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Changelog

Source: NEWS.md

OpenSpecy 2.0.0

  • The public app, pkgdown site, canonical metadata, sitemap, and documentation links now use the institutional GitHub Pages route at https://www.openanalysis.org/OpenSpecyV2/.

  • match_spec() now accepts batch_size for bounded spectral-library Top-N searches. The bundled app exposes this limit for dense and file-backed identification so large in-memory maps do not allocate one full correlation matrix.

  • The bundled app now presents one direct-path Choose spectra… control: it opens the native file chooser on Windows and macOS when available and the no-copy filesystem browser elsewhere. It also presents the requested Advanced-control order, scopes pixel calibration to particle collapse, and shows Column ID plus available X/Y coordinates in Simple Metadata. Min-Max Normalize consistently rescales every plotted spectrum, and the Logistic weight legend controls its complete overlay.

  • Quantification ratios and measurements can be defined before upload or Run, persist when a file is selected, and can be cleared together with Remove All. Settings tabs turn green whenever they contain an active feature and use the same dark-panel, blue-outline hover treatment as quality-status controls.

  • The landing contact links now open through the browser’s external mail handler.

  • Reference-library downloads, bundled-app fallback, and Shinylive staging now use the latest unversioned AWS objects by default; explicit S3 versionId downloads remain available for historical comparisons, and hosted staging records the actual SHA-256 and byte size it resolved.

  • automate_particle_analysis() now opens H5/HDF5 paths through bounded FileSpecs chunks and supports streamed all_cell_id identification plus connected Mean collapse, avoiding multi-gigabyte eager map allocations.

  • Reference-build review tables are now coherent and compact instead of sparse unions of unrelated schemas. Review columns are limited to at most 10% missing values, detailed evidence remains attached separately, and model error-mode reporting directly compares with-error and without-error accuracy percentages without retraining.

  • Added split_h5() to natively copy whole-region metadata categories into separate H5 files without loading spectral values into R; an explicit RDS mode remains available for within-region categories.

  • Released logistic models now retain only their selected glmnet lambda and no captured training call, restoring compact model downloads without changing predictions. Routine reference builds no longer train or publish the experimental random-forest models; explicit random-forest training remains available through build_model_lib().

  • Reference builds now derive library_name from organization first and user name second, retain reviewed other plastic and other material sources, and record stage-by-stage source-library retention with explicit reasons for complete drops in assessments.rds.

  • prune_lib() now reassigns each resolved class below min_n as a whole to its most-correlated established class within the same technique and material type; it drops spectra only when no valid destination exists and audits both outcomes.

  • Corrected the bundled raman_hdpe metadata to the package CC BY 4.0 license and moved advanced compact/file-backed/app workflow guidance out of the beginner README and into vignettes.

  • Versioned reference-library releases now keep global cleanup, quality, pruning, comparison, and model-training diagnostics in a standalone assessments.rds. Runtime library, medoid, and model files are stripped to scientific/prediction state for smaller, faster-loading downloads; published accuracy reviews now contain overall and macro class accuracy percentages, evaluated class counts, and adjacent old/new identifying context.

  • Reference-library downloads now use AWS exclusively. get_lib() no longer accepts the obsolete aws switch, and AWS now serves raw.rds.

OpenSpecy 1.7.1

  • Signal metric previews no longer fall back to Signal Over Noise when the threshold mask is off. Recalculate Preview now refreshes both the histogram and Signal map with the selected metric, while the threshold switch controls only its black rejection mask; Map Color and heatmap hover show the active metric name.

  • Raw/Spatial signal/noise always excludes Min-Max Normalize, while Fully Processed signal/noise now honors the complete selected recipe, including Min-Max when enabled. Intensity-unit conversion still occurs before either basis is measured.

  • Added Cluster Buster 1000 particle identification. It builds a temporary processed map-background reference, performs bounded Top-1 pixel matching, rejects background winners and optional low correlations, collapses the remaining connected regions, and re-identifies final particles against the original library. Collapsed Uploaded Metadata selection now also resolves a single representative pixel so Selection Metadata remains populated.

  • Retired the unsupported offline-bundle GitHub Action, Go packager/launcher, dedicated tests, and user instructions. The bundled local Shiny app and hosted Shinylive app remain supported.

  • Processed-particle RDS downloads now round-trip through upload with canonical heatmap coordinates while retaining their unit-bearing metadata columns.

  • File-backed maps now support Fully Processed signal/noise and Collapse-off identification through bounded, spatial-halo-aware chunks. Whole-map state retains only S/N and rank-1 match summaries; selecting a pixel reads and processes that spectrum and calculates its requested Top N matches on demand.

  • Raw / Spatially Smoothed signal thresholds now include the selected intensity conversion, so transmittance and reflectance are measured after conversion to absorbance-like units. The first heatmap remains hidden until its current Plotly result is painted, eliminating the upload-time empty/stale flash.

  • Added optional per-metadata-group Top-N spectral matching with match_spec(..., top_n_by = "organization"); the Shiny app enables this per organization by default and batches both organizations and query spectra. The app also marks ranked derivative-zero peaks on the active processed spectrum, reports standardized model material classes in Summary, lets model matching retain the user-selected Top N, and keeps completed plot/table state stable until Run commits changed identification settings.

  • Large BIP ENVI maps can now stay file-backed through raw/spatial signal/noise thresholding and connected Mean collapse. Retained members are accumulated directly into particle means in bounded blocks instead of assembling and cbinding a dense retained-pixel matrix. Connected geometry is preserved; Advanced pixel calibration supplies unit-bearing coordinates, size/shape, area, and estimated-volume metadata, heatmap axes, summaries, and exports.

  • Particle metadata now distinguishes the legacy area/Feret approximation as rectangular_min and calculates feret_min from the bounding width perpendicular to the maximum-Feret axis. Reported shape, score, and signal/noise values use three significant figures. Spectrum Index maps were removed; material summaries sort largest-first; Thresholded Particles now exports fixed-size legend-free heatmaps with separate legend images.

  • File-backed connected Mean analysis can now apply per-pixel library correlation thresholds by processing and matching bounded spectrum chunks; only each pixel’s winning score and identity are retained before connected collapse. An Advanced opt-in can instead load the complete map into memory for users who deliberately prefer the ordinary dense workflow and have sufficient memory.

  • Selection Metadata now defaults to a concise friendly view, with detailed calibrated metadata available from Advanced, and library filtering initially selects every available organization.

  • Official reference builds now return at most ten nonempty assessment tables nested by cleanup, ref_lib, medoid, model, and functionality. Old/new metrics are wide and adjacent; accuracy, confusion, model-correlation, and warning/error-shift tables are ranked for direct review. Row-level tests and split manifests remain attached as hash-addressed evidence.

  • Reference and model holdouts now group physical IDs and exact transformed spectral duplicates, and both logistic and random-forest assessment models are refit only on grouped training rows. Logistic assessments select their production-matched medoids inside each training fold before fitting, while full spectra remain untouched as test queries. Parallel logistic cross- validation now uses reproducible doRNG streams without backend misuse warnings. Failed CO2 corrections and flat processed spectra fail closed, while releases and checkpoints use SHA-256 payload verification and immutable versioned paths.

  • Replaced the legacy broad plate-ID substring filter with 139 reviewed exact spectrum IDs, restoring 31 valid 7_b10–7_b12 FTIR plastic spectra. Corrected the spreadsheet-mutated 4-5 identity and added an exact PVDC mapping for the newly reviewed dataset.

  • Added experimental estimate_temperature() and calculate_emissivity() diagnostics for calibrated, surface-leaving FTIR spectral radiance. The in-memory method uses bounded matrix blocks for large hyperspectral maps and returns one Planck-weighted, mean, median, or maximum emissivity value per spectrum; full unclipped emissivity curves are materialized only when explicitly requested for selected spectra. Ambiguous fits are reported by aligned statuses, while the physical-range fraction exposes nonphysical emissivity values without clipping. These outputs are contrast and quality diagnostics, not library-identification spectra, and remain experimental pending validation on traceable measured particle/background data.

  • Removed the in-app Walk me through guide while retaining the concise, control-adjacent What this changes guidance. A video tutorial can be linked when its replacement is ready.

  • Restored preprocessing compatibility warnings for derivative and no-baseline identification libraries, made tab-wide actions turn switches off only, and fixed fresh-session startup/Plotly warnings plus first-Run Selection Metadata and Top Matches initialization.

  • Long-running full and medoid library identification in the bundled app now reports completed blocks, total blocks, and the block-completion percentage after every bounded matching block.

  • Hosted progress overlays now remain closed after a completed action, even when late output-only reactive updates render after identification results.

  • Selection Metadata now uses client-side rendering for its single row, and an explicit WebAssembly-safe row-click bridge keeps Top Matches selection synchronized. Package and CI model fitting remains single-worker by default, while production builders can set options(OpenSpecy.build_workers = n) to run logistic cross-validation folds and random forests concurrently. Scientific component checkpoints are keyed by their inputs, runtime, and an explicit component version so presentation-only source edits do not repeat core preprocessing. Immutable promotion reuses existing bytes only when a completed same-signature release manifest verifies their size and SHA-256.

  • Official library partitioning and medoid preparation now remove spectra that become flat only after the technique or model range is applied. Their exact identities remain visible in cleanup/QC evidence, and models cannot reuse checkpoints from before this post-restriction gate.

  • Fixed the bundled app’s logistic model interpretation so Top Matches row selection updates the quantitative coefficient background for the spectrum currently being viewed, including selected spectra within batches and maps. Spectrum trace toggles now stay above the axes while the logistic-weight scale uses a separately reserved right margin.

  • prune_lib() now removes material classes with fewer than min_n spectra within each spectrum type before correlation pruning. Its report records class support, threshold shortfalls, and affected spectrum IDs; complete builds collect the actionable class table in assessments$pruning_excluded_classes so maintainers can reassign classes or target additional reference spectra. Classes exactly at min_n remain.

  • Added train_spec_model() for reusable logistic-regression and experimental full-library ranger probability-forest training. Official builds now retain algorithm-explicit models and assessments, while legacy logistic filenames remain compatible. Random forests cover raw, derivative, and nobaseline data with inverse-frequency balanced sampling, permutation importance, OOB diagnostics, checkpointed training, and leakage-free grouped full-library holdouts.

  • Model matching can now return ranked top class probabilities. The bundled app displays the top logistic scores and updates a quantitative red-yellow-green coefficient background on the selected spectrum when a top class is chosen; plotly_spec() and model_class_weights() expose the same interpretation for package users. The colors show signed model influence, not causal peak attribution.

  • Leveled the hosted homepage video card while retaining its autoplay, privacy-enhanced embed, and responsive aspect ratio.

  • Final full and medoid reference libraries now drop metadata columns that are entirely NA and stably order the remainder from least to most missing. assessments$metadata_finalization records the change. Model holdout outputs now include ranked point-biserial correlations between numeric assess_spec() metrics and incorrect IDs, making the strongest quality/error associations directly reviewable without retraining models.

  • Updated the hosted homepage with the requested Pew-Gerstner Fellows Program acknowledgement and replaced the hero spectrum illustration with an eager, muted autoplay embed of the supplied privacy-enhanced YouTube video.

  • Stabilized the wasm repository build by installing its native HDF5, JPEG, PNG, and Pandoc build prerequisites once in the pinned driver image, with a retried apt refresh that no longer depends on the runtime rig repository.

  • Official build_lib() runs now default to remove_other = TRUE, removing blank spectrum_identity rows and the unresolved literal other class before quality control, while retaining reviewed broad other plastic and other material categories for constrained prune_lib() reassignment. Typed source-level review and before/after counts remain in assessments.

  • Simplified official polymer class names, separated polyethylene from polypropylene, and retained chemically meaningful polyhydroxy(meth)acrylates notation. Confusion tables now flag and rank the largest misidentifications and report each cell’s share of its expected class.

  • Fixed cold-cache failures in the pinned WebAssembly package-repository workflow by letting a dependency-metadata cache key seed from the newest compatible successful repository before rebuilding the exact OpenSpecy commit. The Action now tests this fallback before its full build.

  • Added rebuild_lib_artifacts() to reuse completed type-keyed libraries while checkpointing a new medoid, model, and assessment run. Spectra with at least 10% observed support now enter medoid/model preparation: PAM uses temporary spectrum-mean filling, published medoids restore original missing values, and model training uses wavenumber-mean filling instead of complete-case removal. Lambda is selected by out-of-fold macro class accuracy without changing the calibrated alpha, no-intercept, grouped multinomial, or class-weight policy. mean_replace() now applies an optimized per-spectrum column fill to matrix inputs while preserving its existing vector behavior.

  • Large medoid groups now use deterministic cluster::pam(variant = "faster") initialization, avoiding the prior quadratic-times-k BUILD phase while retaining FasterPAM swaps and reproducible selected identifiers. Groups over 3,000 spectra use five deterministic 1,000-spectrum PAM samples scored against the complete group with correlation distance, avoiding oversized full dissimilarity matrices while preserving reproducible medoid selection.

  • Candidate and legacy medoids now identify their complete corresponding processed libraries, and existing production models likewise identify each complete source dataset without assessment-time retraining. Full reference libraries retain independently stratified source-local holdouts with self-matches removed. Exact class labels, denominators, and provenance remain explicit.

  • Official build_lib() artifacts are now partitioned by FTIR, Raman, and NIR with full ranges of 400–4000, 200–4000, and 4000–12000 respectively; FTIR/Raman medoids and models use 800–3200, while the NIR identification interval is derived from finite coverage. Per-type all-blank metadata columns are dropped, and the bundled app now offers NIR identification.

  • The bundled app now defaults Spectrum Type to All, using complete FTIR/Raman/NIR full or medoid references and every overlapping typed model. Recalculate Preview can materialize staged files before Run, displayed signal-to-noise metadata uses two significant figures, and CO2/silent checks outside a user-restricted axis are reported as successful no-ops.

  • Derivative and no-baseline reference spectra now pass checkpointed quality gates before pruning: FTIR CO2 is selectively flattened when its CO2/silent maximum ratio is greater than two, high-tail detection ignores NA padding and drops failed corrections, and running SNR below two is removed.

  • Model/reference comparisons report macro class accuracy first, with coverage, overall accuracy, per-class results, confusion counts, stable warning schemas, and numeric assessment fields. Models use the package match_spec() filler pathway for partial spectra.

  • build_lib() now provides an end-to-end official workflow from explicit source-library paths and an explicit output directory, returning libraries, medoids, models, and named assessment tables in one object. Curated helper CSVs are discovered under data/ beside the calling script or working directory. Completed components and full old/new assessment stages are exported with input manifests as they finish; reuse = TRUE resumes only compatible checkpoints and validated artifacts are promoted to a versioned release directory.

  • Restored the optimized cluster::pam(pamonce = 6) medoid engine used by the established reference workflow. reduce_lib(progress = TRUE) and delegated build_lib() reduction now report each group size plus separate correlation and PAM timings, making large medoid bottlenecks visible.

  • Optimized identical-input cor_spec(x, x) calls through the symmetric one-matrix tcrossprod() kernel. This preserves the full correlation matrix exactly while avoiding the general two-matrix path used during PAM medoid selection.

  • Full old/new reference holdouts now use one optimized full-matrix cor_spec() call per artifact/source pair instead of repeatedly normalizing the training library in small query blocks. Progress reports the matrix dimensions plus correlation and total identification time.

  • Vectorized assess_spec(report = "all") report expansion so complete in-memory library assessments no longer rescan the full evidence table for every spectrum. build_lib() calls assess_spec() once per complete artifact and reports each artifact/source timing.

  • Fixed the anchored-regex audit so PCRE escapes such as \x2c are classified without compiling an invalid detector expression.

  • Full reference assessment uses a stable-identity-grouped ten-percent holdout across the complete candidate and legacy artifacts, prevents exact reference leakage, records identification metrics, and reports per-check shifts from assess_spec(). Medoid and model evaluation instead exercise each deployed artifact once against its complete corresponding dataset; model assessment never selects fold-local medoids or retrains a model. Evaluation rows live in one tidy tests table with explicit provenance.

  • Reference-build promotion now reports each release artifact and serializes the aggregate build only once after its final manifest is attached, removing a redundant multi-gigabyte in-memory compression pass.

  • The bundled app now treats identification as a Run-captured optional owner: raw or processed spectra remain viewable and quantifiable without matches, while match tables, downloads, and heatmap colors appear only when identification was enabled for that Run.

  • Canonical source metadata is coalesced before external joins, and fallback_by is deprecated. Literal-only anchored class patterns moved from classes_regex.csv to exact entries in classes_reference.csv.

  • Added auditable prune_lib() and recipe-selective build_lib(prune = ...) support for reference-library QA/QC. Generic classes are reassigned only to eligible same-technique candidates: other may match any established class, other plastic only plastic classes, and other material only organic matter or mineral. Reassignment also updates material type. Classes are then processed largest first with one optimized cor_spec() matrix per class/pool pair, reused across removal iterations with deterministic ties and protected minimum sizes. This replaces repeated small blocks that multiplied against ineligible spectra and obscured multi-hour bottlenecks. The official workflow labels remaining blank standards as other, enforces a one-percent cap, and prunes derivative and nobaseline libraries before medoid/model creation while leaving raw unpruned.

  • Applied Clarissa’s reviewed exact-class corrections using OpenSpecy’s existing canonical names: confirmed monomers/non-polymers move to organic matter, polymer-natural blends to other, and reviewed ABS, nylon 6,6, cellulose, polyurethane, SciPoly, and textile-polyester identities to their existing hierarchy values.

  • Harmonized reviewed metadata aliases and made build_lib() lookup keys explicitly selectable, with optional fallback-key merging and fill-only lookup values. The official workflow coalesces username into a missing organization before one type join and verifies complete library/spectrum types. The curated reference tables now separate polyamides from polyacrylamides, classify adipate polymers as polyesters, correct PA, aramid, Nomex, duplicate, and common-name mappings, and cover reviewed organization plus exact user-source fallbacks.

  • Added predict_class_reference() for reviewable class-table curation. Flexible patterns now live in a separate regex reference, run only after the exact lookup, and fill only blank materials when every match agrees. Exact overlaps are allowed and reported; distinct-material clashes stay blank.

  • build_lib() now removes recognizable paths and every read_any()-supported trailing file extension from spectrum_identity before exact metadata lookup. Numeric OPUS suffixes include any terminal period followed only by digits, such as .10. It records an audit attribute and normalizes exact lookup keys the same way. The compressed exact class table no longer carries extension-only aliases, and the source table records all observed spectrum techniques, including MBARI as Raman.

  • Accelerated reference-library Savitzky-Golay derivatives with compiled convolution and polynomial baseline subtraction with reusable QR fits. The retained benchmark compares the former implementations and enforces tight same-output tolerances.

  • Added the opt-in compact map Specs 0.2 format for ENVI/H5/ZIP inputs. Regular coordinates and repeated metadata use validated descriptors, while optional S/N background suppression retains foreground values and maps every rejected source to an exact virtual zero spectrum with auditable reasons. Weighted PCA/K-means and foreground Hilbert transforms preserve full-source multiplicity without expanding compact pixels. The bundled app now stages one local direct path or one hosted WORKERFS mount, reads only after Run, and offers the compact transformed map as an RDS download.

  • automate_particle_analysis() now treats both S/N threshold extremes as valid outcomes. Removing every map pixel emits a message and returns an empty analysis before library matching; retaining every pixel emits a message and continues, allowing connected collapse to identify and measure the full map as one particle per source.

  • Reduced default read_envi() peak memory without changing its public API or returned OpenSpecy format. BIP, BIL, and BSQ files are now read in bounded blocks directly into the final band-by-pixel matrix instead of constructing and permuting multiple complete arrays; spectral_smooth = TRUE retains its existing three-dimensional smoothing path.

  • Reduced read_zip() peak memory for two-member ENVI HDR+DAT archives by streaming the compressed binary directly into the same blockwise band-by-pixel reader. This avoids retaining a complete extracted DAT beside the final matrix in WebAssembly while preserving the returned OpenSpecy data and the existing extraction path for other ZIP layouts and smoothed ENVI reads.

  • Fixed collapsed analysis settings requiring a separate maximize click: the Preprocessing, Identification, Advanced, and Quantification tabs now expand the card and activate the chosen tab with the same click. Run, Recalculate Preview, and download actions again schedule the central loading overlay directly from the browser click, before a blocking local or WebAssembly R task can delay server phase messages. The overlay now follows Shiny’s real idle lifecycle instead of being dismissed after the first reactive flush, which could precede lazy identification and rendering work.

  • Changed the default assess_spec() silent region to 2420–2550 cm-1 and the high-tail/CO2 detection and automatic-correction ratio from 3x to 2x. Explicit caller values remain unchanged.

  • Removed speculative RAM forecasting from the Shiny app. Jobs now proceed until the real read, allocation, or processing operation succeeds or fails, with elapsed-phase recovery guidance while retaining the 10 GiB input limit.

  • The hosted Shinylive app can mount browser-selected files into webR WORKERFS and pass their paths to the ordinary read_any() pipeline, avoiding the copying multipart/R-raw upload bridge while still fully materializing an in-memory OpenSpecy object. Shinylive now presents only that mounted-file picker, while local Shiny presents one direct-path picker that uses the native Windows/macOS dialog when available and otherwise uses shinyFiles. Hosted mount and read/materialization status appears in the central progress popup instead of explanatory/status text below the picker. Mounted text spectra are read through fread()’s text parser to avoid its unsupported 32-bit WORKERFS file memory map while retaining delimiter/type inference and output structure.

  • WebAssembly repository builds now reuse a verified dependency-only CRAN-like cache locally and in GitHub Actions. Every reuse evicts and rebuilds OpenSpecy, refreshes changed dependency versions, regenerates the VFS image, and retains exact commit/artifact checks.

  • Fixed active-spectrum quality findings for collapsed maps: retained units and rejected clicked pixels now use the same one-spectrum object as the plotted trace, and SNR is calculated directly from that object instead of indexing a dataset/heatmap vector. Rejected pixels are labeled and no longer assessed as synthetic zero spectra.

  • Fixed Spatial Smooth running its (potentially expensive) convolution immediately on every toggle/Spatial Standard Deviation change, before Run was ever clicked. An always-on observer that keeps the heatmap’s selection marker in sync with clicks was reading the spatially-smoothed object purely for pixel x/y coordinates, which smoothing never changes, and that incidentally forced the real computation to run live.

  • Changed Remove Isolated Spikes, Flatten Region, and Range Selection to default off. Whether their toggles are on or off, the viewed spectrum’s Warnings/Successes now always include a spike/CO2-region/high-tail/ saturation check (previously these four were only ever reported as part of “Automatic Corrections Made,” which stayed silent when the matching toggle was off, and a leftover filter separately hid them from Warnings/ Successes even after being computed), so turning automatic correction off never hides whether the spectrum actually has the issue. Every one of these checks now also has its own specific success message (e.g. “No isolated single-point spikes were detected”) instead of a generic “check passed” placeholder. A Low Signal/Noise check was considered but left out as redundant with the app’s existing separate SNR Threshold finding.

  • Filled the Warnings/Successes buttons with their semantic color (amber/ green) instead of a thin border on a neutral background, so they read as clickable like the app’s other buttons; Automatic Corrections Made keeps its rainbow identity as a permanent fill (previously only a border shown when something had actually been applied), with a glow ring added to still flag when a correction was actually applied.

  • Fixed the Thresholded Particles download’s Particle Unit and Match ID heatmap images always drawing a legend, even though both are per-particle identifiers with too many categories for a legend to be useful.

  • Fixed a selection feedback loop that snapped a manual heatmap click on a multi-pixel collapsed particle back to that particle’s first/representative pixel instead of staying on the pixel actually clicked: syncing the sidebar metadata table’s selection to match a heatmap click echoed back through the table’s own selection-change handler, which was indistinguishable from a genuine row click.

  • Fixed the Top Matches table staying empty whenever Library type = AI model, even though the Top Matches download and the Selection Metadata table already showed AI predictions. AI mode has one prediction per spectrum rather than a ranked candidate list, so the table now shows that single prediction for the selected spectrum instead of erroring/staying blank.

  • Clicking Run, Recalculate Preview, or a download now shows busy feedback immediately instead of after a multi-second delay (dominated, for Run, by an unannounced whole-map signal-to-noise scan that ran ahead of the first progress message; Recalculate Preview previously had no progress signal at all in its default configuration). Run and Recalculate Preview also get an instant client-side busy indicator on click, and downloads show the same indicator consistently in both the local Shiny app and the hosted Shinylive build.

  • Fixed clicking a row in the Uploaded Metadata table jumping to an unrelated or unchanged map location instead of that particle’s first (lowest raw pixel index) location: the handler treated the table row’s particle/unit index as if it were a raw pixel index, and separately skipped updating the selection whenever the clicked unit happened to already equal the current selection’s default – most visibly on the very first row click, since the app’s initial selection defaults to unit 1. It now resolves both the selected pixel and unit directly, unconditionally, matching the heatmap click handler.

  • Changed the Summary panel’s “Good Signal”/“Good Match Values”/“Good Identifications” bars to show the underlying pixel counts (e.g. “142 / 331,180”) alongside the percentage: shinyWidgets::progressBar() rounds its displayed percentage to the nearest whole number, so a real but small share of passing pixels on a large, sparse map could read as a misleading “0%”.

  • Moved the Signal/Noise Recalculate Preview button out of the histogram card it previously shared with the plot: that card dims when the preview is stale, which was dimming the one control needed to un-dim it. The button now uses the same green (“would change the result”)/dark navy (“already current”) convention as the main Run button, and the histogram itself now visibly resets to blank (instead of freezing on the previous dataset’s chart) when a new file is uploaded.

  • Fixed a bug in canonical_state_gate’s Run-gated result where return() inside tryCatch() exits the enclosing reactive directly, silently skipping the settings snapshot the previous entry’s fixes attached after the tryCatch() call – on every code path except one (collapse with Threshold Correlation on and a successful result), canonical_state()’s settings were NULL, so the heatmap/plot/download fixes below were silently inert whenever Threshold Correlation was off. Settings are now attached at every actual return point instead. This also fixes the particle-size histogram never rendering when collapsed (its req() on the missing settings blocked it silently) and the Map Color selector/ particle-summary gating for the same reason.

  • Added a Signal/Noise Basis choice (Raw / Spatially Smoothed, the previous default; or Fully Processed, which also applies every other enabled preprocessing step to each pixel before scoring it) that decides which pixels are eligible for particle collapsing. The Signal/Noise histogram preview no longer recomputes live on every settings change (which could re-run spatial smoothing or, with Fully Processed, full preprocessing, before Run was ever clicked); it now only updates on Run or a new Recalculate Preview button in the Threshold Signal/Noise box, and dims when the basis, Spatial Smooth, or thresholding settings have changed since its last computation. The memory preflight advisory no longer runs a live spatial smooth either (uses the raw upload’s dimensions only, which is all it ever needed).

  • Fixed a filter_spec() “zero spectra” error when clicking a collapse-rejected/background pixel: the raw-spectrum overlay reactive had no fallback for an invalid selection (unlike the processed-spectrum reactive, which already flat-lines correctly); it now does the same.

  • Fixed the Run-gated reactivity the previous entry introduced: the heatmap, particle/material plots, correlation and signal/noise histograms, download type list, and progress-bar summaries now read only the settings captured at the last Run instead of live checkboxes, so toggling Collapse Particle Spectra, Spatial Smooth, Threshold Signal/Noise, or Threshold Correlation no longer recomputes or re-renders anything before Run is clicked. Added an on/off switch to the Identification Strategy box (default on) that fully skips identification, and one Turn All On/Off button per settings tab that has switches. Processed spectra now flat-line below the enabled signal/noise threshold whether or not Collapse Particle Spectra is on (previously only when it was on). Fixed a race between the six Run-triggered result caches that could leave quantification, quality reports, and other Run-gated results silently stuck at their pre-Run value; results are now populated in an explicit, deterministic order. Fixed the Map Color selector defaulting to Signal/Noise and never updating once Material Class/Match ID/Match Value became available. The Run button’s default (nothing-to-run) color is now the app’s dark background color instead of light blue, and the Spectra card has visible space above it. Vectorized residual spike detection across every spectrum in a map/batch upload at once instead of one small allocation per spectrum per correction pass (same output; see benchmarks/spike_correction.R), and raised the identification blockwise match size from 100 to 1,000 query spectra per block (same output, less chunking overhead). The memory preflight estimate no longer runs the actual spatial smooth as a side effect of estimating memory. Fixed a duplicate id="columns_selected" between the Top Matches column-choice uiOutput wrapper and its inner selectInput.

  • Added a single Run button as the sole trigger for the app’s analysis tranche, replacing the four per-tab owner switches; the button turns bright green whenever a new dataset is uploaded or a setting changes, and returns to the app’s normal accent color once Run has produced current results. Uploading a new dataset now also resets the heatmap, spectrum plot, and quality/automatic-correction reports back to a “click Run” state instead of continuing to show the previous dataset’s results. “Collapse Particle Spectra” and “Spatial Smooth” are silently ignored for a single uploaded spectrum instead of erroring. Fixed a crash (“wasn’t able to determine range of domain”) when a heatmap’s selected color metric has no finite values for any pixel (for example, when no uploaded spectrum clears the correlation threshold).

  • Replaced the Preserve Uploaded Wavenumbers advanced switch with a Mean Up conformation technique (the new default). Mean Up only resamples the uploaded spectra to the selected Wavenumber Resolution when that resolution is finer than what was actually uploaded; otherwise it leaves the uploaded axis untouched and conforms the reference library onto it instead, exactly as the removed switch did.

  • Rebuilt the bundled app around one in-memory OpenSpecy workflow with a unified 10 GiB upload ceiling and best-effort resident/peak-memory guidance. Identification now ranks bounded query blocks and retains only a shared Top N result (10 by default) for the match table and download. Particle analysis calculates signal/noise after optional spatial smoothing but before other processing. Spectral cluster modes now fit source-scoped PCA/K-means first, identify collapsed clusters once, and either retain them as non-spatial particles or project their identities into a second connected same-material spatial collapse without re-identification. Correlation thresholds reuse that first pass. All heatmaps black out rejected pixels, omit inline legends, and expose a formatted legend modal (or a >30-category explanation); rejected clicks return no match and a flat processed trace. Threshold histograms remain on-theme, and only caught errors open alert dialogs. The default-on uploaded-axis option conforms the reference library onto the exact uploaded axis with memory-bounded mean_up averaging/interpolation, and particle ZIPs restore the summary table, both histograms, every heatmap, material summary, and size distribution.

  • Corrected package automate_particle_analysis() partitioning so connected units and source-scoped PCA/K-means clusters never cross source maps or H5 regions; return stable pixel-to-unit membership and aligned unit IDs/metadata; and apply the minimum pixel area inclusively. Connected units retain recomputed shape and signal summaries, while specs_centers remains the public K policy and non-default specs_steps now fails clearly instead of being silently ignored.

  • Added experimental, package-only FileSpecs descriptors for read-only H5 and ENVI maps. They fingerprint immutable sources, keep derived generations in a separate atomic cache, provide bounded decompress_spec() selections and lightweight region views, stream complete rectangular views to new atomic float64 ENVI pairs without wavelength-axis truncation, and fail early for unsupported matrix-only operations while preserving legacy matrix-backed Specs behavior. The first direct large-map workflow streams region-wise S/N and exact particle means through automate_particle_analysis(), retains one exact best match, and lazily caches registered regional H5 mosaics for particle images; it intentionally requires the collapse strategy, mean, and non-entropy S/N. spectral_smooth = TRUE now streams a halo-padded 3-D Gaussian smooth (matching mmand::gaussianSmooth() exactly) instead of erroring, without ever materializing a full region. H5 mosaics retain region, local and stage coordinates, unique pixels, and intersecting image tiles. These APIs remain available to package users but are no longer routed through the app.

  • automate_particle_analysis()/automate_particle_filespecs() now return queryable plot data (particle_image, particle_heatmap, particle_heatmap_thresholded, cor_heatmap, sn_histogram, cor_histogram; each a list with grid/histogram values and a type, or type = "empty" with a reason when nothing passed filtering) instead of stored recordedplot objects; this is a breaking change to the field names and shape of automate_particle_analysis()’s per-sample result. plot() still draws any of these with base graphics, and the app renders them with Plotly for on-theme, interactive maps. Advanced no longer disables its own controls while off, matching the other top-level switches. The Thresholded Particles download drops the duplicative Raw Map object choice, defaults to itself once a particle result exists, and now zips every selected content type including an explanatory details/summary when no particles passed filtering. The redundant “No regions passing threshold” popup is removed in favor of the existing quality warning/success indicators.

  • Unified the app’s numeric, categorical, and particle heatmaps into one Plotly renderer with hover tooltips, an on-demand modal legend, and a selection marker kept in sync via a cheap trace restyle; this replaces the separate base-graphics heatmap, its click/brush handlers, and the metadata popover. Material-class colors are resolved from one shared palette across the heatmap, particle summary, and particle_image(). The Advanced switch and its correlation threshold default on. The Uploaded Metadata tab moves x/y/z and other per-pixel columns to the front for every source, and for sources over 100,000 spectra shows only those columns, dropping duplicated file-level metadata. automate_particle_analysis() now accepts a character vector of file paths, reading and processing each one in turn. Base-graphics particle-plot legends (plot(), particle_image()) now draw in the margin outside the plotted data instead of overlapping it. The as_OpenSpecy() data.table-to-matrix conversion notice is silent when called internally.

  • Added correct_spike() with a conservative wavenumber-aware residual method and the manual and automated prominence/FWHM methods described by Coca-Lopez (2024). Corrections are transactional, preserve the OpenSpecy axis and metadata alignment, avoid boundary extrapolation, and retain auditable accepted/rejected-region diagnostics. Safe correction now repeats while the correctable count decreases, retaining successful passes when later candidates are newly exposed and leaving no-progress candidates unchanged with their safeguard reason.

  • Added opt-in spike and saturation checks plus report = "all" status output to assess_spec(), exact sorted-amplitude breakpoint_snr support to sig_noise(), and optional spike correction at the start of process_spec(). restrict_range() can now remove one guarded union of hard saturation intervals from a whole batch, with irregular-axis coverage accounting and a conservative rollback when the proposed loss exceeds 70% or leaves too few points.

  • Added a default-on app control for isolated spikes and an opt-in saturation control, separated automatic-correction details from warning/success results for the active spectrum, an external adaptive spectrum legend, and bright colorblind-accessible heatmap palettes. Numeric map legends sit horizontally above the plot, default Match Name maps no longer flash a numeric metric, categorical Match Name colors are shared with the material summary, and map selection updates its marker without rebuilding the heatmap. Hosted WebAssembly downloads now use a same-frame validated Blob handoff while local Shiny retains its native download handler; browser smoke tests require genuine CSV and ZIP files from real clicks.

  • Added a dark, accessible static landing page at the hosted-site root with the embedded app, navigation guidance, search and social metadata, tutorial, publications, contacts, and funding context. Conventional README-driven pkgdown documentation now lives at /pkgdown/; the app remains at /app/. Pew-Gerstner Fellowship in Ocean Plastics Research and Walking Softer are credited as Thriving monetary partners.

  • 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, point_intensity() for non-ratio point measurements, and 4S Fill Peaks baseline correction. The app’s Quantification tab now defaults off and lets users save ratios, individual band areas, and individual point intensities from precise numeric inputs. Custom Ratios and Single Measurements now share the single Quantification owner without a redundant child switch. The app calculates any combination from the exact final processed spectra displayed in the app and includes exact definitions, values, and processed-spectrum provenance in Processed Spectra and Top Matches downloads.

  • Made the representative medoid library the interactive app default and cache reference-library preparation by the final processed axis. The complete library remains an explicit local-app option for users who accept its longer initial calculation.

  • 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.

  • Made the contextual download action fill its card, 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. Processing disclosures now explain each spike and saturation input, success findings omit empty interpretation and action fields, and automatic details report the ranges actually corrected by spike, saturation, CO2, and high-tail operations.

  • 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 hosted landing source.

  • Embedded the hosted Shinylive app on the static landing page with real Shiny readiness feedback and a viewport app mode that persists through upload/download dialogs. GitHub retains a normal README, and brief reactive updates no longer flash the app’s processing overlay. Relative app/ and pkgdown/ routes keep GitHub project and hosting-fork deployments portable.

  • 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 static landing page, conventional pkgdown docs, 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 the runtime signal dependency by using internal Savitzky-Golay filtering. Reference-library medoids continue to use the established cluster::pam(pamonce = 6) implementation.

  • 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

CRAN release: 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

CRAN release: 2024-06-13

Minor Improvements

  • updated links

OpenSpecy 1.0.9

Minor Improvements

  • more closing and flexibility options

OpenSpecy 1.0.8

CRAN release: 2024-03-14

Minor Improvements

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

OpenSpecy 1.0.7

CRAN release: 2024-03-11

Minor Improvements

  • Modified manage_na.R
  • Added to NAMESPACE

OpenSpecy 1.0.6

CRAN release: 2023-11-25

Minor Improvements

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

OpenSpecy 1.0.5

CRAN release: 2023-10-31

Minor Improvements

  • Support .tsv files

Bug Fixes

  • Flip xy coordinates in ENVI files

OpenSpecy 1.0.4

CRAN release: 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

CRAN release: 2023-09-13

Minor Improvements

OpenSpecy 1.0.2

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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