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Changelog

Source: NEWS.md

eyeris 1.2.1

🚨 What’s changed

✨ 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

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

CRAN release: 2025-06-07

✨ 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

CRAN release: 2025-04-24

✨ 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 expcted within the glassbox() pipeline.
  • RF: Modify paths to documentation assets to fix broken links at build.

eyeris 1.0.1

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

CRAN release: 2025-03-31

🎉 First CRAN release! (#144)

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

✨ New features (#125)

📚 Documentation (#125)

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

Thanks for checking out eyeris! 🧠👁️

eyeris 0.1.0.9001

🔧 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

💥 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

  • 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