NEWS

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OpenSpecy 1.7.1

• Added a reusable workflow for compressing hyperspectral images with PCA and K-means (k = 100) and plotting pixel cluster groups with heatmap_spec().
• Fixed bundled Shiny app startup when another attached package caused R to resolve dashboard box() calls to graphics::box().
• Restored the empty spectrum canvas and made uploaded spectra render before reference matching completes. Replaced redundant native progress popups with one central status display showing the active phase, elapsed time, and a staged progress bar without fragile completion-time estimates. Spectral, heatmap, and diagnostic plots now use a cohesive bordered dark theme.
• Added ratio-based CO2 and high-tail quality checks that avoid flagging unstructured noise. flatten_range() and restrict_range() can now assess and correct those issues automatically, with guarded batch-wide tail cropping. The bundled app enables both corrections and identification by default, gates reference results on an uploaded spectrum, and prioritizes downloads according to the current upload and identification state. In the app, ordinary preprocessing now runs before range/CO2 assessment, and an automatic correction is retained only when it strictly increases the number of passing spectra; the bundled Test Map exercises both corrections.
• Fixed Test Data, Test Map, Processed Spectra, and Top Matches downloads by restoring the native Shiny download link and validating every generated payload. Added an always-available, timestamped User Metadata CSV containing the current analysis inputs for manual reproducibility, without adding a settings-import compatibility contract. Top Match options are collapsed by default.
• Refined the bundled app workspace with collapsed-by-default settings and download cards, tab-triggered settings expansion, selection-specific download labels, responsive gap-free summary layouts, and one dark navy/cyan theme for the app chrome, cards, controls, tables, progress widgets, and plots.
• Added named area-under-band ratio indices, explicit custom area-ratio composition, peak_ratio() for nearest-point or linearly interpolated point ratios, and 4S Fill Peaks baseline correction. The app's Quantification tab now defaults off and lets users name and save any number of area-band or point-ratio definitions from final-processed-axis sliders. It calculates saved ratios from the exact final processed spectra displayed in the app, uses integer wavenumber sliders, and includes exact definitions, values, and processed-spectrum provenance in Processed Spectra and Top Matches downloads.
• Reimplemented 4S Fill Peaks smoothing and suppression in base R, removing the compiled baseline runtime dependency so the same correction works in local R and the hosted WebAssembly app.
• Widened the contextual download action, changed uploaded spectrum traces to white, standardized enabled switches to green and white, validated all informational disclosures, and restored the historical donation choices in an on-demand right-side header dialog. Removed the inactive help and dark-mode header toggles, aligned the full-width Spectra and Summary cards, and kept disabled child settings inert until their owning analysis switch is enabled. Automatic tail mode now visibly disables its manual bounds and explains that assessment uses the full processed axis.
• Streamlined the app to one analysis workspace with Preprocessing, Identification, and Advanced tabs; moved independent thresholds and map controls to Advanced, removed Google Translate and the informational sidebar, and moved community, partner, and contract information to the pkgdown source.
• Embedded the hosted Shinylive app immediately below the pkgdown title with real Shiny readiness feedback and a viewport full-screen mode that persists through upload/download dialogs. GitHub retains a normal README, and brief reactive updates no longer flash the app's processing overlay. The standalone app is published at /app/ so it resolves to openanalysis.org/openspecy/app/ through the repository-relative Moore Institute hosting fork.
• Added source manifests, app configuration, and GitHub Actions for building a hosted Shinylive/WebAssembly app from inst/shiny/. The hosted app is pinned to a versioned wasm CRAN-like repository containing OpenSpecy and the app dependency closure, stages the small medoid/model libraries, and keeps full library support available in the local bundled app.
• Bundled the action-built, commit-pinned wasm library image into Shinylive so the app loads the package version in DESCRIPTION without waiting for the floating webR package repository. Deployment now smoke-tests the package version, upload, identification, download, and public GitHub Pages endpoint.
• Fixed hosted-app startup by including hard dependencies from R's recommended packages (including Matrix, survival, and their closure), skipping the unavailable Google Translate connectivity probe in WebAssembly mode, and exercising the Shinylive iframe/selectize controls in the browser smoke test.
• Consolidated GitHub Pages publication into one native deployment containing the pkgdown site and the self-contained Shinylive app. The complete wasm package repository is now retained as a pinned Actions build artifact and embedded in the app instead of accumulating public wasm/<commit> trees.
• Bundled the Shiny app in inst/shiny/ from wincowgerDEV/OpenSpecy-shiny commit 60d1bdefff90affcda3353d7c389ea8f3748ca56; run_app() now launches the installed app by default instead of downloading app files from GitHub.
• Added bundled-app path, asset, source-parse, YAML-removal, and app helper regression tests; optimized/pruned Shiny app static assets and fixed app sample-data loading for the current matrix-backed OpenSpecy spectra format.
• Fixed bundled Shiny app smoke-test issues: startup no longer opens a blocking donation modal, bundled UI no longer auto-loads remote image assets, and identification uses existing package/app cached reference libraries before attempting a download.
• Removed built-in YAML read/write support and the YAML example fixture; read_spec() and write_spec() now support JSON, RDS, and CSV formats.
• Removed runtime signal and cluster dependencies by using internal Savitzky-Golay filtering and PAM medoid selection in package workflows.
• Made internal PAM medoid return order deterministic in tied cases so reduce_lib(return = "ids") is stable across platforms.
• Aligned automate_particle_analysis() collapse exports with legacy analyze_features() particle details, summaries, raw maps, and processed particle objects; returned list item names now mirror export filenames and formats.
• Added automate_particle_analysis() image return/export support for particle heatmaps, thresholded particle heatmaps, and correlation heatmaps. Requested image outputs are returned as recorded base-graphics plots, and are written to matching image files when output_dir is supplied.
• Fixed automate_particle_analysis(particle_id_strategy = "all_cell_id") so cell-level match joins preserve x/y map coordinates, collapsed particle spectra are processed to the library wavenumber axis before final matching, H5 mosaic coregistration can drive complete edge-tolerant particle color extraction, and single-class character feature labels define one class instead of erroring.
• particle_image() now leaves particle labels off by default and uses the attached visual image's full map extent when overlaying collapsed particle results. Particle maps are now drawn as categorical rasters with transparent background cells rather than point markers.
• Added a signal/noise heatmap legend, enlarged the correlation heatmap legend, and made automate_particle_analysis(spectral_smooth = TRUE) smooth already-loaded OpenSpecy/Specs maps as well as file-backed maps.
• Fixed visual-image BMP reading without relying on the unavailable grDevices::readbitmap() helper.
• Fixed .xyz text-map reading so coordinate metadata and spectra are aligned.

OpenSpecy 1.7.0

• Improved run_app functionality to allow for version control.
• Added automate_particle_analysis() for package-native batch particle detection, matching, summaries, and optional file output based on OpenSpecy/Specs workflows.
• Added visual-image helpers (add_visual_image(), visual_image(), and detect_image_origin()) so spectral maps can carry aligned visual imagery for feature color extraction and base graphics overlays.
• Added particle_image() for dependency-light particle map plotting with the package material color defaults.
• Added crowd_lookup(), recovery_rate(), minimum_detectable_amount(), and batch_detection_limit() for generalized particle-size crowding, spike recovery, MDA, and single-blank BDL summaries.
• read_h5() now defaults to raw per-region/pixel spectra instead of collapsing by particle, preserves region and stage-position metadata, parses scalar H5 metadata where possible, and attaches mosaic imagery when present.
• Faster ENVI file reading.
• Add area under band calculation.
• Added library-builder helpers for creating lookup templates, auditing metadata joins, reducing libraries with PAM medoids, and training model libraries.
• Expanded build_lib() into the standard end-to-end library workflow with full-range resolution-6 merging, lookup-triggered metadata and material hierarchy joins, editable metadata-name cleanup, automatic NA-aware recipes, signal-to-noise, processing attributes, and optional assess_spec() metadata summaries.
• build_lib() now converts declared reflectance and transmittance sources to absorbance before merging. The intensity_unit object attribute takes precedence over per-spectrum intensity_units metadata, and conversion can be disabled with convert_intensity = FALSE.
• build_lib() now accepts file paths, one OpenSpecy, or a list of OpenSpecy objects. Each RDS path may contain either one object or a list, while other formats continue through read_any(). Named progress stages and elapsed time are reported by default and can be disabled with progress = FALSE. It also accepts optional restrict_range_args before library recipes. Large same-axis source lists are bulk-prepared to avoid repeated legacy object coercion.
• Automatic build_lib() metadata lookups now infer the single shared column with overlapping values and unique lookup keys, skip lookups with no usable shared key, remain strict when multiple usable keys are ambiguous, and coalesce curated lookup values back into existing metadata columns.
• Added optional metadata value normalization with build_lib(clean_metadata_values = TRUE) and lib_clean_metadata(clean_values = TRUE), used by the reference workflow to trim/lowercase metadata values before joins.
• Fixed NA-aware process_spec() dispatch so downstream arguments such as baseline or intensity type reach the intended processing function. NA-aware processing now groups leading/trailing missing-value ranges and bulk-processes complete spectra where possible.
• Optimized sig_noise() for matrix-native signal/noise summaries, including the default run signal-to-noise calculation used by build_lib().
• build_lib() now generates reference-library sample_name hashes at the source stage using the legacy cleanup recipe and removes exclude_ids against both sample_name and sample_name_old, preserving compatibility with the curated bad-ID hash list.
• filter_spec() now treats NA values in logical filters as FALSE and checks logical filter length, preventing spectra/metadata misalignment when filtering metadata columns that contain missing values.
• Added a tracked, package-build-excluded workflows/OpenSpecy_reference_library.R workflow composed only from existing package operations, with canonical lookup and exclusion CSVs under workflows/data/. Repeated filtering, reduction, assessment, model building, and artifact writing are applied across named library lists.
• The reference workflow now prunes legacy raw-source technical metadata using a versioned metadata-drop CSV while retaining modern canonical metadata names.
• Exported metadata-name cleaning helpers with automatic underscore and terminal-s matching, extensible exact aliases, and ambiguity-checked regular expression rules.
• as_Specs() now supports an end-to-end compressed Specs workflow. By default it fits PCA and then Hilbert-encodes the scores into exact high/low 64-bit code rows; K-means can be placed before, between, or after those steps. Hilbert Specs objects can be decoded, decompressed back to approximate OpenSpecy spectra, subset-decompressed by numeric index for plotting, and matched with fast Hilbert-code distance.

OpenSpecy 1.5.0

Major

• Update to vignettes for new functionality.
• Improved plots
• Improved tests for Open Specy format.
• Improved reading of csv files.
• Improved reading of spa files.
• Extended options for library version downloads.
• Simpler function calling
• Extended baseline fitting options.

OpenSpecy 1.3.0

Major

• added 2 new libraries a nobaseline and derivative version of medioid and model
• Created new function for spatial smooth without reading envi files
• Allow adj_intens to work on vectors or Open Specy objects

Minor

• fixed bug with mac reading libraries

OpenSpecy 1.2.0 (2024-09-14)

Potentially Breaking

• Removed share data options in all functions. They just weren't useful to users at all and were more of an administrative thing. Keeping them forced us to be incompatible with webR.

Major

• added support for siMPle files.
• added support for xyz files.
• added support for img files.
• improved interactive plot popups.
• changed how libraries are downloaded to avoid osfr pacakage.
• increased support for options when collapsing maps.
• avoid forcing min-max relative plots in interactive mode.
• create static map option.

OpenSpecy 1.1.0 (2024-06-13)

Minor Improvements

• updated links

OpenSpecy 1.0.9

Minor Improvements

• more closing and flexibility options

OpenSpecy 1.0.8 (2024-03-14)

Minor Improvements

• updated manage_na, spec_res, read_any for easier flow with the app

OpenSpecy 1.0.7 (2024-03-11)

Minor Improvements

• Modified manage_na.R
• Added to NAMESPACE

OpenSpecy 1.0.6 (2023-11-25)

Minor Improvements

• Add attributes to OpenSpecy objects
• More flexible sig_noise()
• Simpler matching

OpenSpecy 1.0.5 (2023-10-31)

Minor Improvements

• Support .tsv files

Bug Fixes

• Flip xy coordinates in ENVI files

OpenSpecy 1.0.4 (2023-10-02)

Minor Improvements

• More contributors
• showlegend argument for interactive plots

Bug Fixes

• Fixes a fatal error in match_spec() probably causing incorrect identifications

OpenSpecy 1.0.3 (2023-09-13)

Minor Improvements

• Simplify check_OpenSpecy()
• Improve unit tests
• Improve interactive plots

OpenSpecy 1.0.2 (2023-09-05)

Bug Fixes

• Set data.table threads to 2 for (CRAN) checks

OpenSpecy 1.0.1

Bug Fixes

• Fixed spelling mistakes
• Reduced example and test run times for CRAN

OpenSpecy 1.0.0

New Features

• Complete package, app, and SOP overhaul!
• The Shiny app has been outsourced to an own GitHub repository: https://github.com/wincowgerDEV/OpenSpecy-shiny
• Spectra are now stored in dedicated OpenSpecy objects, which can be managed with a set of new functions including c_spec() for concatenating spectra or converting them back to tables
• Various functions have been renamed and improved, for instance, to facilitate reading (and writing) spectral files
• New functions include def_features() to identify microplastics in spectral maps and ai_classify() to use AI for matching/identifying spectra

Minor Improvements

• Added pkgdown documentation
• Added code coverage tests

OpenSpecy 0.9.5 (2022-07-06)

Bug Fixes

• Fixed outdated links and redirects

OpenSpecy 0.9.4

Minor Improvements

• UI improvements
• Gitter support

Bug Fixes

• Fixed invalid regex failing CRAN checks

OpenSpecy 0.9.3 (2021-10-13)

Minor Improvements

• Better error handling for .csv formats
• Add funders and goals
• Updated package citation
• CI testing for Mac

Bug Fixes

• Fixed testthat routines occasionally failing CRAN checks

OpenSpecy 0.9.2 (2021-05-20)

New Features

• Manual baseline corrections
• Citable technical note

Minor Improvements

• More generic .spa file reading
• Added funding

Bug Fixes

• UI improvements

OpenSpecy 0.9.1 (2021-04-11)

Bug Fixes

• Checks fail gracefully if api.osf.io is not reachable
• Adjust UI selectors to comply with inverse axis and not exceed ranges

OpenSpecy 0.9.0 (2021-04-09)

New Features

• UI overhaul
• Give more control to the user when starting via run_app()

Minor Improvements

• Reverse spectral axes to comply with most wavenumber scales
• Let users select metadata license
• Improved data sharing and logging capabilities
• Google Analytics removed

Bug Fixes

• Use tempdir for unit tests and examples

OpenSpecy 0.8.2 (2021-03-31)

Minor Improvements

• Compliance with CRAN style guide
• More references with DOIs
• Better error/warning messages during Shiny file input

Bug Fixes

• Fixed bug with Shiny reactive values

OpenSpecy 0.8.1

Bug Fixes

• Fix redirecting URLs

OpenSpecy 0.8.0

New Features

• Use external Open Specy libraries from OSF
• read_asp() for reading Agilent .asp files
• GUI overhaul
• Comprehensive package vignette and function documentation
• Unit testing for main functions

Minor Improvements

• Better error handling
• Stripped down dependencies

OpenSpecy 0.7.0

• Transferred code base from openspecy.org to this R package