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Changelog

Source: NEWS.md

sptrends 1.6.2

sptrends 1.6.1

Full audit: functions, docs, website config, NEWS style, cran-comments.

  • Removed 4 dead duplicate validation checks in benchmark.R/ validation.R left over from the 1.6 audit integration.
  • Added _pkgdown.yml entries for 5 functions exported in 1.5.3.
  • Condensed NEWS from 1.5.4 onward to match the project’s usual telegraphic style.
  • Updated cran-comments.md to reflect confirmed 1.6 results.
  • Cross-checked MK/Theil-Sen against 5 external packages (Kendall, trend, modifiedmk, robslopes, zyp); no real discrepancies found.

sptrends 1.6

Bug fixes

  • Fixed compute_anomalies() climatology/standardisation alignment when start_position is not 1.
  • Fixed read_ordered_stack() annual dates to use 1 January.
  • Preserved constant residuals in Yue-Pilon prewhitening; skipped unavailable DW plots for Zhang’s method.
  • Propagated worker counts in TST/RTA; honoured supplied clusters.
  • Matched original-BKY plotting thresholds to its own decisions.
  • Fixed zero F1 scores; benchmarks now apply evaluation_mask.
  • Handled one-permutation summaries; rejected undefined General G inputs with fewer than two positive cells.
  • Fixed missing-neighbour panels, single-cell histograms, and TST direction plots with BY or no slope estimate.

Documentation

  • Clarified cycle ordering, daily-data limits, calendar anchors.
  • Updated website sources; synchronised exports with 1.5.3.
  • Corrected estimator labels and MMK identification.

sptrends 1.5.9

  • Confirmed 100% coverage holds with SPTRENDS_TEST_PARALLEL=true set. No code changes.

sptrends 1.5.8

  • Fixed workflow_trends()’s example again: finds a valid cell programmatically, keeping real (not synthetic) data.

sptrends 1.5.7

  • Replaced the 1.5.5 example crop (had no valid cells) with synthetic data.

sptrends 1.5.6

  • Skipped 19 parallel-cluster tests by default (SPTRENDS_TEST_PARALLEL=true to run) to cut check time.

sptrends 1.5.5

sptrends 1.5.4

  • Used a null device for three report = TRUE tests to cut check time.

sptrends 1.5.3

Bug fixes

CRAN-requested fixes (submission feedback on 1.5.2):

Found while fixing the above:

  • Fixed a conflicting @inheritParams/duplicate @return in fdr_bky() that corrupted the installed help database.
  • Updated 4 stale tests asserting the newly-exported functions were still internal.

sptrends 1.5.2

Bug fixes

sptrends 1.5.1

Resubmission of 1.5 to CRAN, with no code changes – version bump required to avoid a filename collision on CRAN’s own incoming server from an earlier submission attempt.

sptrends 1.5

New features

  • read_ordered_stack() now supports explicit declaration of a series’ temporal structure (files, time, cycle_type, start, end, time_anchor), as an alternative to automatic detection from file names – recommended whenever the series is not simply annual. Eight unambiguous calendar conventions are supported: "annual", "monthly", "16-day", "semimonthly", "10-day", "8-day", "weekly", and "daily", all built with real calendar arithmetic (leap years included).
  • compute_anomalies()’s own cycle_type now uses the same vocabulary as read_ordered_stack()’s ("monthly", "16-day", "semimonthly", "10-day", "8-day", "weekly"), so a value already used to read a stack can be reused directly here. "annual" and "daily" are deliberately not included – see ?compute_anomalies for why.

Improvements

  • Automatic mode’s gap detection is now scoped to simple annual sequences, avoiding false positives on combined numeric codes.
  • Automatic mode now recommends explicit declaration for series that may not be annual.
  • compute_anomalies() now validates cycle fully (must be one finite integer >= 2), instead of only checking cycle < 2.

sptrends 1.4.4

Improvements

  • trend_test(method = "CMK") now supports connectivity = "rook" as a genuine, working option, alongside the default "queen".

sptrends 1.4.3

Documentation

  • Added the CMK/ConMK external validation note to README.md.

sptrends 1.4.2

Documentation

  • Documented a fresh, independent confirmation of CMK’s external validation against ConMK: the base statistic matches to floating-point precision, and the continuity = TRUE option reproduces ConMK’s own p-values exactly at the specific edge case (Sm == 0) where the two implementations would otherwise be expected to diverge.

sptrends 1.4.1

Improvements

sptrends 1.4

Passed a comprehensive external code audit; several improvements resulted.

Improvements

  • Corrected method-comparison summaries to consistently treat error rates as “lower is better”.
  • Added validation for sim_trend_stack()’s ar1 and noise_sd arguments.
  • Added the software’s own DOI to citation metadata.
  • Unified the package website URL across README.md and DESCRIPTION.
  • fdr_direction_summary() now supports the "BY" method.
  • Refined NaN/NA consistency in replicate-aggregated summaries.
  • Corrected documentation for workflow_tst()/workflow_rta()’s return value and documented a known limitation with irregular time spacing.

Documentation

  • Refreshed cran-comments.md.
  • Softened prescriptive wording around BY in the FDR vignette.

sptrends 1.3.4

Improvements

  • Improved reliability of categorical map rendering.

sptrends 1.3.3

Documentation

  • Streamlined the beta-era NEWS.md history (0.96.4-0.97.1) too: shorter entries.

sptrends 1.3.2

Documentation

  • Streamlined NEWS.md from 1.0 onward: shorter, improvement-focused entries.

sptrends 1.3.1

Improvements

  • Improved robustness of categorical map rendering in edge cases.
  • Improved tolerance of a regression test near signal boundaries.
  • Direction maps: legend now lists “Increase” before “Decrease”.
  • TST vignette example now calls workflow_tst() directly.

sptrends 1.3.0

Improvements

  • read_ordered_stack() now shows live reading progress.
  • summary() on workflow results now leads with the FDR-corrected result, with uncorrected stats shown as diagnostic context.
  • Documented reporting valid cell counts as good practice.
  • Standardised valid-cell and raw/percentage reporting across every summary() table in the package.

sptrends 1.2.5

Improvements

  • Improved “not significant” display consistency in smoothed direction plots.

sptrends 1.2.4

Improvements

  • Refined category-colour assignment in categorical maps.

sptrends 1.2.3

Improvements

  • Categorical maps now always render as discrete colour blocks.
  • Unified category order and grey shade across every map, plot and bar chart. Full symbology audit completed.

sptrends 1.2.2

Improvements

sptrends 1.2.1

Improvements

  • Refined the colour scheme into three distinct identities: diverging maps (ColorBrewer RdBu), categorical direction (Tableau red/blue), and binary significance (its own dedicated colour).

sptrends 1.2.0

Improvements

  • Unified the colour scheme across the package’s plots.

sptrends 1.1.5

Quality assurance

  • Improved test coverage in tst-methods.R, rta.R and workflow_trends-methods.R.

sptrends 1.1.4

Quality assurance

  • Refined test coverage.

sptrends 1.1.3

Improvements

  • Improved consistency of the direction panel across workflows.

sptrends 1.1.2

Documentation

  • Added a “Quality assurance” section to README.md.

sptrends 1.1.1

Documentation

  • Completed citations in the FDR-correction vignette.
  • Audited citations and references across all six vignettes.

sptrends 1.1

Quality assurance

  • Passed a comprehensive integral audit of the whole package.
  • Confirmed via two independent rounds of external testing.

sptrends 1.0.8

Quality assurance

  • Closed the last coverage gap; confirmed 100% test coverage and a clean R CMD check.

sptrends 1.0.7

Improvements

  • Improved test reliability for direction-map testing.
  • Added a round-trip fidelity test for read_netcdf_stack().

sptrends 1.0.6

Improvements

  • Improved test reliability with a stronger reference signal.

sptrends 1.0.5

Improvements

  • Improved test compatibility with fdr_correction() and refined message formatting.

sptrends 1.0.4

Package identity

  • Added README badges: license, lifecycle, Zenodo DOI, pkgdown site.

sptrends 1.0.3

Feature changes

sptrends 1.0.2

Documentation

  • Vignette and documentation improved.

sptrends 1.0.1

Documentation

  • Polished README.md: official citation, author affiliations, reordered examples and modules.
  • Polished vignettes/a-getting-started.Rmd: clarified TST origin, added references, reworked “Common mistakes”.

sptrends 1.0

Package identity

  • Added URL/BugReports to DESCRIPTION.
  • First stable release, confirmed clean on all win-builder platforms.

sptrends 0.97.1

Improvements

  • Fixed four broken DOI links in vignette References sections (URL encoding).

Documentation

  • Added 11 words to inst/WORDLIST.

sptrends 0.97

Last pre-release (beta) version. sptrends 1.0 is the first stable release.

Quality assurance

  • Passed an extensive external test battery covering all 18 exported functions.

sptrends 0.96.7

Improvements

  • Fixed sim_trend_stack(trend_shape = "block") ignoring signal_location/signal_size/signal_angle.

sptrends 0.96.6

Simulation and validation

  • Corrected a validation-metric edge case.
  • Confirmed simulator checks across spatial-dependence and multiple-testing scenarios.

sptrends 0.96.5

Simulation and validation

  • Added field-significance power metric.
  • Removed an R CMD check NOTE from console flushing.

sptrends 0.96.4

Simulation and validation

  • Added progress/timing reporting to simulation, design, validation and benchmarking functions.
  • Recorded a 33-control external validation of the simulation cycle.

sptrends 0.96.3

Simulation and validation

  • Completed regression coverage for shared replicate-level validation inputs.

sptrends 0.96.2

Simulation and validation

  • Expanded regression tests for benchmark scoring, covariance fallback, uncertainty graphics and replicate-specific validation inputs.

sptrends 0.96.1

Simulation and validation

  • Corrected the real-data spatial validation test and limited benchmark stages to currently implemented method families.

sptrends 0.96

Simulation and validation

sptrends 0.95.2

Documentation

  • Vignette and documentation improved.

sptrends 0.95.1

Documentation

  • Vignette and documentation improved.

sptrends 0.95

Documentation

  • Vignette and documentation improved.

sptrends 0.94.10

Vignettes

  • Improved the multiple-testing and workflow vignettes and clarified the binarised workflow map.

sptrends 0.94.9

Vignettes

  • Refined the multiple-testing vignette.

sptrends 0.94.8

Vignettes

  • Improved the multiple-testing vignette.

sptrends 0.94.7

Vignettes

  • Improved the package vignettes.

sptrends 0.94.6

Vignettes

  • Improved the trend-magnitude vignette.

sptrends 0.94.5

Vignettes

  • Improved the trend-inference vignette.

sptrends 0.94.4

Vignettes

  • Improved the serial-correlation vignette.

sptrends 0.94.3

Vignettes

  • Improved the data-loading and exploration vignette.

sptrends 0.94.2

Vignettes

  • Improved the introductory vignettes.

sptrends 0.94.1

Documentation

  • Simplified the README introduction and revised all introductory vignettes to use the bundled NDVI series, including a complete temporal mosaic, interactive animation code and linked navigation.
  • Expanded the fdr_correction() example to show BH, BKY and BY explicitly, and listed additional CRAN packages used as external validation references.

sptrends 0.94

Package identity

  • Renamed the package subtitle to Statistical Inference for Spatiotemporal Trends in Gridded Data, reflecting a general inference framework without restricting every component to robust statistical methods.

sptrends 0.93.3

Quality assurance

  • Removed an invalid assumption about roxygen2’s internal placement of descriptive paragraphs from the documentation contract test.

sptrends 0.93.2

Quality assurance

  • Corrected the documentation contract test to inspect Function type within the parsed description instead of relying on internal Rd ordering.

sptrends 0.93.1

Documentation

  • Standardised Function type placement across the remaining documented helpers.

sptrends 0.93

Documentation

  • Rebuilt six concise introductory vignettes around a common teaching structure, integrating TST and RTA into the trend-workflows guide.

sptrends 0.92.2

Documentation

  • Completed the cross-references in four core help pages.

Quality assurance

  • Cleaned the remaining spelling, URL and style diagnostics.

sptrends 0.92.1

Documentation

  • Clarified that the default CMK region follows Neeti and Eastman (2011), as implemented in TerrSet’s Kendall module.

Quality assurance

  • Made the documentation-architecture test compatible across supported testthat versions.

sptrends 0.92

New features

  • Added configurable odd CMK neighbourhoods while retaining the 3 by 3 region described by Neeti and Eastman (2011), as implemented in TerrSet’s Kendall module, as the default.

sptrends 0.91.9

Documentation

  • Completed and regression-tested the common help-page architecture across the public API.

sptrends 0.91.8

Documentation

  • Standardised the detailed help across the remaining public functions, workflows and shared S3 methods without removing methodological content.

sptrends 0.91.7

Documentation

  • Standardised the detailed help for prewhitening, trend testing, slope estimation and FDR correction while preserving its methodological content.

sptrends 0.91.6

Documentation

  • Confirmed a clean local devtools::check() for 0.91.5 itself: 0 errors, 0 warnings, 0 notes.

sptrends 0.91.5

Documentation

  • Confirmed win-builder R-oldrelease also clean: 0 errors, 0 warnings, 1 (expected) note. All three win-builder platforms now confirmed clean.

sptrends 0.91.4

Documentation

  • Confirmed win-builder R-release also clean: 0 errors, 0 warnings, 1 (expected) note.

sptrends 0.91.3

Documentation

  • Confirmed the LaTeX/PDF manual fix against a fresh win-builder R-devel run: 0 errors, 0 warnings, 1 (expected) note.

sptrends 0.91.2

Bug fixes

  • Fixed a real win-builder R-devel error: a literal Unicode alpha character in fdr.R/workflow_trends.R broke PDF manual generation. Replaced with \eqn{\alpha}/plain text.

sptrends 0.91.1

Quality assurance

  • Covered local verbose, parallel-cleanup and Gi* printing branches.

sptrends 0.91

Quality assurance

  • Hardened documentation tests and completed a static release audit.

Documentation

  • Standardised spatial-correlation terminology and citation metadata.

sptrends 0.90.4

Quality assurance

  • Replaced formatting-sensitive help-text tests with API checks.

sptrends 0.90.3

Quality assurance

  • Restored the consecutive release history.

sptrends 0.90.2

Quality assurance

  • Made small-raster tests explicitly planar.

sptrends 0.90.1

Spatial autocorrelation

  • Corrected sparse-matrix row sums in local calculations.

sptrends 0.90

Spatial autocorrelation

  • Added permutation-based local Moran’s I and Getis-Ord Gi*.
  • Added local maps and FDR forwarding through fdr_correction().

sptrends 0.89.1

Documentation

  • Reorganised the introductory and workflow vignettes around loading, exploration, configurable analysis and the published TST/RTA workflows.
  • Presented all prewhitening, slope and FDR alternatives with clearer guidance on trend preservation, robustness, multiplicity and computational performance.
  • Standardised the pedagogical distinction between raw p-values, per-test α and target FDR q.

Quality assurance

  • Added documentation-contract tests and resolved the remaining source line-length findings.

sptrends 0.89

Simulation

  • Separated spatial scale (smooth_radius) from spatial intensity (spatial_rho) in sim_trend_stack(), preserving the established default output.

API

  • Exposed every compare_detections() metric in Usage while keeping FWER opt-in for replicated validation.
  • Added dependency-free elapsed-time messages to verbose analytical functions; workflow objects continue to retain per-stage timings.

Documentation

  • Added concise Typical use paths to every exported function and distinguished single-run from replicated benchmarking.
  • Clarified that the simulator supports controlled method evaluation, not calibrated environmental-process simulation.

sptrends 0.88.4

Quality assurance

  • Corrected the DCF structure of .lintr so lintr::lint_package() and the lintr stage of goodpractice::gp() can read the project configuration.

sptrends 0.88.3

API

  • Displayed every supported method in public function usage while preserving established defaults; workflow FDR arguments now validate BH, BKY and BY before computation.
  • Extended the default ordered-stack file pattern to common raster formats supported by terra, while retaining custom regular expressions for other GDAL-readable formats.

Documentation

  • Shortened the README to a general package overview and added Luis V. García’s ORCID to package metadata.
  • Distinguished local FDR control at q (BH, BKY and BY) from local FWER control at alpha (permutation maxT) in the reserved spatial-autocorrelation interface.
  • Documented OLS as fastest, repeated median as substantially slower, and Theil-Sen as the recommended general balance of robustness and computational cost.

Quality assurance

  • Excluded Windows shortcut files from source builds and added regression tests for API choices, metadata, raster-format defaults and global/local multiple-testing validation.

sptrends 0.88

API

  • Added an explicit global/local scope and scope-specific S3 hierarchy to spatial_autocorrelation(), preserving the global result while reserving a stable interface for independently validated local statistics.
  • Reserved local multiple-testing choices (none, BH, BKY, BY and permutation-based maxT); global analyses reject non-none adjustments because they contain only one test.

Documentation

  • Reframed spatial_autocorrelation() as a general spatial diagnostic for environmental variables, residuals, coefficients and inferential fields; FDR-assumption assessment is now presented only as one qualified application.
  • Documented that local Moran and Getis-Ord Gi* remain unavailable until their permutation inference and multiple-testing behaviour have been validated.

sptrends 0.87.2

API

  • Exposed configurable trend workflows through the single public interface workflow_trends(); the temporary pre-release alias and compatibility class were removed.

Bug fixes

  • Removed a hardcoded exact-version check from an unrelated ORCID test; it broke on every routine version bump.
  • Kept local quality-assurance logs out of source builds and made the FDR comparison-plot example use a minimal direct input.
  • Added targeted regression tests for empty FDR method sets, malformed or incompatible spatial neighbourhoods, and inconsistent configurable-workflow FDR objects; removed an unreachable OLS time-axis branch already enforced by the common validator.
  • Completed BY support in configurable-workflow printing, direction maps and slope-significance plots.
  • Defined the default CMK result for completely tied, zero-variance neighbourhoods as Z = 0, p = 1.
  • Precomputed spatial neighbourhoods now carry and validate raster geometry, connectivity and the valid-cell pattern before reuse, with type-compatible dimension checks.
  • Added consistent validation for cores, probabilities, seeds, pair limits, convergence controls and Durbin-Watson bounds.
  • Prevented stage argument lists from replacing workflow-managed inputs, methods, reporting or shared-cluster controls.
  • Preserved an initially absent global RNG state during internal Theil-Sen pair sampling and restored graphical parameters after null-distribution plots.
  • Restored the internal sequential fallback for n_cores <= 1 while retaining strict positive-integer validation in exported workflows.
  • Changed the optional Moran diagnostic from an automatic BH/BKY selector to a qualified assessment: positive association is compatible with BH, whereas other outcomes are inconclusive; BKY is no longer presented as a safeguard against arbitrary dependence.
  • Added a shared time-axis validator to reject mismatched, non-finite, duplicated or unordered dates before slope estimation, prewhitening, OLS or MMK.
  • Added explicit validation for FDR levels and p-value inputs, including empty and all-NA cases.
  • Added explicit validation for permutation counts, cores, seeds and precomputed spatial-neighbourhood dimensions.

Documentation

  • Documented that current analytical functions are vectorised and optionally parallel but operate in memory, rather than claiming out-of-core scalability.
  • Added inst/benchmarks/scalability.R for reproducible timing and memory-proxy measurements.
  • Corrected the documented number of prewhitening procedures.

sptrends 0.86

Bug fixes

  • Corrected CMK’s regional variance when ties = TRUE: each cell now contributes its own tie-corrected VarS, and every cross-covariance uses the corresponding pair of variances. The default no-ties calculation is unchanged.

Quality assurance

  • Added an analytical 3 x 3 RAMK regression test with heterogeneous tie patterns and independently calculated Sm, VarSm, and p.
  • Added legitimate spelling terms reported by spelling::spell_check_package() to inst/WORDLIST.
  • The final checks for this patched source are pending; results obtained for 0.85.10 before this correction are not carried forward.

sptrends 0.85

Documentation

  • Documented the substantially faster CMK execution observed against TerrSet on the same validation raster, without presenting the platform-dependent result as a universal benchmark.
  • Updated documentation for slope estimators, FDR methods and prewhitening methods.
  • Updated vignettes, navigation, author metadata and spelling exceptions.

sptrends 0.84

Documentation

  • Added reproducible ConMK and TerrSet validation materials under inst/validation/.
  • Documented CMK’s continuity convention and the limits of the TerrSet comparison.
  • Added an optional rkt comparison for independent validation of CMK’s regional score aggregation.

sptrends 0.83

New features

  • Added continuity to CMK: FALSE follows the published equations; TRUE provides compatibility with ConMK’s convention.

Documentation

  • Documented CMK as the moving-window raster form of analytical RAMK, including their shared cross-correlation correction.
  • Clarified that prewhitening is an upstream operation, not part of the CMK statistic itself.
  • Added method-specific quality-assurance sections across the principal trend workflow functions.

sptrends 0.82

Bug fixes

  • Corrected VCTFPW to use the published variance-ratio correction and 95% lag-1-autocorrelation gate. Cells below the gate remain unchanged, the first time step is retained, and a Modified diagnostic is returned.
  • Updated VCTFPW workflow reporting to show the number and percentage of modified cells.
  • Masked complete VCTFPW series when their rescaling factor is invalid.

sptrends 0.81

Bug fixes

  • Corrected repeated-median inspection and slope-comparison intercepts.
  • Returned the repeated-median intercept as a SpatRaster.
  • Corrected the repeated-median intercept calculation.

sptrends 0.80

New features

Breaking changes

  • inspect_ts_cell() no longer draws a shaded confidence band; the interval is now text-only in the legend.

sptrends 0.79

New features

Bug fixes

sptrends 0.78

New features

  • Added workflow_trends() for user-defined analytical workflows.
  • Added a dedicated vignette for configurable trend workflows.

sptrends 0.77

New features

Bug fixes

  • Added BY support to workflow printing and plotting.

sptrends 0.76

New features

Bug fixes

  • Handled non-positive MMK variance-correction factors.

sptrends 0.75

New features

Bug fixes

  • Corrected AR(1) estimation in prewhiten(method = "TFPW_WS").

sptrends 0.74

Breaking changes

  • Removed prewhiten(method = "PW").

Bug fixes

  • Corrected method citations, links and Moran’s-I guidance.

sptrends 0.73

Breaking changes

  • Changed all method identifiers to uppercase.

New features

  • Standardised package-wide method values to uppercase.

sptrends 0.72

Bug fixes

  • Removed publisher url fields from inst/CITATION/CITATION.cff, keeping only doi. Both publisher URLs returned 403 to CRAN’s own automated checker, a known behaviour toward bots, not a dead link.
  • Fixed a test using expect_s4_class() on an S3 object.
  • Closed the package’s last remaining zero-coverage line (a cluster-sharing seed-handling branch).
  • Investigated a suspected missing \donttest{} wrap; confirmed a false alarm (an earlier grep had missed the closing brace).

sptrends 0.71.0

New features

  • Shared spatial-adjacency caching between trend_test() and spatial_autocorrelation(). Both previously recomputed the identical structure independently; now computed once and reusable via a new precomputed_neighbourhood argument.
  • workflow_tst()/workflow_rta() gain a shared n_cores, reusing one cluster across their own internal parallel steps instead of building and tearing down a separate one for each.

sptrends 0.70

New features

  • compare_detections() gains "fwer" (family-wise error rate) as a requestable metric, only meaningful with replicates = TRUE.

sptrends 0.69.0

Bug fixes

  • Fixed summary.compare_detections()/..._replicates() picking the wrong “best” method for FPR/FDR: both used which.max() unconditionally, but lower is better for these two error-rate metrics.

Documentation

  • Clarified the distinction between FDR (a single run’s realised proportion) and FDR_mean (the actual rate estimate, averaged across replicates), and added the Benjamini & Hochberg (1995) reference to compare_detections()’s own citation list.

sptrends 0.68

New features

  • Added method = "ols" to trend_test(). Provides the classical parametric alternative to CMK/MK, verified against stats::lm().

sptrends 0.67

New features

sptrends 0.66

New features

  • Added a dedicated slope-estimation vignette.

sptrends 0.65

Breaking changes

  • Renamed trend_test()’s and slope_estimator()’s own returned S3 classes ("cmk" to "trend_test", "theil" to "slope"). Reflects that both functions now cover more than one method each.

sptrends 0.64

API changes

  • Renamed fdr_bky()’s variant argument to implementation, and its "definition6" value to "original". The old names did not say what they were a variant/implementation of.

sptrends 0.63

API changes

sptrends 0.62

API changes

  • Renamed 7 internal reporting functions and 5 source files (e.g. contextual_mk.R to trend_test.R, theilsen.R to slope_estimator.R) to match the generic, multi-method scope their own functions and classes already had after the renames above.

sptrends 0.61

Bug fixes

  • Fixed a real bug affecting every diverging map the package draws: fill_range = TRUE was missing from 5 terra::plot() calls, so the highest-magnitude cells rendered blank instead of strongly coloured.

sptrends 0.60

Bug fixes

  • Fixed workflow_tst()/workflow_rta()’s own progress messages always saying “Contextual Mann-Kendall” regardless of the actual method used.

sptrends 0.59

Bug fixes

  • Fixed inconsistent citation formatting (author name, DOI, title) for one paper cited from three separate files.

sptrends 0.58

Bug fixes

  • Closed all remaining test-coverage gaps found by covr, including 4 regressions introduced by adding method = "ols"; the package reached 100% coverage except one line-group left deliberately untested (unreachable without unsafely mocking a base R function).

sptrends 0.57

Documentation

sptrends 0.56

Documentation

  • Corrected trend_test()’s own title (still describing only two of its three methods) and added a missing citation (Douglas, Vogel & Kroll, 2000) for the RAMK connection behind CMK’s own variance correction.
  • Audited the whole package for vignettes/docs describing only one method where more than one now exists; added missing coverage in three vignettes and ?sptrends’s own overview.
  • Finalised the diverging-colour convention (navy, not cyan, for “significant”) across all affected plots.

sptrends 0.55.9

Bug fixes

  • Fixed 2 real R CMD check NOTEs from CITATION.cff living at the package root: excluded it via .Rbuildignore (it is meant for GitHub/Zenodo, not R’s own citation() mechanism, and does not need to be part of the built package).
  • Wrapped compute_anomalies()’s own example in \donttest{} (6.17s, over the 5-second threshold).

sptrends 0.55.8

Documentation

  • Added CITATION.cff at the package root, with both authors, both published references, and the licence.

Bug fixes

  • Fixed inst/CITATION still referring to the old tst()/rta() function names after they were renamed.

sptrends 0.55.7

New features

  • Added verbose = TRUE messaging to inspect_ts_cell(), matching every other function’s own convention.
  • Folded summarise_replicates() into compare_detections()’s own replicates = TRUE argument. One function instead of two for the same task.
  • tst() and rta() renamed to workflow_tst() and workflow_rta(). Clarifies these are complete, opinionated workflows, not the only way to run each analytical step.
  • trend_test(), slope_estimator(), and prewhiten() now fail fast with an informative error on invalid input shapes, instead of a cryptic error partway through computation.
  • spatial_autocorrelation() now errors informatively on two previously-confusing invalid input cases.
  • Established a consistent visual identity (colours, logo, hex sticker) across the package, README, and pkgdown site.

Bug fixes

  • Fixed two real bugs in sim_trend_stack(), including a division-by-zero, found by new edge-case tests written for it, trend_test(), and slope_estimator().
  • Fixed a wrong DOI, caught by devtools::check(remote = TRUE).
  • Fixed a real R CMD check WARNING and a separate ERROR, both in compute_anomalies()’s own documentation.
  • Fixed 2 real test failures and a bug from the previous release’s verbose = addition, found running test-external-validation.R (a new suite comparing sptrends’ own core statistics against independent reference implementations).
  • Removed a broken test added in the previous release, and fixed a broken @examples block and a malformed @section title.
  • Fixed a visible numbering gap in the vignette titles, and used the wrong logo file from the previous release.

Documentation

  • Package title changed to remove “for”, and DESCRIPTION’s own description no longer repeats the package name.
  • Added a runnable simulated-data example alongside the existing real-data one for 5 core functions, and wrapped several long-running examples in \donttest{}.
  • New conceptual pipeline figure and a revised 5-step workflow diagram (from 6).
  • New vignette covering the full workflow end-to-end, filling a real content gap; a separate RTA-only vignette folded into it.
  • Reviewed the package in full against goodpractice::gp() and lintr::lint_package(); addressed genuine findings.

Internal changes

  • A large NEWS.md formatting inconsistency found and corrected across many earlier entries.
  • Established a consistent brand colour palette, replacing an approximate logo blue used in the previous release.
  • Closed several coverage gaps identified individually via covr::zero_coverage(), and removed a small amount of dead code in prewhiten.R found during that same review.
  • 15 compound-semicolon statements split into separate lines for readability.

sptrends 0.54

Internal changes

  • Minor internal maintenance and test upkeep.

sptrends 0.53

Internal changes

  • Minor internal maintenance and test upkeep.

sptrends 0.52

Bug fixes

  • Fixed 4 real test failures (in test code, not package behaviour): incorrect terra::values() matrix-mode usage in two tests, a genuine bug in a hand-computed Theil-Sen reference implementation, and a named-vs-unnamed value mismatch in expect_equal().

sptrends 0.51

Bug fixes

  • Fixed, while completing a rename, a genuinely broken previous state: the earlier moran_permutation_test() to spatial_autocorrelation() rename had been left half-done – neither the old nor the new name was actually callable from outside the package, and fdr_correction()’s own moran_check = TRUE silently called the missing old name internally. Fixed throughout.

sptrends 0.50.0

New features

  • moran_permutation_test() generalised into spatial_autocorrelation(), gaining a second method (method = "getis_ord", global Getis-Ord General G) alongside the existing Moran’s I. Follows the same method = pattern already used elsewhere in the package; verified numerically against the direct definition before being added. Returned field names changed to be generic ($statistic/ $null_dist, were $I/$I_null) – breaking change for code reading the old field names.

sptrends 0.49.0

New features

  • sim_trend_stack() gains structural-break simulation (break_type = "mean"/"slope"), composing independently from the existing monotonic-trend simulation, with its own ground truth (true_break/break_time) for validating a future change-point method – none is implemented yet.
  • inspect_ts_cell() gains slope_method = "ols", matching slope_estimator()’s own second method; the confidence band’s “bowtie” shape was checked and confirmed correct (standard linear-trend theory), not a bug.
  • slope_estimator() gains method = "ols", a fast closed-form alternative to the default Theil-Sen, not a replacement for it (not robust to outliers the way Theil-Sen is).
  • prewhiten() gains method = "yue_pilon" (trend-free prewhitening) alongside the default wang_swail. Loses one time step (classic lag-1 differencing) and has a different diagnostics structure. Fixed three real integration bugs found while adding it – print()/summary()/plot(), tst()’s own print(), and inspect_ts_cell() all hard-assumed the other method’s own structure and would have errored on a yue_pilon result.

Improvements

  • read_ordered_stack() now stores detected years as real terra::time() metadata; inspect_ts_cell()’s x-axis uses them automatically. Found and fixed a related bug while doing this: the prewhitened panel misaligned t by one step for yue_pilon’s own shorter output, silently, with no visible symptom.
  • Fixed 3 real test failures from the previous release’s rename, missed because the old parameter name was passed through a forwarding argument list rather than called directly.

Bug fixes

  • Fixed a critical bug: terra::values(x, mat = FALSE)[, 1] errors on a single-layer raster (already a flat vector, not a matrix) – affected prewhiten(method = "yue_pilon") entirely (every call errored) and two "ols" tests.

Internal changes

  • direction_map() made internal – the FDR-corrected and uncorrected direction are the same computation with an optional filter, not two things needing separate public entry points. Breaking: no longer exported; use plot(x, which = "direction") instead.

sptrends 0.48

Internal changes

  • Reviewed a goodpractice::gp() report; one genuine fix (a missing add = TRUE on an on.exit() call), the rest confirmed as tool limitations.

sptrends 0.47.0

Internal changes

  • API redesign stage 1: contextual_mann_kendall(), theil_sen_slope(), and wang_swail_prewhiten() renamed to trend_test(), slope_estimator(), and prewhiten(), each gaining a method = argument ahead of a planned second method per function. Breaking: update any direct calls to the old names, and neighbourhood = TRUE/FALSE to method = "cmk"/"mk". Fixed a real naming collision caught during the rename (tst()’s own prewhiten flag argument shadowed the new function of the same name).

sptrends 0.46.1

Internal changes

  • Closed one more coverage gap; remaining read_stack.R gaps confirmed as unreachable defensive branches or an ncdf4-only test.

sptrends 0.46.0

New features

  • plot() on "tst"/"rta" results gains 8 new which views (slope_map/slope_direction/slope_hist/slope_bar, pvalue_map/pvalue_significance/pvalue_hist/pvalue_bar), all uncorrected diagnostics, not a final result. Considered and rejected a bigger redesign (separate generics) first, since it would not generalise cleanly across every classed object type this package returns.

sptrends 0.45.1

Improvements

  • workflow_summary()/summary(x, which = "workflow"), added in the same release, removed again immediately on reflection – it competed with summary()’s own simpler default rather than sitting alongside it. No replacement; x$timing has the same data.
  • inspect_ts_cell() gains show_neighbours: a small-multiples grid of each aggregated neighbour cell’s own fit, drawn in a separate window, answering whether the clicked cell’s trend is representative of its neighbourhood.

Internal changes

  • Closed several coverage gaps found via covr::zero_coverage(); documented two read_stack.R branches as genuinely unreachable rather than chased with contrived tests.
  • method_citation() removed entirely – redundant with each function’s own @references; fixed a real bug this surfaced along the way (duplicated, driftable citation text in workflow_summary()). No replacement; see each function’s own help page.
  • classify_moran() folded into print()/summary() of a "moran" object; no longer exported separately.

sptrends 0.44.0

New features

  • workflow_summary() folded into summary(x, which = "workflow") for tst()/rta() results (later removed again in 0.45.1).

Internal changes

  • fdr_direction_map() renamed to direction_map() and moved out of fdr.R into its own file – it isn’t itself an FDR method, it combines a trend test’s direction with an FDR result. Breaking: rename any direct calls.
  • prepare_cmk_neighbourhood() no longer exported – a real, acknowledged capability loss for batch-processing many rasters sharing one grid geometry (no longer precomputable without :::).
  • classify_moran() no longer exported; its category now shown automatically in print()/summary() of a "moran" object.
  • Exported function count: 23 to 20.

Documentation

sptrends 0.43.1

Bug fixes

  • Fixed a real test failure: test-sptrends-methods.R checked S3 methods via getNamespaceExports(), which never reflects S3 methods registered the standard way – fixed to use getS3method(), the actually-correct check.

sptrends 0.43.0

Improvements

  • print.sptrends()/summary.sptrends()/plot.sptrends() now dispatch by naming convention (.print_<class>() lookup) instead of a hardcoded switch() – adding a future class no longer requires editing all three shared generics.
  • API redesign: 18 separate print()/summary()/plot() methods (one per class) consolidated into the 3 shared generics above, mirroring terra’s own single-entry-point convention. Breaking: code calling one of the 18 old method names directly (not via generic dispatch) breaks; ordinary print(x)/summary(x)/plot(x) usage is unaffected. Exported function count: 43 to 28.

Documentation

sptrends 0.42.1

Bug fixes

  • Fixed 2 real R CMD check example errors: 15 internal functions called themselves by bare name in their own @examples, invisible in devtools::test() but not under R CMD check’s external-user context. Prefixed with sptrends:::.

sptrends 0.42.0

Improvements

  • API redesign stages 4-5 of 5: 15 standalone reporting functions (trend_maps(), fdr_summary(), and others) no longer exported – fully covered by the print()/summary()/plot() methods added in earlier stages. Breaking: switch to the equivalent S3 method (see each function’s own docs for the exact mapping). Exported function count: 58 to 43.

sptrends 0.41.1

Bug fixes

  • Fixed 4 real test failures missed in the previous stage’s own verification: a second test file also passed a classed result directly where the raw statistics raster was expected.

sptrends 0.41.0

Improvements

  • API redesign stage 3 of 5: contextual_mann_kendall() now returns a classed object (list(stats = <raster>, neighbourhood = <logical>)) instead of a bare raster, with its own print()/summary()/plot(). Breaking: update trend$p to trend$stats$p.

sptrends 0.40.0

Improvements

  • API redesign stages 1-2 of 5: wang_swail_prewhiten(), fdr_correction(), and theil_sen_slope() now return classed objects with their own print()/summary()/plot(), matching tst()/rta()’s own pattern. theil_sen_slope()’s own change is breaking (was a bare raster, now list(slope = ..., smoothed = ...)). A deliberate 5-stage redesign, done before the associated papers are published rather than after.

sptrends 0.39.2

Documentation

  • R/ and all vignettes brought under the 80-character line-length limit (59 lines fixed), verified line by line, not just visually diffed – caught a real sprintf() mistake introduced during the cleanup itself before it reached the codebase. Test files deliberately left alone (developer-facing only, high volume).

sptrends 0.39.1

Internal changes

  • goodpractice::gp() cleanup, low-risk items only: stop(paste0()) replaced with stop()’s own concatenation, fixed = TRUE added to plain-string grepl() calls, several test assertions replaced with more specific equivalents, one real broken URL fixed in README.md.

sptrends 0.39.0

New features

  • New “Preprocessing” pkgdown category, separating wang_swail_prewhiten()/compute_anomalies() from “Core”/“Support” – documentation/organisation only, no behavioural change.

Improvements

  • Breaking: tst() no longer smooths its Theil-Sen slope by default, matching rta()’s own default and removing an unprincipled asymmetry (neither published method includes this smoothing). Pass theil_sen_args = list(smooth_neighbourhood = TRUE) to keep the old behaviour.

Bug fixes

  • Fixed a real, visually misleading bug found by inspecting an actual plot: queen-3x3 smoothing (smooth_neighbourhood = TRUE, and both plot(which = "slope") methods) used terra::focal()’s own default na.policy = "all", letting a non-significant or no-data cell get painted with a neighbour’s colour/value. Fixed to "omit" in all three call sites, factored into one shared helper.

Documentation

  • Fixed 13 occurrences of a stale “one of the five pillars” phrase across 9 files, now inaccurate after prewhitening’s own reclassification.

sptrends 0.38.1

Bug fixes

  • Fixed a test-suite bug: expect_s3_class() does not accept an info argument (unlike expect_error()); removed it from two new sweep tests.

sptrends 0.38.0

Improvements

  • rta() gained summary.rta()/plot.rta(), closing an asymmetry with tst().
  • Added two systematic combinatorial sweep tests (tst() across 12 argument combinations, rta() across 4).

Internal changes

  • Closed remaining coverage gaps found via covr::zero_coverage() across several reporting functions.

sptrends 0.37.2

Internal changes

sptrends 0.37.1

Improvements

  • Fixed non-ASCII characters in R/method_citation.R’s own string literals (accented names), caught by R CMD check’s portability check – replaced with Unicode escapes.

Bug fixes

  • Fixed a real bug: tst()/rta() called trend_summary() a second, unconditional time with no way to suppress its own printed output, so report = FALSE never achieved full silence and report = TRUE printed the summary twice. Added verbose = to trend_summary().

sptrends 0.37.0

No new statistical methodology in this release – architecture, API and documentation work only.

New features

  • tst()/rta() now record per-step timing in a new $timing list.
  • New workflow_summary(): a Step/Method/Reference/Time table for a tst()/rta() result (later folded into summary(), then removed – see later entries).
  • New method_citation(): looks up a citation by short method name (later removed as redundant – see 0.45.1).
  • New theil_sen_summary()/theil_sen_map(), and theil_sen_slope() gained report = TRUE, closing the one core function still missing companion reporting functions. Found and fixed a real bug while wiring this in: inspect_ts_cell()’s own internal call did not set report = FALSE, so every call would have started auto-printing a spurious one-cell summary/map.

Improvements

  • Added a “Methodological background” section to the top of each core method’s documentation, for a scannable orientation before the argument-level detail.
  • moran_permutation_test() gained report = TRUE (closing the one remaining function requiring a separate manual call to see any report) and proper match.arg() validation on connectivity (previously failed silently deep inside terra::adjacent() on a typo).
  • prewhiten_summary() now prints an informative narrative summary, matching the other *_summary() functions.

Internal changes

  • tst()/rta() results gain a shared "sptrends" superclass, non-breaking, for future common methods to dispatch on.

Documentation

  • Reorganised the pkgdown reference index into four blocks by user intent (“Published workflows”, “Core methods”, “Diagnostics”, “Utilities”) rather than internal function type.
  • inspect_ts_cell() added to README.md for the first time.
  • Rebalanced TST/RTA presentation further, per explicit feedback that an earlier pass still read as TST-first: rewrote the README opening, diagram, and citation section to present both as equal, parallel workflows; rewrote rta()’s own documentation to mirror tst()’s in full; added a new vignette walking through the complete RTA workflow, closing the one remaining asymmetry.

sptrends 0.36.1

New features

  • Documentation review following rta()’s introduction: ?sptrends, README.md, inst/CITATION, and four vignettes updated to present TST and RTA as two workflows, not TST alone (rta() had been missing from several places despite already being complete and tested). theil_sen_slope()/fdr_bh() gained a “used by” note that both are shared infrastructure, not TST-specific.

sptrends 0.36.0

Improvements

  • Completed tst()’s and rta()’s own @references: both previously cited only their own workflow paper, not the individual published methods (Wang & Swail, Neeti & Eastman, Theil, Sen, Benjamini and co-authors) each step builds on.

Bug fixes

  • Fixed a real, visually misleading bug: inspect_ts_cell()’s confidence band was anchored at t = 0 (typically outside the observed range), widening in only one direction instead of the standard symmetric “bowtie” shape. Anchored at the centre of the observed range instead.

sptrends 0.35.0

New features

  • New function rta(): a second, complete, published workflow (Robust Trend Analysis, Gutiérrez-Hernández & García 2024) alongside tst(), not replacing it – Theil-Sen, Contextual Mann-Kendall, and standard FDR-BH (not adaptive BKY), deliberately without prewhitening. Both differences documented at length rather than left implicit, since prewhitening’s own value before a Mann-Kendall test is a genuine, unresolved debate in the published literature (cited both sides). No Moran’s I step and no categorical slope classes, unlike the original published RTA method – kept consistent with how this package treats magnitude and diagnostics elsewhere. New print.rta(). Fixed an inaccurate existing cross-reference: tst()’s own docs had listed the RTA paper as “the same workflow”, no longer true now that RTA is separately implemented.
  • Added a mosaic view and an optional year-by-year animation to the getting-started vignette’s data-loading section.

Bug fixes

  • Fixed a real test-suite bug: a shared test helper lived inside one test file, invisible to another that sorts earlier alphabetically. Moved to a helper-sptrends.R, always sourced first.

sptrends 0.34.0

New features

  • Redesigned inspect_ts_cell(): a single neighbourhood argument (default TRUE) replaces always overlaying two Theil-Sen lines. All aggregation modes now take the per-time-step median of raw values first, then fit one Theil-Sen slope to that aggregated series – deliberately different from the previous “estimate per cell, then median the slopes” order, since only the “aggregate first” order has a standard confidence-interval formula. As a consequence, inspect_ts_cell(neighbourhood = TRUE) no longer numerically matches theil_sen_slope(..., smooth_neighbourhood = TRUE) at the same cell – documented as a genuine, intended difference.
  • A confidence interval is now always shown, using the standard Sen/Gilbert rank-based method; not offered for the old “median-of-slopes” mechanism, since no standard formula exists for it.

Improvements

  • inspect_ts_cell() gained an optional prewhitened argument, drawing a second panel using wang_swail_prewhiten()’s own output side by side with the raw one. Internally refactored into small, reusable helpers shared by both panels.
  • Completed inspect_ts_cell()’s own references, and found and fixed a real gap while doing so: contextual_mann_kendall() itself had never explicitly cited Mann (1945)/Kendall (1975), the foundational statistic its own S/VarS computation rests on.

sptrends 0.33.0

New features

  • New function inspect_ts_cell(): interactive click-to-inspect time series viewer, overlaying the clicked cell’s own Theil-Sen fit against one that borrows its queen neighbourhood – whether the two agree is itself the diagnostic. Split into a public interactive wrapper and an internal, fully testable core (the interactive part cannot be exercised by automated tests). Verified by direct comparison to match theil_sen_slope()’s own output exactly for the same cell.

sptrends 0.32.0

Improvements

  • Replaced the bundled example dataset: annual mean temperature (CRU TS) out, annual mean NDVI (NOAA STAR Blended-VHP, 1982-2023) in – vegetation greening/browning is the motivating application of the TST method itself, so the bundled example now matches the package’s own subject matter. Updated everywhere the old dataset was referenced.

sptrends 0.31.0

Improvements

  • Covered the n_cores-capping message safely for R CMD check, by mocking parallel::detectCores() rather than actually requesting more cores than the machine has.

sptrends 0.30.1

Improvements

  • Simplified plot.tst(which = "slope")’s map title, dropping smoothing/neighbourhood wording from the displayed label.

Internal changes

  • Final coverage pass after a large refactor, closing several gaps identified by exact covr::zero_coverage() line numbers; confirmed (not forced) that the n_cores-capping message and two read_stack.R lines remain deliberately/structurally unreachable.

sptrends 0.30.0

Internal changes

  • Finished the line-length (>80 char) cleanup started in 0.29.1; from 235 offending lines across 14 files down to 35 legitimate exceptions (a few-character string overruns, published reference tables, the package’s own title).

sptrends 0.29.1

Internal changes

  • Started a line-length (>80 char) cleanup across the codebase.

sptrends 0.29.0

New features

  • New variant argument for fdr_bky() ("multtest"/"definition6", two distinct published implementations of the same BKY procedure), forwarded through fdr_correction()/tst(). Confirmed "multtest"’s threshold is never stricter than "definition6"’s.

sptrends 0.28.0

Improvements

  • Simplified d-fdr-correction’s narrative: Moran’s I check reframed as an optional diagnostic, not part of the main flow; now shows both FDR-BH and FDR-BKY direction maps side by side.

Documentation

  • Changed the FDR-corrected significance colour from royal blue to navy, and the general diverging palette from “RdBu” to “Blue-Red 3” (both grDevices::hcl.colors()), across every function and vignette using it. Uncorrected significance stayed red deliberately, to reinforce it is diagnostic-only.
  • tst()’s own examples now also show plot(which = "significance"/ "slope"), not only the default view.

sptrends 0.27.1

Improvements

  • Fixed a test comparing raster values directly: the manually-built comparison object had a different auto-generated layer name, failing expect_equal() on the name alone, not the values. Fixed with unname().

sptrends 0.27.0

Documentation

  • Restructured the vignette narrative into 5 steps: the getting-started vignette is now a true “hello world” (load and visualise only); the full TST demonstration moved into its own new vignette, after prewhitening/trend-test/FDR are each covered alone.

sptrends 0.26.1

Internal changes

  • Fixed 3 real issues surfaced by devtools::check(): 7 tests used bare values() instead of terra::values(); a real portability bug in moran_null_plot() (Unicode arrow characters failing to convert on some locales, replaced with plain ASCII); and a max()-with-no-arguments warning in two all-NA guards, suppressed.

sptrends 0.26.0

New features

  • New plot.tst(which = "slope") view: the Theil-Sen slope, masked to FDR-significant cells, smoothed by default at plot time only. Motivated by real data: comparing CMK’s neighbourhood-averaged statistic sign against Theil-Sen’s own sign on the bundled dataset showed 338 disagreeing cells, always pulled towards the locally dominant trend – this view deliberately uses Theil-Sen’s own sign.
  • New smooth_neighbourhood argument for theil_sen_slope() (default FALSE): queen-3x3 median smoothing of the estimated slope, with an explicit caveat that – unlike CMK’s own published, validated method – this has no equivalent literature backing, since blending neighbouring cells’ magnitudes assumes they share a similar true slope, which does not always hold.

Improvements

  • tst()’s own Theil-Sen step now smooths by default, a deliberate methodological choice despite the caveats above; calling theil_sen_slope() directly is unaffected. Override via theil_sen_args = list(smooth_neighbourhood = FALSE).
  • Changed the package title to emphasise formal statistical inference as the actual differentiator.

Bug fixes

  • Fixed a real, potentially misleading plotting bug: trend_maps()/ prewhiten_maps() did not fix their diverging colour range symmetrically around zero, visually misrepresenting the sign boundary whenever positive and negative values were not equally extreme.

Documentation

  • Added a “Roadmap” section to README.md.

sptrends 0.25.0

Internal changes

  • Final targeted coverage pass across the whole package (46 lines), using exact covr::zero_coverage() results. The single biggest recurring pattern: the path = (write-to-disk) argument had never been tested for most reporting functions – added across 10 of them. Closed several other real per-function gaps. Deliberately left uncovered: the n_cores-capping message and two structurally unreachable read_stack.R checks.

sptrends 0.24.0

Internal changes

  • Used exact covr::zero_coverage() line numbers to close genuine gaps in prewhiten.R (Durbin-Watson out-of-range messages, several verbose branches, path = untested for two reporting functions) and read_stack.R (read_netcdf_stack()’s own messages, never exercised since every existing test used verbose = FALSE). Noted, not forced: two checks appear structurally unreachable given existing upstream guards.

sptrends 0.23.1

Improvements

  • Fixed a test based on a misreading of wang_swail_prewhiten()’s own code: the clamp only catches rho at or beyond exactly +-1, not a general cap at 0.99 – a legitimate 0.995-ish estimate correctly failed the test’s own wrong assertion. Rewritten to check abs(rho) < 1, what the code actually guarantees.

sptrends 0.23.0

Internal changes

  • More coverage for the remaining ~86%-covered files (tst-methods.R, read_stack.R, prewhiten.R); flagged one added test’s own assertion as weak, honestly, since execution could not confirm it actually drove the estimate past the clamping boundary.
  • More coverage for fdr.R (worst-covered file at 84.65%): out-of- range input error, multi-layer input message, full report = TRUE branch, Moran’s I recommendation message, CSV-writing path.

sptrends 0.22.1

Bug fixes

  • Fixed a real bug in the parallel chunk-splitting logic of theil_sen_slope()/contextual_mann_kendall(): cut() errors with only a single item to split, which happens at exactly one valid cell or two time layers. Fixed by switching to parallel::splitIndices().

sptrends 0.22.0

Internal changes

  • Further coverage for theilsen.R/contextual_mk.R: verbose messages previously executed but never asserted, and n_cores exceeding the number of valid cells without erroring.
  • Found and fixed why utils-internal.R’s coverage was stuck at 58.5%: covr::package_coverage() does not set NOT_CRAN, so every skip_on_cran()-guarded test was silently skipped during coverage measurement. Nearly every parallel test used n_cores of 1-2 (already CRAN-compliant), so the guard was unnecessary caution – removed from all 9 affected tests.

sptrends 0.21.1

New features

  • Fixed another type-mismatch test failure: stats::median() of an odd-length integer vector returns an integer, not a double, unlike the even-length case.

sptrends 0.21.0

Internal changes

  • Continued the coverage sweep: contextual_mk.R’s full report = TRUE branch (previously only its own constituent functions were tested in isolation); theilsen.R’s subsampling branch (n*(n-1)/2 > max_pairs), previously completely untested; utils-internal.R’s remaining parallel-lapply arguments (seed, packages); read_stack.R’s NetCDF error path and diagnostic plot path.

sptrends 0.20.1

Improvements

  • Removed a test requesting more cores than available to verify a capping message: R CMD check enforces its own separate hard limit on parallel workers, so the test errored before the function’s own logic ever ran.

sptrends 0.20.0

Internal changes

  • Continued the coverage sweep on the worst-covered files: utils-internal.R (31.7%, every internal helper tested directly), pipeline.R/tst() (71.8%, the flagship function, largely untouched by earlier rounds), theilsen.R (76.1%, including a hand-worked exact reference value, not just a sanity check).

sptrends 0.19.1

Bug fixes

  • Fixed 13 test failures from the previous round’s new tests: several genuine type mismatches (terra::values() on a single layer returns a vector not a matrix; terra::nlyr() returns a double, not integer), two malformed test fixtures (a file-name collision, an NetCDF write missing overwrite = TRUE), and one over-strict expect_silent() where warnings are legitimately expected.

sptrends 0.19.0

Internal changes

  • Added substantial test suites for the three remaining lowest-coverage core files: prewhiten.R (gating behaviour, dw_method, error conditions), fdr.R (raster input, all reporting functions), and contextual_mk.R (hand-worked exact S/variance values, isolated- cell fallback, connectivity comparison).
  • Added a test suite for read_ordered_stack() (previously zero tests, unlike read_netcdf_stack()), plus further NetCDF tests guarded by skip_if_not_installed("ncdf4").
  • Added a substantial test suite for moran.R (previously 40.8% coverage): hand-worked exact Moran’s I values under both connectivity types on a checkerboard pattern, confirming they genuinely differ and are each individually correct.

sptrends 0.18.1

Internal changes

  • Fixed a leftover unname() omission in two tests comparing an extracted raster value against a literal number.

sptrends 0.18.0

Internal changes

  • Added a full test suite for compute_anomalies() (previously 0% coverage), verified against hand-worked expected values, not just “does it run”.

sptrends 0.17.1

Bug fixes

  • Fixed a real bug from the previous round’s testthat idiom cleanup: terra::SpatRaster is S4, not S3 – 4 expect_s3_class() calls fixed to expect_s4_class().

sptrends 0.17.0

Internal changes

  • Addressed goodpractice::gp()’s findings: defensive on.exit(add = TRUE) fixes, removed placeholder URL/BugReports fields pointing to a repository that doesn’t exist yet, fixed a real NA-safety bug introduced while flattening a nested ifelse() in fdr_direction_map(), several idiomatic cleanups (anyDuplicated(), inverted negated conditions), and confirmed two flagged findings as false positives.
  • Added goodpractice and lintr to Suggests, formalising the package’s quality-evaluation toolkit.

sptrends 0.16.0

Improvements

  • Clarified alpha’s own multi-value documentation: 0.05 is the conventional standard actually used for the map/reference message, 0.1/0.01 shown alongside for context, not as interchangeable defaults.

Bug fixes

  • Fixed a real bug affecting default output throughout the package: with the default alpha = c(0.1, 0.05, 0.01), reporting functions used min(alpha) = 0.01 (the strictest) instead of the conventional 0.05, silently under-reporting significance in every default run. Fixed via a new .reference_alpha() helper.

Internal changes

  • Added covr to Suggests, formalising test coverage as a quality standard.

Documentation

  • Pedagogical sweep: every @examples block across the package now has at least one explanatory comment, verified programmatically.

sptrends 0.15.0

Internal changes

  • Renamed sptrends_example() to example_data() (inconsistent prefix), and two identifiers to British spelling (summarise_replicates(), standardise) – done now, before the package reaches CRAN.

Documentation

  • Made several functions’ and vignettes’ examples more pedagogical, and switched to the bundled real dataset where a synthetic one was less intuitive.
  • Final exhaustive British-English sweep across the whole package; confirmed clean beyond the two renames above and identifiers that must keep American spelling (not ours to rename).

sptrends 0.14.0

Documentation

  • tst()’s own examples and all four vignettes switched to the bundled real temperature dataset instead of sim_trend_stack(), a more recognisable example for the package’s flagship function and walkthroughs specifically.

sptrends 0.13.1

Improvements

  • Fixed a stale test asserting "accuracy" should error, left over from before Accuracy became a valid metric.

sptrends 0.13.0

New features

  • New bundled real-world example dataset (annual mean temperature, CRU TS v4.10, 1976-2025) and new function example_data() to access it, doubling as a realistic read_ordered_stack() example.

Improvements

  • compare_detections() gained Accuracy and MCC (Matthews correlation coefficient, generally preferred under class imbalance) as two more metrics, both included by default.

Internal changes

Documentation

sptrends 0.12.0

New features

  • New functions summarise_replicates() and plot_detection_comparison(), completing the validation toolkit.
  • New function compare_detections(): a confusion-matrix comparison of one or more trend-detection results against a known ground truth, deliberately agnostic to where either side comes from.

Improvements

  • sim_trend_stack() gained noise_dist = "gaussian"/"t", generating heavy-tailed noise – the condition under which rank-based methods’ robustness argument over a parametric one like OLS actually shows up.

Bug fixes

  • Fixed a real bug in sim_trend_stack()’s own trend-assignment logic: sign flips were applied cell-by-cell at random (“salt-and-pepper”), silently defeating CMK’s whole rationale (borrowing strength from a plausibly-trending neighbourhood). Switched to coarse, spatially contiguous blocks.
  • Fixed a real documentation bug: an internal helper had ended up inside sim_trend_stack()’s own roxygen block, documenting the wrong function as exported.

sptrends 0.11.0

Documentation

  • Fixed the package logo’s background: solid white instead of transparent, showing a visible rectangle on any non-white background.

sptrends 0.10.0

New features

  • sim_trend_stack() gained noise_sd, trend_fraction (proportion of cells keeping a non-zero true slope; 0 gives a complete null field for false-positive-rate checks), and trend_shape (“radial”/“gradient”/“block”).

Improvements

  • Breaking: sim_trend_stack() now returns list(series = ..., true_slope = ...) instead of the raster directly – what makes it a simulator with known ground truth, comparable directly against a fitted slope or a method’s own significance calls.

Documentation

  • Added a package logo.

sptrends 0.9.0

Documentation

  • sim_trend_stack()’s examples now demonstrate smooth_radius’s own effect directly via Moran’s I (~0.07 vs ~0.65).

sptrends 0.8.0

New features

  • sim_trend_stack() now genuinely generates spatial autocorrelation between neighbouring cells, via a new smooth_radius argument – previously documented but not actually implemented (noise was independent per cell).

Improvements

  • moran_permutation_test() documentation now explains why the permutation approach matters for this package’s own use case (bounded and/or skewed trend statistics, not normally distributed).
  • Removed sptrends_pipeline() entirely – a deprecated alias for tst(), never part of a public release.
  • read_netcdf_stack() now issues a real warning(), not just a documentation note, when the detected time step looks sub-annual.
  • Behaviour change: tst()’s default fdr_method changed from c("BH", "BKY") to "BKY" only, the method actually used in the published TST methodology.

sptrends 0.7.0

Improvements

  • Benjamini & Yekutieli (2001) now cited explicitly in all 11 fdr_* functions, not only fdr_bh().
  • tst()’s own argument order regrouped for logical proximity (alpha with moran_check, fdr_method with q); named-argument code is unaffected.
  • Strengthened the alpha/q note: applying a per-test alpha cell by cell across a raster is the multiple-testing error FDR exists to fix, not a harmless simplification.

Internal changes

  • Prose switched to British English throughout the package. Left unchanged, deliberately: identifiers that must keep American spelling (not ours to rename) and every quoted paper title.
  • Renamed “multiple comparisons” to “multiple testing” throughout.

Documentation

  • Corrected a co-author’s affiliation, mistakenly duplicated from the other author’s.
  • Description rewritten twice more for clarity, naming each workflow component explicitly before citing the TST paper.
  • Fixed vignette ordering in browseVignettes() (sorts by title, not file name) by prefixing the getting-started vignette’s own title.

sptrends 0.6.0

Internal changes

  • Vignettes renamed with an a-/b-/c-/d- prefix so browseVignettes() lists them in reading order.

Documentation

  • Added a “Citation” section to README.md.

sptrends 0.5.0

Improvements

  • Every exported function’s help page now has a “Function type” section, and a runnable @examples block (previously missing on 21 of 34 functions).

Documentation

  • Strengthened the package’s identity messaging (official R implementation of the published TST framework) across README.md and package docs; finalised Title/Description around a reproducible-framework framing; added _pkgdown.yml for a grouped future reference index; fixed a duplicated header in README.md.

sptrends 0.4.0

Improvements

  • Title finalised, deliberately not naming TST or “monotonic” in the title itself, since TST is meant to be the flagship workflow, not necessarily the only one going forward.

Documentation

  • Description rewritten to lead with the reproducible-framework framing before naming TST.
  • Corrected imprecise use of “adaptive” – only BKY is adaptive in the technical sense, BH is not.
  • New “Getting started” vignette.

sptrends 0.3.0

New features

  • tst() now includes Theil-Sen as a fourth, optional step, completing the four-component TST workflow as published.

Improvements

  • Every exported function’s help page now states its Function type (Core/Support/Reporting-derived).
  • tst() now returns a classed object with print()/summary()/ plot() methods.

Internal changes

  • New main function tst(), renamed from sptrends_pipeline() (matching the published workflow’s own name); the old name kept as a deprecated alias.

Documentation

  • DESCRIPTION and README.md rewritten to lead with the general monotonic-trend framing before naming TST by name.

sptrends 0.2.0

New features

Improvements

  • Added second author; added inst/CITATION; added the package-level help page; report = TRUE added as the default across the core functions; moran_check added to fdr_correction()/the pipeline; parallel computation (n_cores) added to the CMK and Moran’s I steps; documentation overhaul with verified/corrected DOIs throughout.

Internal changes

  • DESCRIPTION rewritten around the three-step workflow.

Documentation

  • Vignettes restructured from one combined vignette into three step-by-step ones.

sptrends 0.1.0

Initial release, built from four standalone scripts to reproduce the TST workflow described at the top of this file: selective AR(1) prewhitening (Wang & Swail, 2001), Contextual Mann-Kendall (Neeti & Eastman, 2011), pixel-wise FDR correction (Benjamini-Hochberg 1995; Benjamini-Krieger-Yekutieli 2006), and Moran’s I permutation testing, plus compute_anomalies(), raster/NetCDF reading, a convenience pipeline wrapper, and a synthetic data generator for examples and tests.