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eyeris: Flexible, Extensible, & Reproducible Pupillometry Preprocessing

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Install

install.packages('eyeris')

Monthly Downloads

269

Version

3.0.1

License

MIT + file LICENSE

Issues

2

Pull Requests

1

Stars

5

Forks

5

Maintainer

Shawn Schwartz

Last Published

October 7th, 2025

Functions in eyeris (3.0.1)

check_time_monotonic

Check time series monotonicity
cleanup_source_figures_post_render

Clean up source figures after report generation
compute_baseline

Compute baseline correction for epoch data
check_epoch_input

Check epoch input for plotting
cleanup_temp_database

Cleanup temporary database
cleanup_run_dir_images

Clean up individual image files in run directories after HTML generation
check_start_end_timestamps

Check start and end timestamps are balanced
clean_string

Clean string by removing non-alphanumeric characters
deblink

NA-pad blink events / missing data
detransient

Remove pupil samples that are physiologically unlikely
convert_nested_dt

Convert nested data.table objects to tibbles
check_limits

Check limits in wildcard mode
check_duckdb

Check for DuckDB availability
detransient_pupil

Internal function to remove transient artifacts from pupil data
create_table_name

Create table name for eyeris data
connect_eyeris_database

Create or connect to eyeris project database
check_pupil_cols

Check if pupil_raw column exists
create_temp_eyeris_database

Create temporary database for parallel processing
count_epochs

Count epochs and validate data is epoched
detrend

Detrend the pupil time series
epoch_and_baseline_block

Block-by-block epoch and baseline handler
counter_bar

Create a counter progress bar
deblink_pupil

Internal function to remove blink artifacts from pupil data
downsample_pupil

Internal function to downsample pupil data
disconnect_eyeris_database

Disconnect from eyeris database
detrend_pupil

Internal function to detrend pupil data
epoch

Epoch (and baseline) pupil data based on custom event message structure
downsample

Downsample pupil time series with anti-aliasing filtering
draw_random_epochs

Draw random epochs for plotting
create_epoch_images_zip

Create zip file from epoch images
epoch_manually

Manually epoch using provided start/end data frames of timestamps
epoch_only_start_msg

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

Draw vertical lines at NA positions
eyelink_asc_binocular_demo_dataset

Access example EyeLink .asc binocular mock dataset file provided by the eyeris package.
epoch_pupil

Main epoching and baselining logic
export_confounds_to_csv

Export confounds data to CSV files and/or database
evaluate_pipeline_step_params

Evaluate pipeline step parameters
epoch_start_end_msg

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

Read eyeris data from database
eyeris_db_disconnect

Disconnect from eyeris database (user-facing)
eyeris_db_reconstruct_from_chunks

Reconstruct eyerisdb from chunked files
eyelink_asc_demo_dataset

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

Extract and aggregate eyeris data across subjects from database
extract_baseline_epochs

Extract baseline epochs from time series data
error_handler

Handle errors with custom error classes
extract_event_ids

Extract event identifiers from event messages
epoch_start_msg_and_limits

Epoch using a start message with fixed limits around it
eyeris_db_list_tables

List available tables in eyeris database
eyeris_color_palette

Default color palette for eyeris plotting functions
eyeris-package

eyeris: Flexible, Extensible, & Reproducible Pupillometry Preprocessing
eyelogger

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

Connect to eyeris project database (user-facing)
filter_epochs

Filter epoch names from eyeris object
eyeris_db_summary

Get summary statistics for eyeris database
eyeris_db_split_for_sharing

Split eyerisdb for data sharing and distribution
find_baseline_structure

Find baseline structure name for a given epoch
eyeris_db_to_chunked_files

Export eyeris database to chunked files
eyeris_db_to_parquet

Split eyeris database into N parquet files by data type
get_log_timestamp

Get formatted timestamp for logging
get_confounds_for_step

Calculate confounds for a single pupil data step
interpolate

Interpolate missing pupil samples
index_metadata

Index metadata from data frame
log_info

Log an informational message
get_block_numbers

Extract block numbers from eyeris object or character vector
interpolate_pupil

Interpolate missing pupil data using linear interpolation
load_asc

Load and parse SR Research EyeLink .asc files
format_call_stack

Format call stack information for display
get_timestamps

Obtain timestamps from events data
log_error

Log an error message and abort
glassbox

The opinionated "glass box" eyeris pipeline
log_success

Log a success message
make_bids_fname

Make a BIDS-compatible filename
glassbox_internal

Internal glassbox function for processing individual eyes
is_binocular_object

Check if object is a binocular eyeris object
lpfilt_pupil

Internal function to lowpass filter pupil data
make_gallery

Create interactive epoch gallery report
lpfilt

Lowpass filtering of time series data
make_epoch_label

Generate epoch label from events and data
make_baseline_label

Create baseline label for epoch data
log_warn

Log a warning message
log_message

Core logging function with timestamp and glue support
logging

Standardized logging functions for eyeris
pipeline_handler

Build a generic operation (extension) for the eyeris pipeline
plot.eyeris

Plot pre-processed pupil data from eyeris
plot_binocular_correlation

Plot binocular correlation between left and right eye data
make_md_table

Create markdown table from data frame
plot_gaze_heatmap

Create gaze heatmap of eye coordinates
print_lightbox_img_html

Print lightbox image HTML for zip-based gallery
process_chunked_query

Process large database query in chunks
parse_eyelink_info

Parse EyeLink version and model information
normalize_gaze_coords

Normalize gaze coordinates to screen-relative units
make_prog_summary_plot

Create progressive preprocessing summary plot
make_md_table_multiline

Create multiline markdown table from data frame
merge_temp_database

Merge temporary database into main database
read_eyeris_parquet

Read parquet files back into R
print_plots

Print plots in markdown format
plot_pupil_distribution

Plot pupil distribution histogram
print_lightbox_img_html_legacy

Print lightbox image HTML (legacy)
merge_events_with_timeseries

Process event messages and merge with time series
process_eyeris_data

Process eyeris data and create eyeris object
make_report

Create eyeris report
plot_with_seed

Plot with seed handling for glassbox pipeline
prompt_user

Prompt user for continuation
parse_call_stack

Parse call stack information
progress_bar

Create a progress bar for tracking operations
plot_detrend_overlay

Internal helper to plot detrending overlay
robust_plot

Robust plotting function with error handling
save_detrend_plots

Save detrend plots for each block
process_epoch_and_baselines

Epoch and baseline processor
run_bidsify

Internal function to run bidsify on a single eye
slice_epoch

Slice epoch from raw time series data
save_progressive_summary_plots

Save progressive summary plots for each block
should_plot_binoc_cors

Check if binocular correlations should be plotted
render_report

Render R Markdown report
sanitize_event_tag

Sanitize event tag string into canonical epoch label
speed

Calculate pupil speed using finite differences
slice_epochs_no_limits

Slice epochs with no explicit limits
tick

Tick a progress bar
slice_epochs_with_limits

Slice epochs with explicit limits
tag_gaze_coords

Tag gaze coordinates as on/off screen
summarize_confounds

Extract confounding variables calculated separately for each pupil data file
tag_blinks

Tag blinks in pupil data
zscore_pupil

Internal function to z-score pupil data
zscore

Z-score pupil time series data
write_eyeris_data_to_db

Write eyeris data to database
zip_and_cleanup_source_figures

Zip and cleanup source figure files
write_csv_and_db

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

Calculate Euclidean distance between points
bidsify

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

Bin pupil time series by averaging within time bins
check_and_create_dir

Check and create directory if it doesn't exist
check_epoch_manual_input_dfs

Check epoch manual input data frame format
add_unique_event_identifiers

Add unique event identifiers to handle duplicate event messages
check_baseline_epoch_counts

Check baseline and epoch counts match
check_data

Check if object is of class eyeris
check_arrow

Check for Arrow availability
check_epoch_manual_input_data

Check epoch manual input data structure
calculate_epoched_confounds

Calculate confounds for epoched data
add_unique_identifiers_to_df

Add unique identifiers to a single events data frame
bin_pupil

Bin pupil data into specified time bins
check_baseline_inputs

Check baseline input arguments
check_column

Check if column exists in data frame
check_epoch_msg_values

Check epoch message values against available events
check_baseline_mean

Check if baseline mean is zero
check_input

Check if input argument is provided