Changelog

Source: NEWS.md

sntutils 2.0.0 (2026-06-11)

Documentation

• New pkgdown site with workflow vignettes covering data cleaning, spatial preparation, climate downloads and raster processing. README rewritten to point at the site.
• New hex sticker logo at man/figures/logo.png.

New features

Climate and earth-observation downloads

• download_nasapower() pulls NASA POWER climate variables (temperature, precipitation, humidity, wind, radiation) plus dewpoint, elevation and 11 more added in this release. Samples multiple points per polygon (default 3) for better representativeness.
• download_modis() and modis_options() pull NASA MODIS imagery directly, replacing the earlier download_appeears() wrapper.
• download_worldpop_urbanicity() downloads WorldPop urbanicity layers.
• download_worldpop_age_band() gains a sex parameter, handles the 80+ band correctly, and respects a quiet flag.
• get_worldpop_paths() wraps multi-group WorldPop download and path building in a single call.
• download_worldpop() now uses the t (total) variant by default and exposes a GLOBAL mosaic option.

Raster processing

• process_rasters_by_year() wraps process_raster_collection() for pipelines where the admin boundary changes year over year.
• process_raster_with_boundaries() gains optional population weighting and an optional time-pattern detection switch.
• Rasters are cropped to the shapefile extent before extraction, cutting runtime substantially on large global rasters.
• Compact YYYYMM date pattern now supported by process_rasters() helpers alongside YYYY and YYYY-MM.

Mapping and visualization

• facetted_map_bins() and facetted_map_gradient() draw faceted choropleths for discrete and continuous data. Both support caption, fixed colour-scale limits and configurable text sizes.
• Insecticide-resistance trend plotting functions added, with built-in PNG compression.
• auto_bin() rewritten with robust outlier handling and adaptive labels; companion colour palette utilities added.

EMOD pipeline

• write_emod_demog() writes EMOD demographics JSON with correct nested AgeDistribution arrays.
• read_emod_weather() and write_emod_weather_by_adm2() added, with a folder_case parameter and correct filename handling when climate_profile is empty.

Reporting and data quality

• New reporting-rate functions computed directly from date columns.
• Reporting-rate plots and outlier detection extended with more diagnostics and standardized plot filenames for OneDrive sync.
• Outlier correction and cascade logic refined.

Spatial validation

• validate_process_spatial() runs a multi-stage boundary-artifact cleaning pass (make_valid, s2 toggling, zero-width buffer, hole removal) so aggregated geometries are always valid and render cleanly without double lines or polygon overlap.
• .clean_coord_string() helper hardens coordinate parsing against varied input formats.
• crosswalk_shapefiles_sf() exported and now works at adm1 without requiring an adm2 column.

Dictionary and variable tree

• var_tree.yml extended with ACT, IRS, ANC, EPI, SMC, IPTp4+, ITN, N5 cascade, care-seeking adjustment factors, severe anemia, household size, vaccine, health-facility variables, trained-provider care-seeking, and rate/incidence/coverage indicators.

File handling

• clean_filenames() refactored as a pure string operation with an explicit path-mapping helper.

Bug fixes

• crosswalk_shapefiles_sf() no longer requires an adm2 column when matching at adm1.
• auto_bin() rounding bug corrected.
• clean_filenames() no longer drops column names when piped through as.data.frame().
• download_worldpop_age_band() recovers from corrupt cached files.
• download_worldpop() and friends handle download timeouts gracefully.
• fuzzy_match_facilities() adds error handling for cloud-storage timeouts.
• NASA POWER download no longer emits unnamed-column warnings when n_sample = 1.
• Two pre-existing test flakes fixed.

Breaking changes

• download_appeears() and its documentation removed in favour of download_modis(). Migrate by replacing calls with download_modis() and pulling product/band names from modis_options().

Internals

• Atomic write path hardened on Windows: retrying fs::file_move, resilience to path and lock failures, tests skipped on Windows where reliable behaviour can’t be guaranteed.
• CI workflows slimmed down - live integrations gated, oldrel-1 dropped now that ggrepel requires R >= 4.5.0; Windows dependency install step added.
• System-dependency install script for macOS, Ubuntu and Fedora.
• Workflow added to block AI mentions in commit messages.

sntutils 1.12.6 (2026-04-23)

New features

• tidy_malaria_raster_names() normalizes filenames emitted by malariaAtlas::getRaster() (strips bounding-box coordinates and download stamps, keeps ...Rate.YYYY.tiff). Idempotent; also removes the getRaster/ artifact directory when it renames files.
• extract_time_components() gains a year_extractor argument. Pass a custom function (filename -> year) when the default “last plausible 4-digit year in 1980-2099” heuristic picks the wrong token.
• process_raster_collection() and process_weighted_raster_collection() expose year_extractor as a pass-through to extract_time_components().

Breaking changes

• detect_time_pattern() now uses base::all() instead of base::any() when deciding whether a batch of filenames belongs to a given time pattern. Batches containing files of mixed granularity no longer get silently misclassified as the most specific pattern present. Callers relying on the previous lenient behaviour should pre-filter their file lists.
• detect_time_pattern() tightens its yearly regex to plausible years only (19[89]\d or 20\d{2}) with digit word boundaries, so tokens like 202005 (a YYYYMM stamp) no longer match as a year.

Internals

• process_weighted_raster_collection() and process_raster_collection() now iterate via purrr::map() with .progress = ..., replacing the hand-rolled progress::progress_bar and for loop. Population rasters are matched using word-boundary regex ((?<!\d)YYYY(?!\d)) so year substrings no longer false-match longer digit runs.
• purrr (>= 1.0.0) moved from Suggests to Imports.

sntutils 1.12.5 (2026-03-02)

New features

• download_modis() and modis_options() for NASA MODIS imagery.
• EMOD pipeline: write_emod_demog(), read_emod_weather() and write_emod_weather_by_adm2().
• facetted_map_gradient() for continuous-data faceted choropleths. facetted_map_bins() gains caption, fixed colour-scale limits and text-sizing controls.
• Insecticide-resistance trend plotting (with PNG compression).
• WorldPop: get_worldpop_paths() multi-group wrapper; download_worldpop_age_band() gains a sex parameter, fixes the 80+ band, and respects a quiet flag.
• correct_outliers() for temporal outlier correction.
• Compact YYYYMM date pattern in process_rasters helpers.
• Togo climate-download example scripts (EN + FR).
• DHS indicator definitions for ACT, IRS, ANC, EPI, SMC and IPTp4+ added to var_tree.

Bug fixes

• validate_process_spatial() runs a multi-stage boundary-artifact cleaning pass (make_valid, s2 toggling, zero-width buffer, hole removal) so aggregated geometries are always valid and render cleanly without double lines or polygon overlap.
• crosswalk_shapefiles_sf() no longer requires an adm2 column at adm1 level.
• download_worldpop_age_band() recovers from corrupt cached files; download timeout fixed.
• fuzzy_match_facilities() handles cloud-storage timeouts.
• clean_filenames() no longer drops column names through piped as.data.frame().
• auto_bin() rounding bug.
• NASA POWER no longer emits unnamed-column warnings when n_sample = 1.
• EMOD weather filename correct when climate_profile is empty.
• R CMD check warnings and notes.

Breaking changes

• download_appeears() removed in favour of download_modis().

Internals

• clean_filenames() refactored as a pure string operation with an explicit path-mapping helper.
• Workflow added to block AI mentions in commit messages.
• macOS/Ubuntu/Fedora system-dependency install script.
• CI: oldrel-1 dropped (ggrepel requires R >= 4.5.0).

sntutils 1.12.4 (2026-02-02)

New features

• download_appeears() and appeears_options() for NASA AppEEARS data (later replaced by download_modis() in 1.12.5).
• facetted_map_bins() works without facets, and gains text sizing control and optional title/subtitle.
• PNG compression applied to dictionary outputs.

Bug fixes

• auto_bin() rounding bug.
• Variable-tree apostrophe preservation in names.
• IDP population paths added to folder structure.

sntutils 1.12.3 (2026-01-09)

New features

• download_nasapower() for NASA POWER climate data. Samples multiple points per polygon (default 3) for better representativeness.
• crosswalk_shapefiles_sf() exported.
• New reporting-rate function computed directly from date columns.
• auto_bin() and companion colour palette utilities for mapping.
• ahadi_path() for resolving OneDrive shared-library paths.
• var_tree extended with incidence cascade, MBG estimates, trained-provider care-seeking variables and rate/coverage terms.

Bug fixes

• prep_geonames UTF-8 handling.
• ISO country-code joins use names rather than coordinates.
• rnaturalearth no longer prompts to download already-cached data.
• Population data enforces unique admin-year rows.

Breaking changes

• validation_terms dataset deprecated; migrate to var_tree.
• rate / rate_cat renamed to incid_rate / incid_rate_cat.

Internals

• arrow moved to Suggests.
• Windows dependency install step added to CI.

sntutils 1.12.2 (2025-12-16)

New features

• facetted_map_bins() for faceted choropleth mapping.
• crosswalk_shapefiles_sf() added (initial).
• New climate variables in var_tree.
• DHS severe anemia indicators in var_tree.

Enhancements

• Plot filenames shortened and standardized for OneDrive sync.
• Translation logic improvements and variable label updates.
• Tighter data_name validation.

Bug fixes

• Context-specific name matching in user interaction.

sntutils 1.12.1 (2025-12-11)

Enhancements

• Reporting-rate plots and outlier detection extended with more diagnostics.
• Outlier correction and cascade logic refined.

Bug fixes

• Validation output trims neighbor_values.

Internals

• CI: missing system dependencies installed.
• System dependencies and R package versions updated.

sntutils 1.12.0 (2025-12-05)

Enhancements

• Validation and outlier-correction workflow consolidated and overhauled, building on the foundation laid in 1.11.x.

sntutils 1.11.9 (2025-11-28)

New features

• correct_outliers() for temporal outlier correction.
• validation_terms dictionary and data-dictionary support.
• Consensus colour visualization in outlier_plot().
• hf_name_col support in consistency checks.

Enhancements

• Caching for SNT variable tree, with improved dictionary filtering.
• dhis2_map() mapping validation improved.
• Missing-data checks extended with detailed summaries.

sntutils 1.11.8 (2025-11-20)

New features

• consistency_map() for spatial violation mapping.
• require_all parameter for complete-data reporting metrics.
• check_snt_var() gains fuzzy matching and dynamic DHS ITN age-group support.
• show_outbreaks and return_plots parameters in outlier_plot().
• x_axis_breaks parameter in reporting_rate_plot().

Enhancements

• Consistency-plot layering and styling improvements.
• Project folder structure and path setup refactor.
• reporting_rate_map() shows CLI config message.

Bug fixes

• Facility-count inconsistencies in reporting_rate_map().
• Pairing-list input in data-check function.

sntutils 1.11.7 (2025-11-14)

New features

• get_active_facilities() helper.
• Multilingual plot captions with facility counts.
• Reporting-rate functions gain flexible facility analysis and CLI feedback.

Bug fixes

• S3 object splicing error in facility_reporting_plot().
• Each facet now has its own axis range.
• Default hf_col set; test failures fixed.

sntutils 1.11.6 (2025-10-31)

New features

• get_dhs_data() for DuckDB-backed DHS dataset access.
• Climate variables added to raster download logic.

Enhancements

• Facility activity classification and plots refactor.
• Outlier-detection summary message simplified.
• CHIRPS file detection improved; snt_var_tree rebuilt.
• Default spatial_level = "hf_uid" in outlier functions.
• consistency_check axis expansion.

sntutils 1.11.5 (2025-10-30)

Enhancements

• fuzzy_match_facilities() step order refactored; docs updated.

sntutils 1.11.4 (2025-10-29)

Enhancements

• fuzzy_match_facilities() enforces one-to-one matching.
• mfl_only_count calculation refactored.

Bug fixes

• NA facet handling in facility_reporting_plot().

Breaking changes

• All hashing functionality removed from write_snt_data().

sntutils 1.11.3 (2025-10-28)

New features

• facet_col parameter validated and preserved in facility_reporting_plot().
• Universal console-clearing helper added.
• Column-width parameter.

sntutils 1.11.2 (2025-10-27)

Enhancements

• Admin-level parameters refactored.
• Facility-activeness checks enhanced.
• Outlier-detection defaults updated and output streamlined.

sntutils 1.11.1 (2025-10-27)

New features

• Advanced outlier-detection parameters.

sntutils 1.11.0 (2025-10-27)

New features

• trailing_tolerance passed through any function using classify_facility_activity().

sntutils 1.10.1 (2025-10-27)

New features

• Time-series plot added to compare_methods_plot().

Enhancements

• Facility activity classification logic refactored.

sntutils 1.10.0 (2025-10-24)

• Version bump; no user-visible changes.

sntutils 1.9.0 (2025-10-21)

New features

• compare_methods_plot() for comparing outlier-detection methods.
• Facility activity classification options on reporting functions.
• Outbreak classification in outlier detection.
• SNT variable tree sourced from package dataset.
• Translation overrides for statistical labels (e.g. “mean” → “Moyenne” in French).

Enhancements

• detect_outliers() now considers the same month in both past and future years.
• Method-description captions on facility reporting plots.

Breaking changes

• Seasonality feature removed from the outlier function.

Bug fixes

• Line-width warning.
• Deprecated label.padding parameter.

sntutils 1.8.0 (2025-10-13)

New features

• SNT variable dictionary added; build_dict() can use the package data dictionary.
• New function to display the data dictionary.
• extrapolate_pop() supports multiple population columns.
• Option to drop columns if not mapped.
• Facility plotting can output binary active/inactive results.
• classify_facility_activity() methods 2 and 3 added; configurable breaks parameter.

Enhancements

• Reduced dependency footprint: foreach dropped; ggrepel replaces shadowtext.
• write_snt_data() n_saved switch for version retention (replaces archiving).
• renv setup added to the repo.

Bug fixes

• standardize_names() no longer introduces auto-generated names from vapply().
• FOSA naming.
• Reporting-function translation and factoring.

sntutils 1.7.0 (2025-10-10)

New features

• File-based caching for outlier detection.
• Parallelized testing.

Enhancements

• Outlier-detection performance optimization.
• outlier_plot() works at the health-facility level.

Bug fixes

• Outlier save-path.

sntutils 1.6.4 (2025-08-30)

New features

• validate_process_coordinates() and validate_process_spatial() - the full spatial-validation pipeline.
• read_snt_data() / write_snt_data() with standardized formats; qs2 save/read format.
• build_dictionary(), prep_geonames(), standardize_names().
• setup_project_paths() and create_data_structure().
• fuzzy_match_facilities() with comprehensive matching stats.
• classify_facility_activity() and facility_reporting_plot().
• plot_admin_map_distinct().
• dhis2_map().
• download_era5() for ERA5 climate data.
• Parquet and Feather support in read() / write().
• GeoJSON support in read() / write().
• consistency_check() gains a facet_by parameter.
• outlier_plot() gains save/translate options, year_breaks, and a meaningful return value.
• Reporting-rate weighting.
• Health-facility data validation (prep_health_facilities).

Enhancements

• Translation system: multilingual plot captions, French acronyms, cached translations.
• Excel sheet formatting.
• Outlier detection with seasonality and guardrails (later removed in 1.9.0).
• UTF-8 handling for data and sheet names.

Internals

• qs2 adopted for save/read.
• pngquant detection improvements.
• Critical packages moved from Suggests to Imports.

sntutils 1.6.3 (2025-08-22)

New features

• New function to download WHO shapefiles.

Documentation

• Various updates.

sntutils 1.6.2 (2025-08-14)

New features

• prep_geonames() enhancements: casing preservation, alternate unmatched-data export.
• calculate_match_stats() properly excludes NA before counting.

Breaking changes

• download_chirps2.0() renamed to download_chirps().
• who_region parameter and stratify functionality removed.

sntutils 1.6.1 (2025-08-05)

Enhancements

• Reporting rate uses proportion in plots, 0–1 elsewhere.

sntutils 1.6.0 (2025-08-05)

• Version bump; paired with 1.6.1 on the same day.

sntutils 1.5.1 (2025-07-25)

New features

• Clinical-pathway streams used for imputation.

Documentation

• README and reporting-rate page refactor.

sntutils 1.5.0 (2025-07-14)

New features

• fallback_diff() and fallback_row_sum().

Enhancements

• Raster-processing weighting updates and improved documentation.

Breaking changes

• na_to_zero options removed.

sntutils 1.4.0 (2025-03-03)

Initial public version of the package, established as sntutils (renamed mid-development from snt / snt-utils).

Core features

• Data I/O - read() and write() supporting CSV, XLSX, GeoJSON, shapefiles and more.
• Data quality - consistency_check(), missing_plot(), auto_parse_types(), autoparse_dates(), standardize_names(), outlier detection.
• Spatial - initial shapefile validation and cleaning.
• Reporting - initial reporting-rate function.
• Translation system with caching, plus vectorized translate_text().
• PNG compression (compress_png()).
• impute_higher_admin() for admin-level imputation.

Raster processing

• process_raster_collection() and process_raster_with_boundaries().
• normalize_raster_by_polygon().
• extrapolate_pop() for population extrapolation.

Downloads

• download_worldpop() (and age-band variant).
• download_chirps() for CHIRPS precipitation data plus available dates check.
• DHS indicator download functions.

Project utilities

• create_data_structure() for the SNT folder hierarchy.
• clean_filenames() for date-laden file paths.

Internals

• vdigest() - vectorized digest.
• GitHub Actions for R CMD check and test coverage.