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eyeris 2.0.0 “Lumpy Space Princess”

This is the largest update yet for eyeris, introducing a wealth of new features and addressing numerous small issues to significantly enhance functionality, robustness, and user experience (#215).

✨ New features

Enhanced reporting and visualization:

• Progressive preprocessing summary plots can now be generated and saved, visualizing the effects of each preprocessing step on pupil data and updating report structures to include these visualizations. The plot.eyeris() function now includes an add_progressive_summary parameter to optionally generate these plots by @shawntz in #212.

• Gaze heatmap generation is added for both runs and epoch groups within bidsify(), enabling visualizations of eye coordinate distributions, data quality, and participant attention when eye tracking and screen dimension data are available. A new plot_gaze_heatmap() function is introduced for this purpose by @gustxsr and @shawntz in #213.

• Interactive HTML reports now include a floating table of contents, enhancing navigation for longer reports by @shawntz in #182.

• The html_report parameter in bidsify() now defaults to TRUE by @shawntz in #212.

Core data processing functions:

• New bin() and downsample() functions are introduced for pupil time series data processing, including anti-aliasing filtering for downsampling and averaging for binning. Both functions are integrated into the eyeris::glassbox() pipeline by @shawntz and @mh105 in #204.

• Unique identifiers (text_unique) are now added to event messages in eyeris::load_asc() to prevent duplicate event merges, and the merge_events_with_timeseries() function is updated to utilize these for correct event matching and merging by @shawntz in #181.

• Confounds calculation and export are integrated into the processing pipelines, with eyeris::summarize_confounds() now included in eyeris::glassbox() and eyeris::epoch() pipelines by @shawntz in #182.

Pipeline robustness and reproducibility:

• Tracking of pipeline step provenance is improved, adding the original function call and parameters for each step via a new call_info argument. This metadata is passed to eyeris functions to enhance reproducibility and debugging by @shawntz in #209.

• The eyelogger() utility documentation has been updated with a new section in the README, detailing its purpose, usage examples, parameters, and generated log files for improved reproducibility and debugging by @shawntz in #214.

🔧 Minor improvements and fixes

Robustness and error handling:

• Enhanced plotting robustness includes tryCatch blocks to handle errors and display informative messages in plots, and time series plotting now iterates over all intermediate steps to ensure plots are generated even with missing or incomplete data by @shawntz in #181, #183.

• Handling of missing valid samples in random epoch plotting has been improved in plot.eyeris(), adding warning messages and placeholder plots when no valid samples are found by @shawntz in #181, #183.

• Stricter validation checks are added for the prev_op argument in the eyeris::zscore_pupil() internal function to catch missing, non-existent, or corrupted column names early, improving error handling by @shawntz in #207.

• Validation for pupil data in the eyeris::lpfilt_pupil() internal function ensures data is numeric, non-empty, and contains only finite values before filtering, preventing errors related to invalid matrix extents by @shawntz in #210.

• Stricter checks for corrupted or empty latest pointers and output column names are added in eyeris::pipeline_handler(), improving error handling and transitioning operation calls to use do.call for flexible argument passing by @shawntz in #211.

• The eyeris::load_asc() function now correctly sets the latest pointer as a named list for multi-block structures and as a single value for single block data, enhancing multi-block support by @shawntz in #211.

• Fixes an edge case where mad_val is NA in the eyeris::detransient_pupil() internal function (occurring when all pupil data is NA), ensuring the original pupil data is returned unchanged and preventing comparison to zero when mad_val is NA by @shawntz in #193.

• Baseline handling in eyeris::epoch() is simplified by deprecating calc_baseline and apply_baseline in favor of a single baseline parameter, also resolving bugs related to baseline computation and event mismatches by @shawntz in #177.

Pipeline and data logic:

• The eyeris::glassbox() function has been refactored to process each block in the time series individually (except load_asc), improving modularity and ensuring correct error handling of multi-block data by @shawntz in #189.

• The calculation of mean_gaze_distance_from_center_px now correctly uses the screen center coordinates (cx, cy) instead of defaulting to the origin, ensuring the metric reflects distance from the actual screen center by @shawntz in #199.

• The eyeris::bidsify() function is refactored to handle cases where no epochs are present, preventing errors and unnecessary processing for users who want summary reports of the entire pupil time series without prior epoching by @shawntz in #201.

• The eyeris::bidsify() function now properly allows manual specification of the run_num for single-block data, while still auto-numbering multi-block files for improved naming consistency by @shawntz in #203.

• The recalculation of epoched confounding variables is now performed when new epochs are created by @shawntz in #182.

Documentation and internal clean-up:

• Extensive documentation cleanup has been performed, including fixing various spelling errors/typos in multiple function documentations by @shawntz in #179, #214.

• The pdf_report parameter is eyeris::bidsify() has been deprecated in favor of html_report = TRUE, with associated removal of PDF rendering logic from the render_report() internal function by @shawntz in #197.

• Updates to _pkgdown.yml, README, NAMESPACE, and R/zzz.R to support new features and functionality, including exposing the eyeris_color_palette() and other global variables by @shawntz in #214.

• The structure of the latest field in mock data for unit tests was fixed to be a named list to ensure tests do not fail due to incorrectly specified data structures by @shawntz in #208.

• Added MASS, viridis, and fields package dependencies to Imports to support new gaze heatmaps functionality by @shawntz in #213.

eyeris 1.2.1 “Tree Trunks”

✨ New features

• eyelogger(): a new utility function to automatically capture and record R console output, errors, and the evaluated eyeris command into timestamped log files (.out, .err, and .cmd) for improved reproducibility, record keeping, and debugging by @shawntz in #171

  eyelogger() usage example

  Logging your eyeris commands with eyelogger() is as simple as wrapping your command like this:

  eyelogger({
    glassbox(eyelink_asc_demo_dataset(), interactive_preview = FALSE)
  }, log_dir = file.path("~/Documents", "eyeris_logs"))

🐛 Bugs fixed

• Fixed edge case related to non-finite samples in bidsify epoch plotting function by @gustxsr in #166
• Fixed multi-block epoch bug by extracting data from blocks using their names rather than their indices by @hyang336 in #168
• Fixed plotting bug (#165) by @shawntz in #169

🔧 Other minor improvements and fixes

• ENH: make plot color scheme more accessible/easier to read by @shawntz in #169
• FF: missing x-axis labels on histograms in rendered reports by @shawntz in #169
• NF: add detrend fitted values diagnostic plot to rendered reports by @shawntz in #169

eyeris 1.2.0 “Tree Trunks”

✨ New features

• NF: Add vertical lines to plots to indicate where missing data (such as blinks and/or removed artifacts) are located in the time series
• ENH: Plotting now takes time ranges in seconds directly and does the conversion to row index using tracker Hz on the backend, making plotting in eyeris more intuitive. To demonstrate:

plot(eyeris_preproc,
  steps = c(1, 5),
  preview_window = c(0, max(eyeris_preproc$timeseries$block_1$time_secs))
)

🐛 Bug fixes

• BF: NA slot offset in diagnostic plotting (#161)
• BF: normalize physical machine time bins and convert to seconds / start at 0 seconds (#162)
• BF: unit displayed on the x-axis doesn’t match the unit listed on the x-axis text label in plots (#162)
• BF: minor issue where a manually specified block number in load_asc() wasn’t being translated to the column block in the resulting list of time series data frames
• BF: minor issue where setting block = NULL in load_asc() didn’t actually omit the block column values from the resulting data frames within the returned eyeris list object

🔧 Minor improvements and fixes

• RF: update package title to match that of the published bioRxiv preprint
• RF: Deprecated the num_previews parameter in plot().
  • Please use preview_n instead.
• DOC: manually update citation file to include all authors + bioRxiv preprint DOI (#152)
• DOC: incorrect URIs in eyeris documentation for load_asc() function (#160)
• DOC: standardize default values for deblink() standalone [previously 40ms] vs. in glassbox() [now all 50ms] (#163)
• DOC: updates to pkgdown documentation website:
  • Matching accent color theme with the eyeris hex logo
  • New nav bar items (buttons/links to access the bioRxiv preprint and socials)
  • Update funders and contributors list
  • Add funders disclaimer statement to the footer

eyeris 1.1.0 “Princess Bubblegum”

✨ New features

• NF: Simplify glassbox() caller with redesigned parameters that enhance continuity across all pipeline steps (#148)

📚 Documentation

• DOC: Improved function documentation across the package and added more usage notes for clarity.
• DOC: Updated styling of documentation website.

🔧 Minor improvements and fixes

• ENH: Make histograms disabled by default when plotting an eyeris object (#156).
• RF: Deprecated the confirm parameter in glassbox().
  • Please use interactive_preview instead.
• RF: Deprecated the num_previews parameter in glassbox().
  • Please use preview_n instead.
• BF: Random seed assignment was not behaving as expected within the glassbox() pipeline.
• RF: Modify paths to documentation assets to fix broken links at build.

eyeris 1.0.1 “Ice King”

This non-CRAN release patches a small handful of documentation-related chores that have no direct impact on the functionality of eyeris for the end user. The minor improvements and fixes contained within this release will soon be bundled with a more substantial feature upgrade when submitted to CRAN to reduce burden on the CRAN reviewers at this time. Stay tuned!

🔧 Minor improvements and fixes (#159)

• CHORE: fix duplicate LICENSE file issue in release/** branches (#145)
• CHORE: update funders list on DESCRIPTION (#149)
• CHORE: add DOI badge to README (#150)
• CHORE: fix citation years in DESCRIPTION (i.e., put them in parentheses, per request of CRAN reviewer) (#151)
• DOC: update README to include CRAN install code + option for @latest dev branch via download with devtools/GitHub (#153)
• DOC: fix version titles + urls on changelog webpage (#154)
• CHORE: change pkgdown docs website deployment rules so that public webpage only updates on pushes to official release branches, and not the dev branch (#155)
• DOC: add CONTRIBUTING.md guidelines file for GitHub (#157)
• DOC: fix /man/figures/... image ref issues which is leading to broken links on the R CRAN read-only GitHub mirror repo (#158)

eyeris 1.0.0 “Ice King”

🎉 First CRAN release! (#144)

This version marks the official launch of the eyeris package on CRAN.

✨ New features (#125)

• Added example vignettes to demonstrate core functionality:
  • Preprocessing pipelines with glassbox()
  • Event-based epoching with epoch()
  • BIDS-style export with bidsify()
  • Custom pipeline extensions using pipeline_handler()

📚 Documentation (#125)

• Improved function documentation across the package
• Added citation guidance and reproducibility tips

Thanks for checking out eyeris! 🧠👁️

Pre-CRAN dev GitHub releases:

eyeris 0.1.1.9000 “Jake the Dog”

🔧 Minor improvements and fixes

• FF (#115): add more aggressive handling of edge cases in eyeris::detransient() (#121)
  • Specifically, situations where pupil data appear to have already undergone some type of online filtering directly from the EyeLink Host PC machine.
  • There is now detailed instructions on what to do if this exception is raised.
  • Furthermore, a new mad_thresh override parameter has been added to eyeris::detransient() for advanced users to override the mad_thresh computed property. Note: this new mad_thresh parameter defaults to NULL (and should pretty much always stay as such).
• FF (#122): fixed issue with incompatible unicode character in plot titles (#123)

eyeris 0.1.0.9000 “Jake the Dog”

💥 Breaking changes

• NF (#10): add support for .asc files containing multiple recording segments within the same file (#120)
  • There is a new block argument added to the load_asc() function
  • The default setting is “auto”, which aims to automatically handle multiple recording segments within the same .asc file. We recommend using this default as this is likely the safer choice rather than assuming a single-block recording. Furthermore, add downstream functions are intentionally designed to support any N number of blocks; using the “auto” setting automatically enables this support for .asc files containing single recording blocks by labeling the single recording session as block_1
  • You can also manually specify a different block value (numeric) instead of “auto”, which can be helpful for multi-block experiments where each block/run was recorded to a separate .asc file. This is especially important to consider when running the downstream epoch() and bidsify() functions so that derived files and summary reports are properly labeled with the correction block/run number
  • Currently, there is also a NULL option; however, this is likely going to just be a part of beta testing and will probably be removed in a future version given the foregoing 2 options should cover most (if not all) use cases

✨ New features

• NF: robust HTML and PDF output summary sidecar reports within bidsify() (#120)
  • Here, reports are well-organized both by block/run and any specific event message epochs that have been processed using the epoch() function
  • For epoched data, we now provide a useful interactive utility within the epoch-specific HTML reports: you can now use your mouse and/or keyboard to swiftly navigate through an interactive gallery of pupil plot segments from every single trial from any given subject, right out-of-the-box! We hope this alleviates some of the complexities/roadblocks users might face when needing to perform manual inspections of their data for quality assurance and/or diagnostic purposes.

🔧 Minor improvements and fixes

• FF (#118): resolved a minor bug in the EyeLink EDF header model and version fields for data collected on newer EyeLink hardware/software (#120)
• ENH: event epoching is now both more robust and super fast (#120)
  • We have implemented more efficient data structures to swiftly handle large sets of pupil samples in rapid time
  • We have also added in better visual feedback within the console regarding epoching progress
  • Similarly, these added benefits coincide nicely with the new multi-block support (#10)
• General bug fixes and enhancements to codebase and front-end UX (#120)

eyeris 0.0.0.9000 “Finn the Human”

• Initial beta release

Commit message tags reference:

• BF: bug fix (in the release branch)
• FF: feature fix (bug fixes in the dev branch)
• RF: refactoring
• NF: new feature
• ENH: enhancement
• DOC: for documentation-related updates and changes
• TEST: for commits that add or change unit tests
• CHORE: like RF but usually less important changes

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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