Package: soilKey 0.9.191

soilKey: Automated Soil Profile Classification per WRB 2022, 'SiBCS' 5 and USDA Soil Taxonomy 13

Implements deterministic classification keys for the World Reference Base for Soil Resources 2022 (4th edition) and the Brazilian System of Soil Classification ('SiBCS', 5th edition). Provides a unified profile representation with explicit per-attribute provenance, multimodal extraction from field reports and photos via vision-language models, spatial priors from 'SoilGrids' and national soil maps, and gap-filling of soil attributes from Vis-NIR or MIR spectra via the Open Soil Spectral Library ('OSSL'). The taxonomic key itself is never delegated to a language model; LLMs are restricted to schema-validated extraction. Each classification result reports a key trace, a provenance-aware evidence grade, and ambiguities that further measurement would resolve.

Authors:Hugo Rodrigues [aut, cre]

soilKey_0.9.191.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
soilKey/json (API)

# Install 'soilKey' in R:
install.packages('soilKey', repos = c('https://hugomachadorodrigues.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hugomachadorodrigues/soilkey/issues

Pkgdown/docs site:https://hugomachadorodrigues.github.io

Datasets:

On CRAN:

Conda:

7.28 score 7 stars 42 scripts 404 downloads 326 exports 5 dependencies

Last updated from:221239bdbb. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE328
source / vignettesOK327
linux-release-x86_64NOTE327
macos-release-arm64NOTE235
macos-oldrel-arm64NOTE223
windows-devel-x86_64NOTE613
windows-release-x86_64NOTE545
windows-oldrel-x86_64NOTE444
wasm-releaseOK142

Exports:%||%abrupt_textural_differenceacrisolaeolic_materialalbeluvic_glossaealbicalisolandic_propertiesandosolannotate_wrb_from_usdaanthraquicanthric_horizonsapply_soilgrids_depth_priorapply_spectral_preprocessingarenic_textureargicargic_aqpargic_with_strong_clay_filmsargillic_clay_films_testartefactsas_aqpattach_lucas_spectraaudit_argic_strong_filmsauto_set_proj_envavailable_esdb_attributesB_espodicoB_incipienteB_latossolicoB_niticoB_planicoB_texturalbatch_robustnessbenchmark_afspbenchmark_bdsolosbenchmark_lucas_2018benchmark_performancebenchmark_redapebenchmark_run_classificationbenchmark_spectral_fillbenchmark_unifiedbenchmark_wrb_vs_usdabuild_taxon_profilescalcaric_materialcalciccambiccambic_aqpcanonical_referencecanonicalise_kst13ed_ggcerosidadechernicchernozemchernozem_strictclaric_materialclassification_robustnessClassificationResultclassify_allclassify_by_spectral_neighboursclassify_csvclassify_from_documentsclassify_from_photosclassify_sibcsclassify_sibcs_familiaclassify_usdaclassify_usda_familyclassify_via_smartsolos_apiclassify_with_engine_heuristicclassify_with_uncertaintyclassify_wrb2022clear_kst13_cacheclear_ossl_cachecohesiccombine_priorscompare_enginescompare_smartsoloscompute_kicompute_krcompute_per_attribute_evidence_gradecontinuous_rockcoverage_reportcryic_conditionscryic_horizonDiagnosticResultdistroficodolomitic_materialdownload_bdsolosdownload_extdata_cachedownload_ossl_subsetdownload_ossl_subset_with_labelsdownload_redape_datasetduric_horizonduripaensure_horizon_schemaeutroficoevaluate_rsg_testsextract_horizons_from_pdfextract_munsell_from_photoextract_site_from_fieldsheetfamilia_mineralogia_argila_geralFamilyAttributefebr_index_munsellferralicferralsolferricfibricofill_from_spectrafill_munsell_from_spectrafluvic_materialfolicformat_wrb_namefragicfragipafrom_aqpgapfill_by_predicted_taxongapfill_derive_horizongapfill_within_pedonget_perturbation_scalegleyic_propertiesgleysolGSM_DEPTHSgypsicgypsiric_materialharmonize_to_gsmhemicohistic_horizonhorizon_column_spechortichydragrichypersulfidic_materialhyposulfidic_materialinspect_bdsolos_csvirragrickastanozemkastanozem_strictkey_trace_tablekst13_canonicalkst13_codeskst13_criterialeptic_featureslimnic_materiallimoniclithic_discontinuitylixisolload_afsp_pedonsload_afsp_sampleload_bdsolos_csvload_embrapa_pedonsload_febr_pedonsload_kssl_nasis_sampleload_kssl_pedonsload_kssl_pedons_gpkgload_kssl_pedons_with_nasisload_kssl_sampleload_lucas_pedonsload_lucas_soil_2018load_ossl_modelsload_redape_pedonsload_rulesload_wosis_sampleload_wosis_stratified_samplelookup_esdblookup_mapbiomas_soloslookup_soilgridsluvisolmake_acrisol_canonicalmake_alisol_canonicalmake_andosol_canonicalmake_anthrosol_canonicalmake_arenosol_canonicalmake_argissolo_canonicalmake_calcisol_canonicalmake_cambisol_canonicalmake_cambissolo_canonicalmake_chernossolo_canonicalmake_chernozem_canonicalmake_cryosol_canonicalmake_durisol_canonicalmake_empty_horizonsmake_espodossolo_canonicalmake_ferralsol_canonicalmake_fluvisol_canonicalmake_gleissolo_canonicalmake_gleysol_canonicalmake_gypsisol_canonicalmake_histosol_canonicalmake_kastanozem_canonicalmake_latossolo_canonicalmake_leptosol_canonicalmake_lixisol_canonicalmake_luvisol_canonicalmake_luvissolo_canonicalmake_neossolo_canonicalmake_nitisol_canonicalmake_nitossolo_canonicalmake_organossolo_canonicalmake_phaeozem_canonicalmake_planosol_canonicalmake_planossolo_canonicalmake_plinthosol_canonicalmake_plintossolo_canonicalmake_podzol_canonicalmake_retisol_canonicalmake_solonchak_canonicalmake_solonetz_canonicalmake_stagnosol_canonicalmake_synthetic_pedon_with_spectramake_technosol_canonicalmake_umbrisol_canonicalmake_vertisol_canonicalmake_vertissolo_canonicalmineral_materialMockVLMProvidermollicmudanca_textural_abruptamulmic_materialnatric_horizonnitic_horizonnormalise_febr_sibcsnormalise_febr_usdanormalise_febr_wrbnormalise_kssl_subgroupollama_is_runningorganic_materialorganotechnic_materialornithogenic_materialossl_library_templateoxic_usdapanpaicpedon_json_schemapedon_to_spcPedonRecordpedons_from_spectral_tablepetrocalcicpetroduricpetrogypsicpetroplinthicphaeozempi_to_confidencepick_enginepick_engine_batchpisoplinthicplaggicplanic_featuresplanosolplinthicposterior_classifypredict_from_spectrapredict_lab_from_spectrapredict_munsell_from_spectrapredict_ossl_mblpredict_ossl_plsr_localpredict_ossl_pretrainedpredict_xyz_from_spectrapreprocess_spectrapreticprior_consistency_checkprotocalcic_propertiesprotogypsic_propertiesprotoverticread_febr_pedonsread_pedon_csvread_spectral_libraryreducing_conditionsreportreport_htmlreport_pdfreport_to_qgisresolve_wrb_qualifiersretic_propertiesrun_all_benchmarksrun_classify_apprun_demorun_sibcs_grande_gruporun_sibcs_keyrun_sibcs_subgruporun_sibcs_subordemrun_taxa_listrun_taxonomic_keyrun_usda_great_grouprun_usda_keyrun_usda_subgrouprun_usda_suborderrun_wrb_keysalicsapricosave_ossl_modelsshrink_swell_crackssideralic_propertiessoil_classes_at_locationsoil_organic_carbonsoilgrids_usda_lutsoilgrids_wrb_lu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Dependencies:clidata.tableR6rlangyaml

Começando com soilKey (PT-BR)
0. O começo de 30 segundos | A. Interface Shiny (sem código) | B. Uma chamada R, uma fixture | 1. Construindo um PedonRecord do zero | 2. Classificando nos três sistemas | Atalho: classificar nos três sistemas em uma chamada | 3. Inspecionando o key trace | 4. Provenance + evidence grade | 5. Cross-system: o mesmo perfil em três taxonomias | 6. Onde ir a partir daqui | 7. Onde reportar bugs / sugerir features / pedir ajuda | Referências canônicas
Rendered fromv01_getting_started_pt.Rmdusingknitr::rmarkdown

Last update: 2026-06-21
Started: 2026-05-04

Getting started with soilKey
0. The 30-second on-ramp | A. Zero-code GUI | B. One R call, one fixture | 1. Building a PedonRecord from scratch | 2. Canonical fixtures | 3. Calling the diagnostics directly | 4. Diagnostic matrix across the canonical fixtures | 5. RSG-derived diagnostics: argic and mollic families | 6. End-to-end WRB classification | 7. Provenance and evidence grade | 8. Interoperability with aqp | 9. Module 4 -- OSSL spectroscopy bridge (gap-filling) | 10. Module 3 -- SoilGrids / Embrapa spatial prior (sanity check) | 11. Module 2 -- Multimodal extraction via ellmer | 12. SiBCS 5ª edição (Embrapa, 2018) | 13. v0.7 scope and the v0.3.3+ roadmap
Rendered fromv01_getting_started.Rmdusingknitr::rmarkdown

Last update: 2026-06-21
Started: 2026-04-30

KSSL + NASIS: multi-level USDA Soil Taxonomy benchmark
1. The KSSL + NASIS join (load_kssl_pedons_with_nasis) | 2. The four levels (benchmark_run_classification) | 3. Headline numbers (v0.9.31, n=2638, ±1.7 pp CI) | 4. Release-by-release trajectory | 5. The four levels are independently measurable | 6. v0.9.25 -- the KST canonicaliser story | 7. What's missing (roadmap) | Summary
Rendered fromv08_kssl_nasis_multilevel.Rmdusingknitr::rmarkdown

Last update: 2026-06-21
Started: 2026-05-03

Um perfil real do A ao Z (estilo Embrapa, em portugues)
Introducao | O perfil: Argissolo Vermelho-Amarelo distrofico tipico | Diagnosticos manuais (sanity check) | Tres classificacoes paralelas | SiBCS 5a edicao | WRB 2022 | USDA Soil Taxonomy 13a edicao | Comparacao cross-system | Relatorio HTML | Cruzamento com priore espacial (opcional) | Cruzamento com SoilGrids 250m (global) | Resumo
Rendered fromv09_perfil_embrapa_pt.Rmdusingknitr::rmarkdown

Last update: 2026-06-21
Started: 2026-05-05

End-to-end WRB 2022 classification with Ch 6 names
1. Build the pedon | 2. Run the WRB key | 3. Inspect the principal qualifier resolution | 4. Inspect the supplementary qualifier resolution | 5. Compose the Ch 6 name | 6. Family suppression | 7. Evidence grade | 6. Render a self-contained pedologist-facing report | 7. Tier-3 strict mode for borderline pedons | Summary
Rendered fromv02_classify_wrb_end_to_end.Rmdusingknitr::rmarkdown

Last update: 2026-05-23
Started: 2026-04-30

Field-photo-only classification
The pipeline | A minimal run | The provider argument is required | The SoilGrids depth prior | Reading the evidence grade | When to use it
Rendered fromv11_photo_only.Rmdusingknitr::rmarkdown

Last update: 2026-05-23
Started: 2026-05-23

Provenance-weighted classification uncertainty
The idea | A first run | Provenance changes the answer | The sensitivity ranking | Backward compatibility | In the Shiny app
Rendered fromv12_uncertainty.Rmdusingknitr::rmarkdown

Last update: 2026-05-23
Started: 2026-05-23

The soilKey Pro Shiny app
Launching the app | The eight tabs | Pedon | Classify | Photo | Spectra | Spatial | Uncertainty | Report | Settings | Notes
Rendered fromv10_shiny_pro.Rmdusingknitr::rmarkdown

Last update: 2026-05-23
Started: 2026-05-23

Benchmarking soilKey against WoSIS
1. Protocol overview | 2. Mini-benchmark on the canonical fixtures | 3. Confusion at the qualifier level | 4. Benchmark protocol against WoSIS (run-once, paper-grade) | 5. Reporting standards | 6. Offline canonical-fixture run (release-time sanity check) | Summary | 7. v0.9.27 -- per-page retry + graceful degradation | 8. v0.9.30 -- bundled WoSIS sample for offline / CI testing
Rendered fromv06_wosis_benchmark.Rmdusingknitr::rmarkdown

Last update: 2026-05-03
Started: 2026-04-30

End-to-end pipeline: Gemma 4 + spatial + spectral + key + GIS export
1. Set the scene | 2. Spatial guide -- before any pedon data | 3. Multimodal extraction with local Gemma 4 | 4. Spectral analogy | 5. Deterministic classification | 6. HTML report | 7. GIS export | 8. The complete picture | Summary
Rendered fromv07_end_to_end_pipeline.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2026-04-30

Vision-language extraction of pedon data (Module 2)
1. The mock provider | 2. Schemas and prompts | 3. Walking the extraction loop with the mock | 4. Merging extraction into a PedonRecord | 5. Provenance and evidence grade | 6. Production: swap the mock for an ellmer chat | 6a. Local-first with Gemma 4 (Ollama) | 6b. Cloud providers (Anthropic, OpenAI, Google) | 6c. The one-liner: classify_from_documents()
Rendered fromv04_vlm_extraction.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2026-04-30

Cross-system classification: WRB 2022, SiBCS 5, USDA Soil Taxonomy
1. The same Ferralsol through three keys | 2. Cross-system table on the canonical fixtures | 3. Where the systems diverge | 4. Recovering the qualifier-level correspondence | 5. Validating the SiBCS ↔ WRB alignment | 6. Use cases for cross-system classification
Rendered fromv03_cross_system_correlation.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2026-04-30

Spatial prior + OSSL spectra pipeline (Modules 3 & 4)
1. Start from a partially-described pedon | 2. Module 3 -- spatial prior consistency check | 3. Module 4 -- OSSL gap-filling | 4. Re-classify with the gap-filled pedon | 5. Combining priors and posteriors | Summary
Rendered fromv05_spatial_spectra_pipeline.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2026-04-30

Readme and manuals

Help Manual

Help pageTopics
Abrupt textural difference (WRB 2022 Ch 3.2.1)abrupt_textural_difference
Acrisol RSG diagnostic (WRB 2022)acrisol
Aeolic material (WRB 2022 Ch 3.3.1)aeolic_material
Albeluvic glossae (WRB 2022 Ch 3.2.2)albeluvic_glossae
Albic horizon (WRB 2022)albic
Alisol RSG diagnostic (WRB 2022)alisol
Andic properties (WRB 2022)andic_properties
Andosol RSG gate (WRB 2022 Ch 4, p 104)andosol
Annotate KSSL/NASIS pedons with a derived WRB Reference Soil Groupannotate_wrb_from_usda
Anthraquic horizon (WRB 2022): puddled-rice / paddy plough layer. v0.3.3 detects via designation pattern 'Apl|Ap|Hh'.anthraquic
Anthric horizons (WRB 2022)anthric_horizons
Fill missing horizon attributes from a SoilGrids depth priorapply_soilgrids_depth_prior
Apply a step-by-step Vis-NIR / MIR preprocessing pipelineapply_spectral_preprocessing
Arenic texture (WRB 2022)arenic_texture
Argic horizon (WRB 2022)argic
Argic / argillic horizon via aqp::getArgillicBounds()argic_aqp
Test whether a pedon's argic horizon has strong clay filmsargic_with_strong_clay_films
Test for clay-illuviation evidence (KST 13ed Ch 3 p 4)argillic_clay_films_test
Artefacts (WRB 2022 Ch 3.3.2)artefacts
Convert one or more PedonRecord objects to an aqp SoilProfileCollectionas_aqp
Attach LUCAS 2018 Vis-NIR spectra to a list of PedonRecord objectsattach_lucas_spectra
Audit the strong-clay-films exclusion across a list of pedonsaudit_argic_strong_films
Auto-detect PROJ_LIB and GDAL_DATA directoriesauto_set_proj_env
List ESDB Raster Library attributes available at a given rootavailable_esdb_attributes
Horizonte B espodico (SiBCS Cap 2, p 62-65; v0.7)B_espodico
Horizonte B incipiente (SiBCS Cap 2, p 59-61; v0.7)B_incipiente
Horizonte B latossolico (SiBCS Cap 2, p 57-59; v0.7 strict)B_latossolico
Horizonte B nitico (SiBCS Cap 2, p 61-62; v0.7)B_nitico
Horizonte B planico (SiBCS Cap 2, p 65-66; v0.7)B_planico
Horizonte B textural (SiBCS Cap 2, p 54-57; v0.7 strict)B_textural
Batch robustness across many pedonsbatch_robustness
Benchmark soilKey WRB predictions against AfSP ground truthbenchmark_afsp
Benchmark soilKey classifiers against BDsolos national reference labelsbenchmark_bdsolos
Run the LUCAS Soil 2018 / ESDB WRB benchmarkbenchmark_lucas_2018
Run the soilKey performance benchmarkbenchmark_performance
Benchmark soilKey SiBCS predictions against the Redape gold standardbenchmark_redape
Run a benchmark across one of the loaded pedon listsbenchmark_run_classification
Benchmark the accuracy lift of spectral gap-fill (ON vs OFF), k-foldbenchmark_spectral_fill
Unified cross-dataset benchmark across SiBCS / WRB / USDAbenchmark_unified
Benchmark soilKey WRB predictions against a USDA-derived ground truthbenchmark_wrb_vs_usda
Build per-taxon mean depth profiles for predicted-taxon gap-fillbuild_taxon_profiles
Calcaric material (WRB 2022 Ch 3.3.3): \>= 2% CaCO3 throughout the fine earth, primary carbonates from the parent material.calcaric_material
Calcic horizon (WRB 2022)calcic
Cambic horizon (WRB 2022)cambic
Cambic horizon via aqp::getCambicBounds()cambic_aqp
Load a canonical reference dataset from soilKey or SoilTaxonomycanonical_reference
Canonicalise a USDA Great Group label to a KST 13ed-compatible keycanonicalise_kst13ed_gg
Cerosidade quantitativa (SiBCS Cap 13, p 207; Cap 1)cerosidade
Chernic horizon (WRB 2022): the cherozemic-style mollic with very high biological activity (worm holes, casts, coprolites). v0.3.3: delegates to mollic + worm_holes_pct >= 50 (proxy for "biological homogenization").chernic
Chernozem RSG diagnostic (WRB 2022)chernozem
Chernozem RSG gate (strengthened, WRB 2022 Ch 4, p 111)chernozem_strict
Claric material (WRB 2022 Ch 3.3.4): light-coloured fine earth with Munsell criteria.claric_material
Robustness of classification under input perturbationclassification_robustness
ClassificationResult: structured outcome of running a keyClassificationResult
Classify a pedon across all three taxonomic systemsclassify_all
Classify a soil by spectral similarity to OSSL reference profilesclassify_by_spectral_neighbours
Classify a horizon spreadsheet in all three systems - one file, one lineclassify_csv
Build a fully-classified `PedonRecord` from documents in one callclassify_from_documents
Classify a soil profile from field photographs aloneclassify_from_photos
Classifica um pedon segundo o SiBCS 5a edicao (1o + 2o + 3o + 4o niveis)classify_sibcs
Classifica um perfil no 5o nivel categorico do SiBCS (Familia)classify_sibcs_familia
Classify a pedon under USDA Soil Taxonomy (13th edition)classify_usda
Classify the USDA family (5th level) of a pedonclassify_usda_family
Classify a PedonRecord via Embrapa's SmartSolosExpert REST APIclassify_via_smartsolos_api
Classify a pedon with the engine chosen by `pick_engine()`classify_with_engine_heuristic
Posterior distribution over classification outcomesclassify_with_uncertainty
Classify a pedon under WRB 2022classify_wrb2022
Clear the in-memory KST13 cacheclear_kst13_cache
Clear the soilKey OSSL cacheclear_ossl_cache
Cohesic horizon (WRB 2022, Chapter 3.1.7)cohesic
Combine multiple spatial priors via weighted geometric meancombine_priors
Side-by-side comparison of soilKey vs aqp diagnostic enginescompare_engines
Cross-validate the local SiBCS classifier against the SmartSolosExpert APIcompare_smartsolos
Ki (silica:alumina molar) - SiBCS Cap 1, p 32compute_ki
Kr (silica:sesquioxidos molar) - SiBCS Cap 1, p 32compute_kr
Per-attribute provenance-aware evidence gradecompute_per_attribute_evidence_grade
Continuous rock (WRB 2022 Ch 3.2.5)continuous_rock
Honest taxonomic-completeness reportcoverage_report
Cryic conditions (WRB 2022)cryic_conditions
Cryic horizon (WRB 2022, Chapter 3.1.8)cryic_horizon
DiagnosticResult: structured outcome of a diagnostic testDiagnosticResult
Solo distrofico (SiBCS Cap 1, p 30)distrofico
Dolomitic material (WRB 2022 Ch 3.3.5): \>= 2% Mg-rich carbonate, CaCO3/MgCO3 < 1.5. v0.3.3: detects via designation pattern 'kdo|do|magn' as proxy when ratio data missing.dolomitic_material
Download the BDsolos consulta-publica CSV (experimental, requires chromote)download_bdsolos
Download one or more soilKey lazy-fetch caches from GitHub Releasedownload_extdata_cache
Download an OSSL subset and return an `ossl_library` artefactdownload_ossl_subset
Download an OSSL subset and attach WRB / SiBCS / USDA labelsdownload_ossl_subset_with_labels
Download the curated Redape GeoTab dataset (Vaz et al 2023)download_redape_dataset
Duric horizon (WRB 2022)duric_horizon
Duripa (SiBCS Cap 2, p 74; v0.7)duripa
Coerce a horizons-like data.frame to the canonical schemaensure_horizon_schema
Solo eutrofico (SiBCS Cap 1, p 30)eutrofico
Evaluate the test block of a single RSGevaluate_rsg_tests
Extract horizons from a soil description PDFextract_horizons_from_pdf
Extract Munsell color from a profile photoextract_munsell_from_photo
Extract site metadata from a field-sheet imageextract_site_from_fieldsheet
Familia: mineralogia da fracao argila (geral, nao-Latossolos)familia_mineralogia_argila_geral
Classe S4-like para atributos de Familia (5o nivel SiBCS)FamilyAttribute
Curated index of FEBR datasets that carry Munsell colorsfebr_index_munsell
Ferralic horizon (WRB 2022)ferralic
Ferralsol RSG gate (WRB 2022 Ch 4, p 110)ferralsol
Ferric horizon (WRB 2022)ferric
Material organico fibrico (SiBCS Cap 14)fibrico
Fill missing soil attributes from spectra via OSSLfill_from_spectra
Fill missing Munsell colors on a PedonRecord from Vis-NIR spectrafill_munsell_from_spectra
Fluvic material (WRB 2022)fluvic_material
Folic horizon (WRB 2022, Chapter 3.1.12)folic
Format a WRB 2022 soil name with qualifiersformat_wrb_name
Fragic horizon (WRB 2022): a high-bulk-density horizon with restricted rooting. v0.3.3: detects via bulk_density_g_cm3 >= 1.65 AND structure grade massive/very firm OR designation pattern 'x'/'Bx'.fragic
Fragipa (SiBCS Cap 2, p 73-74; v0.7)fragipa
Convert an aqp SoilProfileCollection back to a list of PedonRecordfrom_aqp
Fill missing horizon attributes from the predicted taxon's mean profilegapfill_by_predicted_taxon
Fill horizon attributes derivable BY DEFINITION from the same horizongapfill_derive_horizon
Fill interior missing horizon attributes by within-pedon depth interpolationgapfill_within_pedon
Monte-Carlo perturbation scale for an evidence gradeget_perturbation_scale
Gleyic properties (WRB 2022)gleyic_properties
Gleysol RSG gate (WRB 2022 Ch 4, p 103)gleysol
Default-value-for-NULL operator%||% grapes-or-or-grapes
Default GlobalSoilMap depth intervals (cm)GSM_DEPTHS
Gypsic horizon (WRB 2022)gypsic
Gypsiric material (WRB 2022 Ch 3.3.7): \>= 5% gypsum that is primary (not secondary). Without a "secondary fraction" schema column, v0.3.3 treats any layer with caso4_pct >= 5 as gypsiric unless it explicitly carries gypsic-horizon designation.gypsiric_material
Harmonise pedons to GlobalSoilMap depth intervalsharmonize_to_gsm
Material organico hemico (SiBCS Cap 14)hemico
Histic horizon (WRB 2022)histic_horizon
Canonical horizon column specificationhorizon_column_spec
Hortic horizon (WRB 2022): garden / kitchen-midden topsoil. Diagnostic criteria: thickness \>= 20 cm, dark colour (mollic-like), high P (Mehlich-3 P >= 100 mg/kg or P2O5_1pct_citric >= 175 mg/kg), high SOC.hortic
Hydragric horizon (WRB 2022): subsoil hydric horizon under anthraquic. v0.3.3 detects via designation pattern 'Bg|Brg' immediately below an anthraquic-like topsoil.hydragric
Hypersulfidic material (WRB 2022 Ch 3.3.8): \>= 0.01% inorganic sulfidic S, pH \>= 4, capable of severe acidification on aerobic incubation.hypersulfidic_material
Hyposulfidic material (WRB 2022 Ch 3.3.9): same inorganic sulfidic S and field pH as hypersulfidic but does NOT consist of hypersulfidic (criterion 3 - does not acidify to pH < 4 on aerobic incubation, usually self-neutralised by carbonate). Reachable from v0.9.128: when 'incubation_ph' is measured, a sulfidic + pH>=4 layer that stays >= 4 on incubation is the set-complement of 'hypersulfidic_material' and is reported here. Without an incubation pH the two cannot be told apart, so this returns empty (the layer is reported as potential hypersulfidic instead).hyposulfidic_material
Diagnostic inspection of a BDsolos CSV before loadinginspect_bdsolos_csv
Irragric horizon (WRB 2022): topsoil thickened by irrigation deposits. v0.3.3: thickness >= 20 cm + sediment-derived structure proxied via designation 'Apk|Apg|Au'.irragric
Kastanozem RSG diagnostic (WRB 2022)kastanozem
Kastanozem RSG gate (strengthened, WRB 2022 Ch 4, p 112)kastanozem_strict
Flatten a classification key trace into a tabular formkey_trace_table
Keys to Soil Taxonomy 13th edition canonical referencekst13_canonical
Load the canonical KST 13ed code -> taxon-name lookup tablekst13_codes
Load the canonical KST 13ed criteria for a single taxon codekst13_criteria
Leptic features (WRB 2022)leptic_features
Limnic material (WRB 2022 Ch 3.3.10): subaquatic deposits (coprogenous earth, diatomaceous earth, marl, gyttja). v0.3.3: detects via 'rock_origin %in% c("lacustrine", "marine")' or designation pattern.limnic_material
Limonic horizon (WRB 2022 Ch 3.1)limonic
Lithic discontinuity (WRB 2022 Ch 3.2.7)lithic_discontinuity
Lixisol RSG diagnostic (WRB 2022)lixisol
Load Africa Soil Profiles (AfSP) v1.2 as PedonRecord objectsload_afsp_pedons
Load the bundled AfSP stratified sample (v0.9.77)load_afsp_sample
Load a BDsolos CSV export as a list of PedonRecord objectsload_bdsolos_csv
Load Embrapa dadosolos pedons with reference SiBCS classificationload_embrapa_pedons
Load the Embrapa FEBR superconjunto into a list of PedonRecordsload_febr_pedons
Load the bundled KSSL + NASIS morphological-enriched sample (v0.9.75)load_kssl_nasis_sample
Load NCSS / KSSL pedons with reference USDA Soil Taxonomy classificationload_kssl_pedons
Load KSSL / NCSS pedons from the ncss_labdata GeoPackageload_kssl_pedons_gpkg
Load KSSL pedons enriched with NASIS morphologyload_kssl_pedons_with_nasis
Load the bundled KSSL/NCSS lab-data sample (v0.9.74)load_kssl_sample
Load EU-LUCAS / ESDB pedons with reference WRB classificationload_lucas_pedons
Load the LUCAS Soil 2018 Topsoil release as a list of PedonRecord objectsload_lucas_soil_2018
Load curated soil profiles from the Embrapa Redape GeoTab datasetload_redape_pedons
Load a soilKey rule set (YAML)load_rules
Load the bundled WoSIS South-America sampleload_wosis_sample
Load the bundled WoSIS stratified RSG-balanced sample (v0.9.73)load_wosis_stratified_sample
Look up an ESDB raster value at WGS84 coordinateslookup_esdb
Look up a MapBiomas Solos raster value at WGS84 coordinateslookup_mapbiomas_solos
Look up a SoilGrids 250m soil property at WGS84 coordinateslookup_soilgrids
Luvisol RSG diagnostic (WRB 2022)luvisol
Build the canonical Acrisol fixturemake_acrisol_canonical
Build the canonical Alisol fixturemake_alisol_canonical
Build the canonical Andosol fixturemake_andosol_canonical
Build the canonical Anthrosol fixturemake_anthrosol_canonical
Build the canonical Arenosol fixturemake_arenosol_canonical
Perfil canonico de Argissolo (SiBCS 5a ed., Cap 5)make_argissolo_canonical
Build the canonical Calcisol fixturemake_calcisol_canonical
Build the canonical Cambisol fixturemake_cambisol_canonical
Perfil canonico de Cambissolo (SiBCS 5a ed., Cap 6)make_cambissolo_canonical
Perfil canonico de Chernossolo (SiBCS 5a ed., Cap 7)make_chernossolo_canonical
Build the canonical Chernozem fixturemake_chernozem_canonical
Build the canonical Cryosol fixturemake_cryosol_canonical
Build the canonical Durisol fixturemake_durisol_canonical
Build an empty horizons data.table with the canonical schemamake_empty_horizons
Perfil canonico de Espodossolo (SiBCS 5a ed., Cap 8)make_espodossolo_canonical
Build the canonical Ferralsol fixturemake_ferralsol_canonical
Build the canonical Fluvisol fixturemake_fluvisol_canonical
Perfil canonico de Gleissolo (SiBCS 5a ed., Cap 9)make_gleissolo_canonical
Build the canonical Gleysol fixturemake_gleysol_canonical
Build the canonical Gypsisol fixturemake_gypsisol_canonical
Build the canonical Histosol fixturemake_histosol_canonical
Build the canonical Kastanozem fixturemake_kastanozem_canonical
Perfil canonico de Latossolo (SiBCS 5a ed., Cap 10)make_latossolo_canonical
Build the canonical Leptosol fixturemake_leptosol_canonical
Build the canonical Lixisol fixturemake_lixisol_canonical
Build the canonical Luvisol fixturemake_luvisol_canonical
Perfil canonico de Luvissolo (SiBCS 5a ed., Cap 11)make_luvissolo_canonical
Perfil canonico de Neossolo Litolico (SiBCS 5a ed., Cap 12)make_neossolo_canonical
Build the canonical Nitisol fixturemake_nitisol_canonical
Perfil canonico de Nitossolo Vermelho (SiBCS 5a ed., Cap 13)make_nitossolo_canonical
Perfil canonico de Organossolo (SiBCS 5a ed., Cap 14)make_organossolo_canonical
Build the canonical Phaeozem fixturemake_phaeozem_canonical
Build the canonical Planosol fixturemake_planosol_canonical
Perfil canonico de Planossolo (SiBCS 5a ed., Cap 15)make_planossolo_canonical
Build the canonical Plinthosol fixturemake_plinthosol_canonical
Perfil canonico de Plintossolo (SiBCS 5a ed., Cap 16)make_plintossolo_canonical
Build the canonical Podzol fixturemake_podzol_canonical
Build the canonical Retisol fixturemake_retisol_canonical
Build the canonical Solonchak fixturemake_solonchak_canonical
Build the canonical Solonetz fixturemake_solonetz_canonical
Build the canonical Stagnosol fixturemake_stagnosol_canonical
Build a synthetic PedonRecord with attached spectra (testing aid)make_synthetic_pedon_with_spectra
Build the canonical Technosol fixturemake_technosol_canonical
Build the canonical Umbrisol fixturemake_umbrisol_canonical
Build the canonical Vertisol fixturemake_vertisol_canonical
Perfil canonico de Vertissolo (SiBCS 5a ed., Cap 17)make_vertissolo_canonical
Mineral material (WRB 2022 Ch 3.3.11): < 20% SOC AND < 35% volume artefacts containing >= 20% organic carbon. The complement of organic_material / organotechnic_material.mineral_material
Mollic horizon (WRB 2022)mollic
Mudanca textural abrupta (SiBCS Cap 1, p 30-31)mudanca_textural_abrupta
Mulmic material (WRB 2022 Ch 3.3.12): mineral material developed from organic material; \>= 8% SOC, with low BD, structural / chroma criteria.mulmic_material
Natric horizon (WRB 2022)natric_horizon
Nitic horizon (WRB 2022)nitic_horizon
Canonicalise FEBR SiBCS names to match soilKey rule outputs.normalise_febr_sibcs
Normalise FEBR USDA taxon strings to USDA Soil Taxonomy Ordernormalise_febr_usda
Normalise FEBR WRB taxon strings to RSG-onlynormalise_febr_wrb
Normalise KSSL USDA subgroup labels for benchmark comparisonnormalise_kssl_subgroup
Is the local Ollama HTTP API reachable?ollama_is_running
Organic material (WRB 2022 Ch 3.3.13): \>= 20% SOC + recognisability criteria. v0.3.3: SOC threshold only.organic_material
Organotechnic material (WRB 2022 Ch 3.3.14): \>= 35% volume of artefacts that themselves contain \>= 20% organic C. Soil itself has < 20% SOC.organotechnic_material
Ornithogenic material (WRB 2022 Ch 3.3.15): bird-influenced topsoil. Mehlich-3 P >= 750 mg/kg + designation pattern 'Aornit|Bornit'.ornithogenic_material
Synthetic OSSL South America demo subsetossl_demo_sa
Canonical schema for an `ossl_library` objectossl_library_template
Oxic horizon (USDA Soil Taxonomy)oxic_usda
Panpaic horizon (WRB 2022 Ch 3.1)panpaic
JSON Schema for a soilKey PedonRecordpedon_json_schema
Convert a soilKey PedonRecord to an aqp SoilProfileCollectionpedon_to_spc
PedonRecord: structured representation of a single pedonPedonRecord
Build PedonRecords with attached Vis-NIR/MIR spectra from a tablepedons_from_spectral_table
Petrocalcic horizon (WRB 2022)petrocalcic
Petroduric horizon (WRB 2022): cemented duric.petroduric
Petrogypsic horizon (WRB 2022): cemented gypsic.petrogypsic
Petroplinthic horizon (WRB 2022): cemented plinthic.petroplinthic
Phaeozem RSG diagnostic (WRB 2022)phaeozem
Map a 95% prediction interval to a [0, 1] confidence scorepi_to_confidence
Choose the best diagnostic engine for a single pedonpick_engine
Per-pedon batch engine recommendationpick_engine_batch
Pisoplinthic horizon (WRB 2022): pisolitic plinthic. v0.3.3 detects via designation pattern 'Bspl' / 'Bvpi' or via plinthite \>= 15% AND structure_type containing 'pisol'.pisoplinthic
Plaggic horizon (WRB 2022): sod-derived topsoil >= 20 cm with low BD AND independent evidence of human input.plaggic
Planic features (WRB 2022)planic_features
Planosol RSG gate (WRB 2022 Ch 4, p 107)planosol
Plinthic horizon (WRB 2022)plinthic
Bayesian posterior classifier (optional)posterior_classify
Predict soil properties from spectrapredict_from_spectra
Predict CIE Lab from Vis-NIR reflectance spectrapredict_lab_from_spectra
Predict Munsell hue / value / chroma from Vis-NIR reflectance spectrapredict_munsell_from_spectra
Memory-based learning prediction against the OSSL librarypredict_ossl_mbl
Local PLSR prediction against the OSSL librarypredict_ossl_plsr_local
Pre-trained OSSL predictionpredict_ossl_pretrained
Predict CIE XYZ tristimulus values from Vis-NIR reflectance spectrapredict_xyz_from_spectra
Predict from a soilKey_pls_modelpredict.soilKey_pls_model
Pre-process Vis-NIR or MIR spectrapreprocess_spectra
Pretic horizon (WRB 2022): "Amazonian Dark Earth" (terra preta de indio) horizon - thick anthropogenic surface with high P, SOC, and incorporated charcoal / pottery.pretic
Print method for soilKey_pls_modelprint.soilKey_pls_model
Check consistency between a deterministic RSG assignment and a spatial priorprior_consistency_check
Protocalcic properties (WRB 2022 Ch 3.2.8)protocalcic_properties
Protogypsic properties (WRB 2022 Ch 3.2.9): visible secondary gypsum \>= 1% but below the gypsic gate.protogypsic_properties
Protovertic horizon (WRB 2022 Ch 3.1)protovertic
Load FEBR datasets as a list of PedonRecord objectsread_febr_pedons
Read a horizon spreadsheet (CSV/TSV) into a PedonRecordread_pedon_csv
Read a Vis-NIR / MIR reflectance + lab table into an OSSL-shaped libraryread_spectral_library
Reducing conditions (WRB 2022 Ch 3.2.10) - per-pedon test wrapping 'test_reducing_conditions'.reducing_conditions
Render a soilKey classification reportreport
Render a soilKey classification report as self-contained HTMLreport_html
Render a soilKey classification report as PDFreport_pdf
Export a classification result + pedon to a QGIS GeoPackagereport_to_qgis
Resolve WRB 2022 qualifiers for a Reference Soil Groupresolve_wrb_qualifiers
Retic properties (WRB 2022)retic_properties
Run the full soilKey benchmark suite and (optionally) write a reportrun_all_benchmarks
Launch the soilKey interactive classification Shiny apprun_classify_app
Launch the soilKey Shiny demo (one-screen GUI)run_demo
Resolve o grande grupo (3o nivel) de um pedon classificado em uma subordem SiBCSrun_sibcs_grande_grupo
Roda a chave SiBCS 5a edicao sobre um pedonrun_sibcs_key
Resolve o subgrupo (4o nivel) de um pedon classificado em um Grande Grupo SiBCSrun_sibcs_subgrupo
Resolve a subordem de um pedon ja classificado em uma ordem SiBCSrun_sibcs_subordem
Iterate a flat taxa list and evaluate tests in canonical orderrun_taxa_list
Run a taxonomic key (system-agnostic engine)run_taxonomic_key
Run the USDA Great Group key for a given Suborderrun_usda_great_group
Run the USDA Soil Taxonomy Order key over a pedonrun_usda_key
Run the USDA Subgroup key for a given Great Grouprun_usda_subgroup
Run the USDA Suborder key for a given Orderrun_usda_suborder
Run the WRB 2022 key over a pedonrun_wrb_key
Salic horizon (WRB 2022)salic
Material organico saprico (SiBCS Cap 14)saprico
Save / load trained OSSL-backed PLSR modelsload_ossl_models save_ossl_models
Shrink-swell cracks (WRB 2022 Ch 3.2.12) - per-pedon test wrapping 'test_shrink_swell_cracks'.shrink_swell_cracks
Sideralic properties (WRB 2022 Ch 3.2.13)sideralic_properties
Likely soil classes at a geographic location (spatial classification aid)soil_classes_at_location
Soil organic carbon (WRB 2022 Ch 3.3.16): organic C that does NOT belong to artefacts. v0.3.3: any layer with oc_pct >= 0.1 and artefacts_industrial_pct < 35.soil_organic_carbon
SoilGrids -> USDA Soil Order lookup table (placeholder)soilgrids_usda_lut
SoilGrids -> WRB code lookup tablesoilgrids_wrb_lut
Solimovic material (WRB 2022 Ch 3.3.17): hetero genous mass-movement material on slopes / footslopes (formerly "colluvic"). v0.3.3: detects via 'rock_origin == "colluvial"' OR 'layer_origin == "solimovic"'.solimovic_material
Sombric horizon (WRB 2022): subsurface accumulation of humus that qualified neither as spodic nor as a true mollic-like horizon (low-base-saturation cool tropical highlands). v0.3.3 detects via designation pattern + OC criteria (BS < 50, OC > 0.6, depth > 25 cm).sombric
Spatial prior over RSGs (or Orders) at a pedon's locationspatial_prior
Embrapa national soil-class spatial prior (Brazil only)spatial_prior_embrapa
SoilGrids spatial priorspatial_prior_soilgrids
Spodic horizon (WRB 2022)spodic
USDA Soil Taxonomy diagnostic features canonical tablest_features_canonical
Stagnic properties (WRB 2022)stagnic_properties
Subgrupo "espessos" de Planossolos (B planico profundo, > 100 cm)subgrupo_planossolo_espessos
Subgrupo "mesicos" de Planossolos (B planico topo em [50, 100] cm)subgrupo_planossolo_mesicos
Subgrupo "endico" de Plintossolos Concrecionarios (topo de horizonte concrecionario >= 40 cm)subgrupo_plintossolo_endico_concrecionario
Subgrupo "endico" de Plintossolos Litoplinticos (topo de horizonte litoplintico >= 40 cm)subgrupo_plintossolo_endico_litoplintico
Subgrupo "espessos" de Plintossolos (horizonte plintico topo > 100 cm)subgrupo_plintossolo_espessos
Takyric properties (WRB 2022 Ch 3.2.15) - per-pedon test wrapping 'test_takyric_surface'.takyric_properties
Technic features (WRB 2022)technic_features
Technic hard material (WRB 2022 Ch 3.3.18): consolidated human-made material (asphalt, concrete, worked stones).technic_hard_material
Tephric material (WRB 2022 Ch 3.3.19): \>= 30% volcanic glass in 0.02-2 mm fraction AND no andic / vitric properties.tephric_material
Terric horizon (WRB 2022): topsoil thickened by long-term application of mineral material (sediment / sand additions). v0.3.3: thickness >= 20 cm + designation Au / Apc.terric
NRCS texture-class shorthand from clay / silt / sand percenttexture_class_from_pct
Thionic horizon (WRB 2022): post-oxidation acid sulfate horizon. Requires sulfidic_s_pct >= 0.01 AND pH(H2O) <= 4.thionic
Train pre-trained PLSR models from an OSSL librarytrain_pls_from_ossl
Tsitelic horizon (WRB 2022 Ch 3.1)tsitelic
Umbric horizon (WRB 2022)umbric_horizon
USDA Soil Taxonomy <-> WRB Reference Soil Group correlation tableusda_to_wrb_rsg
Validate horizon depth geometryvalidate_horizon_geometry
Validate a PedonRecord against the JSON schemavalidate_pedon_json
Vertic horizon (WRB 2022 Ch 3.1)vertic_horizon
Vertic properties (WRB 2022)vertic_properties
Vertisol RSG gate (WRB 2022 Ch 4, p 101)vertisol
Vitric properties (WRB 2022 Ch 3.2.16)vitric_properties
Pick the best available VLM providervlm_pick_provider
Construct a VLM provider chat objectvlm_provider
WRB 2006 RSG code -> 2022 RSG namewrb06_code_to_rsg
WRB 2022 canonical reference (parsed IUSS Working Group WRB 2022)wrb2022_canonical
Yermic properties (WRB 2022 Ch 3.2.17) - per-pedon test wrapping 'test_yermic_surface'.yermic_properties