Man pages for eyeris
Flexible, Extensible, & Reproducible Pupillometry Preprocessing

add_unique_event_identifiersAdd unique event identifiers to handle duplicate event...
add_unique_identifiers_to_dfAdd unique identifiers to a single events data frame
alertDisplay formatted alert messages
bidsifySave out pupil timeseries data in a BIDS-like structure
binBin pupil time series by averaging within time bins
bin_pupilBin pupil data into specified time bins
calc_euclidean_distCalculate Euclidean distance between points
calculate_epoched_confoundsCalculate confounds for epoched data
check_and_create_dirCheck and create directory if it doesn't exist
check_baseline_epoch_countsCheck baseline and epoch counts match
check_baseline_inputsCheck baseline input arguments
check_baseline_meanCheck if baseline mean is zero
check_columnCheck if column exists in dataframe
check_dataCheck if object is of class eyeris
check_epoch_inputCheck epoch input for plotting
check_epoch_manual_input_dataCheck epoch manual input data structure
check_epoch_manual_input_dfsCheck epoch manual input dataframe format
check_epoch_msg_valuesCheck epoch message values against available events
check_inputCheck if input argument is provided
check_limitsCheck limits in wildcard mode
check_pupil_colsCheck if pupil_raw column exists
check_start_end_timestampsCheck start and end timestamps are balanced
check_time_monotonicCheck time series monotonicity
clean_stringClean string by removing non-alphanumeric characters
compute_baselineCompute baseline correction for epoch data
convert_nested_dtConvert nested data.table objects to tibbles
count_epochsCount epochs and validate data is epoched
counter_barCreate a counter progress bar
deblinkNA-pad blink events / missing data
deblink_pupilInternal function to remove blink artifacts from pupil data
detransientRemove pupil samples that are physiologically unlikely
detransient_pupilInternal function to remove transient artifacts from pupil...
detrendDetrend the pupil time series
detrend_pupilInternal function to detrend pupil data
downsampleDownsample pupil time series with anti-aliasing filtering
downsample_pupilInternal function to downsample pupil data
draw_na_linesDraw vertical lines at NA positions
draw_random_epochsDraw random epochs for plotting
epochEpoch (and baseline) pupil data based on custom event message...
epoch_and_baseline_blockBlock-by-block epoch and baseline handler
epoch_manuallyManually epoch using provided start/end dataframes of...
epoch_only_start_msgEpoch based on a single event message (without explicit...
epoch_pupilMain epoching and baselining logic
epoch_start_end_msgEpoch using a start and an end message (explicit timestamps)
epoch_start_msg_and_limitsEpoch using a start message with fixed limits around it
error_handlerHandle errors with custom error classes
evaluate_pipeline_step_paramsEvaluate pipeline step parameters
export_confounds_to_csvExport confounds data to CSV files
extract_baseline_epochsExtract baseline epochs from timeseries data
eyelink_asc_demo_datasetAccess example EyeLink .asc demo dataset file provided by the...
eyeloggerRun 'eyeris' commands with automatic logging of R console's...
eyeris_color_paletteDefault color palette for eyeris plotting functions
eyeris-packageeyeris: Flexible, Extensible, & Reproducible Pupillometry...
filter_epochsFilter epoch names from eyeris object
find_baseline_structureFind baseline structure name for a given epoch
format_call_stackFormat call stack information for display
get_block_numbersExtract block numbers from eyeris object or character vector
get_confounds_for_stepCalculate confounds for a single pupil data step
get_timestampsObtain timestamps from events data
glassboxThe opinionated "glass box" 'eyeris' pipeline
index_metadataIndex metadata from dataframe
interpolateInterpolate missing pupil samples
interpolate_pupilInterpolate missing pupil data using linear interpolation
load_ascLoad and parse SR Research EyeLink '.asc' files
lpfiltLowpass filtering of time series data
lpfilt_pupilInternal function to lowpass filter pupil data
make_baseline_labelCreate baseline label for epoch data
make_epoch_labelGenerate epoch label from events and data
make_galleryCreate interactive epoch gallery report
make_md_tableCreate markdown table from dataframe
make_md_table_multilineCreate multiline markdown table from dataframe
make_prog_summary_plotCreate progressive preprocessing summary plot
make_reportCreate eyeris report
merge_events_with_timeseriesProcess event messages and merge with timeseries
normalize_gaze_coordsNormalize gaze coordinates to screen-relative units
parse_call_stackParse call stack information
parse_eyelink_infoParse EyeLink version and model information
pipeline_handlerBuild a generic operation (extension) for the 'eyeris'...
plot_detrend_overlayInternal helper to plot detrending overlay
plot.eyerisPlot pre-processed pupil data from 'eyeris'
plot_gaze_heatmapCreate gaze heatmap of eye coordinates
plot_pupil_distributionPlot pupil distribution histogram
plot_with_seedPlot with seed handling for glassbox pipeline
print_lightbox_img_htmlPrint lightbox image HTML
print_plotsPrint plots in markdown format
process_epoch_and_baselinesEpoch and baseline processor
progress_barCreate a progress bar for tracking operations
prompt_userPrompt user for continuation
render_reportRender R Markdown report
robust_plotRobust plotting function with error handling
sanitize_event_tagSanitize event tag string into canonical epoch label
save_detrend_plotsSave detrend plots for each block
save_progressive_summary_plotsSave progressive summary plots for each block
slice_epochSlice epoch from raw timeseries data
slice_epochs_no_limitsSlice epochs with no explicit limits
slice_epochs_with_limitsSlice epochs with explicit limits
speedCalculate pupil speed using finite differences
summarize_confoundsExtract confounding variables calculated separately for each...
tag_blinksTag blinks in pupil data
tag_gaze_coordsTag gaze coordinates as on/off screen
tickTick a progress bar
zscoreZ-score pupil timeseries data
zscore_pupilInternal function to z-score pupil data
eyeris documentation built on July 3, 2025, 9:08 a.m.