpass filtering of time series data

Create baseline label for epoch data

Make a BIDS-compatible filename

Generate epoch label from events and data

Create interactive epoch gallery report

Create multiline markdown table from data frame

Create markdown table from data frame

Create progressive preprocessing summary plot

Create eyeris report

Process event messages and merge with time series

Merge temporary database into main database

Normalize gaze coordinates to screen-relative units

Parse call stack information

Parse EyeLink version and model information

Build a generic operation (extension) for the eyeris pipeline

Plot binocular correlation between left and right eye data

Internal helper to plot detrending overlay

Create gaze heatmap of eye coordinates

Plot pupil distribution histogram

Plot with seed handling for glassbox pipeline

Plot pre-processed pupil data from eyeris

Print lightbox image HTML (legacy)

Print lightbox image HTML for zip-based gallery

Print plots in markdown format

Process large database query in chunks

Epoch and baseline processor

Process eyeris data and create eyeris object

Create a progress bar for tracking operations

Prompt user for continuation

Read parquet files back into R

Render R Markdown report

Robust plotting function with error handling

Internal function to run bidsify on a single eye

Sanitize event tag string into canonical epoch label

Save detrend plots for each block

Save progressive summary plots for each block

Check if binocular correlations should be plotted

Slice epoch from raw time series data

Slice epochs with no explicit limits

Slice epochs with explicit limits

Calculate pupil speed using finite differences

Extract confounding variables calculated separately for each pupil dat...

Tag blinks in pupil data

Tag gaze coordinates as on/off screen

Tick a progress bar

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

Write eyeris data to database

Zip and cleanup source figure files

Internal function to z-score pupil data

Z-score pupil time series data