Extract and aggregate eyeris data across subjects from database

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

# \donttest{
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
)
#> ✔ [2026-02-01 01:11:18] [OKAY] Running eyeris::load_asc()
#> ℹ [2026-02-01 01:11:19] [INFO] Processing block: block_1
#> ✔ [2026-02-01 01:11:19] [OKAY] Running eyeris::deblink() for block_1
#> ✔ [2026-02-01 01:11:19] [OKAY] Running eyeris::detransient() for block_1
#> ✔ [2026-02-01 01:11:19] [OKAY] Running eyeris::interpolate() for block_1
#> ✔ [2026-02-01 01:11:19] [OKAY] Running eyeris::lpfilt() for block_1

#> ! [2026-02-01 01:11:19] [WARN] Skipping eyeris::downsample() for block_1
#> ! [2026-02-01 01:11:19] [WARN] Skipping eyeris::bin() for block_1
#> ! [2026-02-01 01:11:19] [WARN] Skipping eyeris::detrend() for block_1
#> ✔ [2026-02-01 01:11:19] [OKAY] Running eyeris::zscore() for block_1
#> ℹ [2026-02-01 01:11:19] [INFO] Block processing summary:
#> ℹ [2026-02-01 01:11:19] [INFO] block_1: OK (steps: 6, latest:
#> pupil_raw_deblink_detransient_interpolate_lpfilt_z)
#> ✔ [2026-02-01 01:11:19] [OKAY] Running eyeris::summarize_confounds()
#> ℹ [2026-02-01 01:11:19] [INFO] Epoching pupil data...
#> ℹ [2026-02-01 01:11:19] [INFO] Block 1: found 10 matching events for
#> PROBEstartstoptrial
#> ✔ [2026-02-01 01:11:19] [OKAY] Done!
#> ✔ [2026-02-01 01:11:19] [OKAY] Block 1: pupil data from 10 unique event
#> messages extracted
#> ✔ [2026-02-01 01:11:19] [OKAY] Pupil epoching completed in 0.12 seconds
#> ℹ [2026-02-01 01:11:19] [INFO] Recalculating epoched confounds for new
#> epochs...
#> ℹ [2026-02-01 01:11:19] [INFO] Starting BIDSify for sub-001 (monocular)
#> ℹ [2026-02-01 01:11:19] [INFO] Only 1 block detected...
#> ℹ [2026-02-01 01:11:19] [INFO] Using run_num = 03 for single block data
#> ℹ [2026-02-01 01:11:19] [INFO] Filtered epochs: epoch_prePostProbe
#> ℹ [2026-02-01 01:11:19] [INFO] Epoch names to save: epoch_prePostProbe
#> ℹ [2026-02-01 01:11:19] [INFO] Parallel processing detected for job unknown
#> (PID: 7280), using temporary database
#> ✔ [2026-02-01 01:11:19] [OKAY] Created temporary database:
#> /tmp/RtmpQNSozO/derivatives/my-project_temp_7280_20260201_011119_589.eyerisdb
#> ℹ [2026-02-01 01:11:19] [INFO] epoch_prePostProbe:
#> ℹ [2026-02-01 01:11:19] [INFO] block_1: data.frame with 20000 rows
#> ℹ [2026-02-01 01:11:19] [INFO] info: list with 1 elements
#> ! [2026-02-01 01:11:19] [WARN] '/tmp/RtmpQNSozO' already exists. Skipping
#> creation...
#> ! [2026-02-01 01:11:19] [WARN] '/tmp/RtmpQNSozO/derivatives' already exists.
#> Skipping creation...
#> ! [2026-02-01 01:11:19] [WARN] '/tmp/RtmpQNSozO/derivatives/sub-001' already
#> exists. Skipping creation...
#> ! [2026-02-01 01:11:19] [WARN] '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01'
#> already exists. Skipping creation...
#> ! [2026-02-01 01:11:19] [WARN] '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01/eye'
#> already exists. Skipping creation...
#> ℹ [2026-02-01 01:11:19] [INFO] Writing blinks data to
#> /tmp/RtmpQNSozO/derivatives/sub-001/ses-01/eye/sub-001_ses-01_task-assocret_run-03_desc-blinks.csv...
#> ✔ [2026-02-01 01:11:19] [OKAY] Wrote blinks data (1 rows) to CSV and database
#> ℹ [2026-02-01 01:11:19] [INFO] Writing events data to
#> /tmp/RtmpQNSozO/derivatives/sub-001/ses-01/eye/sub-001_ses-01_task-assocret_run-03_desc-events.csv...
#> ✔ [2026-02-01 01:11:19] [OKAY] Wrote events data (67 rows) to CSV and database
#> ℹ [2026-02-01 01:11:19] [INFO] Processing single-run epoch: epoch_prePostProbe
#> (label: prePostProbe)
#> ℹ [2026-02-01 01:11:19] [INFO] Block block_1 for epoch epoch_prePostProbe has
#> 20000 rows
#> ! [2026-02-01 01:11:19] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ℹ [2026-02-01 01:11:19] [INFO] Found epoch events in structure:
#> PROBE_{startstop}_{trial}
#> ! [2026-02-01 01:11:19] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ! [2026-02-01 01:11:19] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ! [2026-02-01 01:11:19] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote epochs data (20000 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote timeseries data (20767 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote run_confounds data (6 rows) to CSV and
#> database
#> ! [2026-02-01 01:11:20] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ℹ [2026-02-01 01:11:20] [INFO] Created epoch summary for epoch_prePostProbe
#> with 9 fields
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote epoch_summary data (1 rows) to CSV and
#> database
#> ! [2026-02-01 01:11:20] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ℹ [2026-02-01 01:11:20] [INFO] Found epoch events in structure:
#> PROBE_{startstop}_{trial}
#> ! [2026-02-01 01:11:20] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ! [2026-02-01 01:11:20] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_summary data (1 rows) to CSV and
#> database
#> ! [2026-02-01 01:11:20] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ℹ [2026-02-01 01:11:20] [INFO] Found epoch events in epoch structure:
#> PROBE_{startstop}_{trial}
#> ! [2026-02-01 01:11:20] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ! [2026-02-01 01:11:20] [WARN] No baseline structure found for epoch label:
#> prePostProbe
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ✔ [2026-02-01 01:11:20] [OKAY] Wrote confounds_events data (6 rows) to CSV and
#> database
#> ! [2026-02-01 01:11:20] [WARN]
#> '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures' already exists.
#> Skipping creation...
#> ! [2026-02-01 01:11:20] [WARN]
#> '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03' already
#> exists. Skipping creation...
#> ℹ [2026-02-01 01:11:20] [INFO] Plotting block 3 with sampling rate 1000 Hz from
#> possible blocks: 3
#> ℹ [2026-02-01 01:11:20] [INFO] Plotting block 3 with sampling rate 1000 Hz from
#> possible blocks: 3
#> ℹ [2026-02-01 01:11:21] [INFO] Plotting block 3 with sampling rate 1000 Hz from
#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
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#> possible blocks: 3
#> ℹ [2026-02-01 01:11:22] [INFO] Plotting block 3 with sampling rate 1000 Hz from
#> possible blocks: 3
#> ! [2026-02-01 01:11:22] [WARN]
#> '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03' already
#> exists. Skipping creation...
#> ✔ [2026-02-01 01:11:23] [OKAY] Created gaze heatmap for run-03
#> ! [2026-02-01 01:11:23] [WARN]
#> '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03' already
#> exists. Skipping creation...
#> ℹ [2026-02-01 01:11:23] [INFO]
#> '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03/epoch_prePostProbe'
#> does not exist. Creating...
#> ✔ [2026-02-01 01:11:23] [OKAY] BIDS directory successfully created at:
#> '/tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03/epoch_prePostProbe'
#> ✔ [2026-02-01 01:11:30] [OKAY] Created epoch images zip:
#> /tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03/epoch_prePostProbe/run-03.zip
#> (70 images)
#> ℹ [2026-02-01 01:11:30] [INFO] Using absolute zip file path:
#> /tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03/epoch_prePostProbe/run-03.zip
#> ✔ [2026-02-01 01:11:30] [OKAY] Embedded zip file as data URL (7969936 bytes)
#> 
#> 
#> processing file: sub-001_epoch-prePostProbe_run-03.Rmd
#> 1/5               
#> 2/5 [citation]    
#> 3/5               
#> 4/5 [session-info]
#> 5/5               
#> output file: sub-001_epoch-prePostProbe_run-03.knit.md
#> /opt/hostedtoolcache/pandoc/3.1.11/x64/pandoc +RTS -K512m -RTS sub-001_epoch-prePostProbe_run-03.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001_epoch-prePostProbe_run-03.html --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/runner/work/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /home/runner/work/_temp/Library/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpQNSozO/rmarkdown-str1c7074560226.html 
#> 
#> Output created: sub-001_epoch-prePostProbe_run-03.html
#> ! [2026-02-01 01:11:37] [WARN] Skipping block info for epoch 1 - no valid data
#> ℹ [2026-02-01 01:11:37] [INFO] Removing duplicate plain epoch directory:
#> /tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/figures/run-03/epoch_prePostProbe
#> ! [2026-02-01 01:11:37] [WARN] Metadata file already exists for 1:
#> /tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/logs/run-01_metadata.json
#> ! [2026-02-01 01:11:37] [WARN] Metadata file already exists for 3:
#> /tmp/RtmpQNSozO/derivatives/sub-001/ses-01/source/logs/run-03_metadata.json
#> ! [2026-02-01 01:11:37] [WARN] No detrend data found for run-03
#> 
#> 
#> processing file: sub-001.Rmd
#> 1/5               
#> 2/5 [citation]    
#> 3/5               
#> 4/5 [session-info]
#> 5/5               
#> output file: sub-001.knit.md
#> /opt/hostedtoolcache/pandoc/3.1.11/x64/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/runner/work/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /home/runner/work/_temp/Library/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpQNSozO/rmarkdown-str1c704840323c.html 
#> 
#> Output created: sub-001.html
#> ℹ [2026-02-01 01:11:39] [INFO] Merging temporary database from job unknown
#> (PID: 7280) into main database
#> ℹ [2026-02-01 01:11:39] [INFO] Merging 8 tables from temporary database to main
#> database
#> ℹ [2026-02-01 01:11:39] [INFO] Created new table 'blinks_001_01_assocret_run03'
#> with 1 rows
#> ℹ [2026-02-01 01:11:39] [INFO] Created new table
#> 'confounds_events_001_01_assocret_run03_prepostprobe' with 60 rows
#> ℹ [2026-02-01 01:11:40] [INFO] Created new table
#> 'confounds_summary_001_01_assocret_run03_prepostprobe' with 10 rows
#> ℹ [2026-02-01 01:11:40] [INFO] Created new table
#> 'epoch_summary_001_01_assocret_run03' with 1 rows
#> ℹ [2026-02-01 01:11:40] [INFO] Merged 20000 rows into existing table
#> 'epochs_001_01_assocret_run01_prepostprobe'
#> ℹ [2026-02-01 01:11:40] [INFO] Created new table 'events_001_01_assocret_run03'
#> with 67 rows
#> ℹ [2026-02-01 01:11:40] [INFO] Created new table
#> 'run_confounds_001_01_assocret_run03' with 6 rows
#> ℹ [2026-02-01 01:11:40] [INFO] Created new table
#> 'timeseries_001_01_assocret_run03' with 20767 rows
#> ✔ [2026-02-01 01:11:40] [OKAY] Successfully merged 8/8 tables
#> ✔ [2026-02-01 01:11:40] [OKAY] Successfully merged job unknown (PID: 7280) data
#> into main database
#> ℹ [2026-02-01 01:11:40] [INFO] Disconnected from temporary database
#> ✔ [2026-02-01 01:11:40] [OKAY] Cleaned up temporary database file
#> ℹ [2026-02-01 01:11:40] [INFO] Finished BIDSify for sub-001 (Duration: 21.09
#> seconds)

# extract all data for all subjects (returns list of data frames)
all_data <- eyeris_db_collect(tempdir())
#> ℹ [2026-02-01 01:11:40] [INFO] Connecting to eyeris database...
#> ✔ [2026-02-01 01:11:40] [OKAY] Connected to eyeris database:
#> /tmp/RtmpQNSozO/derivatives/my-project.eyerisdb
#> ℹ [2026-02-01 01:11:40] [INFO] Found 15 tables in database
#> ℹ [2026-02-01 01:11:40] [INFO] Extracting data types: blinks, events,
#> timeseries, epochs, epoch_summary, run_confounds, confounds_events,
#> confounds_summary
#> ℹ [2026-02-01 01:11:40] [INFO] Processing blinks...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "blinks_001_01_assocret_run01" UNION ALL SELECT * FROM
#> "blinks_001_01_assocret_run03") as combined_data WHERE 1=1
#> ℹ [2026-02-01 01:11:40] [INFO] Processing events...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "events_001_01_assocret_run01" UNION ALL SELECT * FROM
#> "events_001_01_assocret_run03") as combined_data WHERE 1=1
#> ℹ [2026-02-01 01:11:40] [INFO] Processing timeseries...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "timeseries_001_01_assocret_run01" UNION ALL SELECT * FROM
#> "timeseries_001_01_assocret_run03") as combined_data WHERE 1=1
#> ℹ [2026-02-01 01:11:40] [INFO] Processing epochs...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "epochs_001_01_assocret_run01_prepostprobe") as combined_data WHERE 1=1
#> ℹ [2026-02-01 01:11:40] [INFO] Processing epoch_summary...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "epoch_summary_001_01_assocret_run01" UNION ALL SELECT * FROM
#> "epoch_summary_001_01_assocret_run03") as combined_data WHERE 1=1
#> ℹ [2026-02-01 01:11:40] [INFO] Processing run_confounds...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "run_confounds_001_01_assocret_run01" UNION ALL SELECT * FROM
#> "run_confounds_001_01_assocret_run03") as combined_data WHERE 1=1
#> ℹ [2026-02-01 01:11:40] [INFO] Processing confounds_events...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "confounds_events_001_01_assocret_run01_prepostprobe" UNION ALL SELECT * FROM
#> "confounds_events_001_01_assocret_run03_prepostprobe") as combined_data WHERE
#> 1=1
#> ℹ [2026-02-01 01:11:40] [INFO] Processing confounds_summary...
#> ℹ [2026-02-01 01:11:40] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "confounds_summary_001_01_assocret_run01_prepostprobe" UNION ALL SELECT * FROM
#> "confounds_summary_001_01_assocret_run03_prepostprobe") as combined_data WHERE
#> 1=1
#> ✔ [2026-02-01 01:11:40] [OKAY] Successfully extracted 8 data types
#> ℹ [2026-02-01 01:11:40] [INFO] blinks: 3 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] events: 201 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] timeseries: 62301 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] epochs: 40000 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] epoch_summary: 2 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] run_confounds: 18 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] confounds_events: 120 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] confounds_summary: 20 rows across 1 subjects
#> ℹ [2026-02-01 01:11:40] [INFO] Disconnected from eyeris database

# view available data types
names(all_data)
#> [1] "blinks"            "events"            "timeseries"       
#> [4] "epochs"            "epoch_summary"     "run_confounds"    
#> [7] "confounds_events"  "confounds_summary"

# 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")
)
#> ℹ [2026-02-01 01:11:41] [INFO] Connecting to eyeris database...
#> ✔ [2026-02-01 01:11:41] [OKAY] Connected to eyeris database:
#> /tmp/RtmpQNSozO/derivatives/my-project.eyerisdb
#> ℹ [2026-02-01 01:11:41] [INFO] Found 15 tables in database
#> ℹ [2026-02-01 01:11:41] [INFO] Extracting data types: blinks, epochs,
#> timeseries
#> ℹ [2026-02-01 01:11:41] [INFO] Processing blinks...
#> ℹ [2026-02-01 01:11:41] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "blinks_001_01_assocret_run01" UNION ALL SELECT * FROM
#> "blinks_001_01_assocret_run03") as combined_data WHERE 1=1 AND subject_id =
#> '001'
#> ℹ [2026-02-01 01:11:41] [INFO] Processing epochs...
#> ℹ [2026-02-01 01:11:41] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "epochs_001_01_assocret_run01_prepostprobe") as combined_data WHERE 1=1 AND
#> subject_id = '001'
#> ℹ [2026-02-01 01:11:41] [INFO] Processing timeseries...
#> ℹ [2026-02-01 01:11:41] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "timeseries_001_01_assocret_run01" UNION ALL SELECT * FROM
#> "timeseries_001_01_assocret_run03") as combined_data WHERE 1=1 AND subject_id =
#> '001'
#> ✔ [2026-02-01 01:11:41] [OKAY] Successfully extracted 3 data types
#> ℹ [2026-02-01 01:11:41] [INFO] blinks: 3 rows across 1 subjects
#> ℹ [2026-02-01 01:11:41] [INFO] epochs: 40000 rows across 1 subjects
#> ℹ [2026-02-01 01:11:41] [INFO] timeseries: 62301 rows across 1 subjects
#> ℹ [2026-02-01 01:11:41] [INFO] Disconnected from eyeris database

# extract epoch data for specific epoch label
epoch_data <- eyeris_db_collect(
  bids_dir = tempdir(),
  data_types = "epochs",
  epoch_labels = "prepostprobe"
)
#> ℹ [2026-02-01 01:11:41] [INFO] Connecting to eyeris database...
#> ✔ [2026-02-01 01:11:41] [OKAY] Connected to eyeris database:
#> /tmp/RtmpQNSozO/derivatives/my-project.eyerisdb
#> ℹ [2026-02-01 01:11:41] [INFO] Found 15 tables in database
#> ℹ [2026-02-01 01:11:41] [INFO] Extracting data types: epochs
#> ℹ [2026-02-01 01:11:41] [INFO] Processing epochs...
#> ℹ [2026-02-01 01:11:41] [INFO] Executing query: SELECT * FROM (SELECT * FROM
#> "epochs_001_01_assocret_run01_prepostprobe") as combined_data WHERE 1=1
#> ✔ [2026-02-01 01:11:41] [OKAY] Successfully extracted 1 data types
#> ℹ [2026-02-01 01:11:41] [INFO] epochs: 40000 rows across 1 subjects
#> ℹ [2026-02-01 01:11:41] [INFO] Disconnected from eyeris database

# }