eyeris_db_collect: Extract and aggregate eyeris data across subjects from...

In eyeris: Flexible, Extensible, & Reproducible Pupillometry Preprocessing

Extract and aggregate eyeris data across subjects from database

Description

A comprehensive wrapper function that simplifies extracting eyeris data from the database. Provides easy one-liner access to aggregate data across multiple subjects for each data type, without requiring SQL knowledge.

Usage

eyeris_db_collect(
  bids_dir,
  db_path = "my-project",
  subjects = NULL,
  data_types = NULL,
  sessions = NULL,
  tasks = NULL,
  epoch_labels = NULL,
  eye_suffixes = NULL,
  verbose = TRUE
)

Arguments

bids_dir	Path to the BIDS directory containing the database
db_path	Database name (defaults to "my-project", becomes "my-project.eyerisdb")
subjects	Vector of subject IDs to include. If NULL (default), includes all subjects
data_types	Vector of data types to extract. If NULL (default), extracts all available types. Valid types: "blinks", "events", "timeseries", "epochs", "epoch_summary", "run_confounds", "confounds_events", "confounds_summary"
sessions	Vector of session IDs to include. If NULL (default), includes all sessions
tasks	Vector of task names to include. If NULL (default), includes all tasks
epoch_labels	Vector of epoch labels to include. If NULL (default), includes all epochs. Only applies to epoch-related data types
eye_suffixes	Vector of eye suffixes to include. If NULL (default), includes all eyes. Typically c("eye-L", "eye-R") for binocular data
verbose	Logical. Whether to print progress messages (default TRUE)

Value

A named list of data frames, one per data type

Examples

demo_data <- eyelink_asc_demo_dataset()

demo_data |>
eyeris::glassbox() |>
eyeris::epoch(
  events = "PROBE_{startstop}_{trial}",
  limits = c(-1, 1),
  label = "prePostProbe"
) |>
eyeris::bidsify(
  bids_dir = tempdir(),
  participant_id = "001",
  session_num = "01",
  task_name = "assocret",
  run_num = "03", # override default run-01 (block_1) to use run-03 instead
  db_enabled = TRUE # enable database storage
)

# extract all data for all subjects (returns list of data frames)
all_data <- eyeris_db_collect(tempdir())

# view available data types
names(all_data)

# access specific data type
blinks_data <- all_data$blinks
epochs_data <- all_data$epochs

# extract specific subjects and data types
subset_data <- eyeris_db_collect(
  bids_dir = tempdir(),
  subjects = c("001"),
  data_types = c("blinks", "epochs", "timeseries")
)

# extract epoch data for specific epoch label
epoch_data <- eyeris_db_collect(
  bids_dir = tempdir(),
  data_types = "epochs",
  epoch_labels = "prepostprobe"
)

eyeris documentation built on June 19, 2026, 9:08 a.m.