Package: h3sdm 0.1.5

Manuel Spínola

h3sdm: Species Distribution Modeling with H3 Grids

Provides tools for species distribution modeling using H3 hexagonal grids (Uber Technologies Inc., 2022, <https://h3geo.org>). Facilitates retrieval of species occurrence records, generation of H3 grids, computation of landscape metrics, and preparation of spatial data for modern species distribution models workflows. Designed for biodiversity and landscape ecology research.

Authors:Manuel Spínola [aut, cre]

h3sdm_0.1.5.tar.gz
h3sdm_0.1.5.tar.gz(r-4.7-any)h3sdm_0.1.5.tar.gz(r-4.6-any)
h3sdm_0.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
h3sdm/json (API)
NEWS

# Install 'h3sdm' in R:
install.packages('h3sdm', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/manuelspinola/h3sdm/issues

Datasets:
  • cr_outline - Costa Rica Full Outline
  • cr_outline_c - Costa Rica Continental Outline
  • records - Presence/pseudo-absence records for Silverstoneia flotator

On CRAN:

Conda:

3.70 score 20 scripts 638 downloads 28 exports 244 dependencies

Last updated from:cd7097e710. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK263
source / vignettesOK340
linux-release-x86_64OK259
wasm-releaseOK256

Exports:h3sdm_aoah3sdm_calculate_it_metricsh3sdm_classifyh3sdm_compare_modelsh3sdm_count_from_recordsh3sdm_datah3sdm_eval_metricsh3sdm_explainh3sdm_extract_cath3sdm_extract_numh3sdm_filter_outliersh3sdm_fit_modelh3sdm_fit_modelsh3sdm_get_gridh3sdm_get_recordsh3sdm_get_records_by_hexagonh3sdm_pah3sdm_pa_from_recordsh3sdm_predicth3sdm_predictorsh3sdm_presh3sdm_recipeh3sdm_recipe_gamh3sdm_spatial_cvh3sdm_stack_fith3sdm_workflowh3sdm_workflow_gamh3sdm_workflows

Dependencies:abindade4adehabitatHRadehabitatLTadehabitatMAaskpassassertthatbackportsbase64encBHbiomod2bitbit64blobbroombslibbutchercachemcallrcellrangercheckmateclassclassIntclicliprclockclustercodetoolscolorspaceconflictedcowplotcpp11crayoncrosstalkcrulcurlDALEXdata.tableDBIdbplyrdiagramdialsDiceDesigndigestdismodoFuturedplyrdtplyre1071ecodistecospatevaluateexactextractrfarverfastmapFNNfontawesomeforcatsforeachforeignFormulafsfurrrfuturefuture.applygargleGauProgbmgenericsgeojsonsfgeometriesggplot2glmnetglobalsgluegoogledrivegooglesheets4gowergridExtragtablegtoolsh3jsrhardhathavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttriBreakDownidsigraphingredientsipredisobanditeratorsjquerylibjsonifyjsonlitekableExtrakernelshapkernlabKernSmoothknitrkslabelinglandscapemetricslatticelavalazyevallbfgsleafletleaflet.providerslifecyclelistenvlobstrlubridatemagrittrmapsMASSMatrixmatrixStatsmclustmemoisemgcvmimemixoptmodelenvmodelrmulticoolmvtnormnabornlmennetnumDerivoaiopensslotelparallellyparsnippermutepillarpixmappkgconfigplyrpngpoibinpracmaPresenceAbsenceprettyunitspROCprocessxprodlimprogressprogressrproxypspurrrR6raggrapidjsonrrappdirsrasterrbiodatacrRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrebirdrecipesrematchrematch2reprexreshapereshape2rgbifridigbiorlangrmarkdownrpartrsamplerstudioapirvertnetrvests2S7sassscalesselectrsfsfdsfheadersshapesliderspsparsevctrsspatialsamplesplitfngrspoccSQUAREMstacksstringistringrsurvivalsvglitesyssystemfontstailorterratextshapingtibbletidyrtidyselecttidyversetimechangetimeDatetinytextriebeardtunetzdbunitsurltoolsutf8uuidV8vctrsveganvipviridisLitevroomwarpwhiskerwithrwkworkflowsxfunxml2yamlyardstick

h3sdm workflow for a single model

Rendered fromh3sdm.Rmdusingknitr::rmarkdownon Jun 13 2026.

Last update: 2026-06-12
Started: 2026-04-15

Readme and manuals

Help Manual

Help pageTopics
Current bioclimatic rasterbioclim_current
Future bioclimatic rasterbioclim_future
Costa Rica Full Outline (Continental + Islands)cr_outline
Costa Rica Continental Outlinecr_outline_c
Area of Applicability (AOA) of spatial prediction modelsh3sdm_aoa
Calculate Information Theory Landscape Metrics for Hexagonal Gridh3sdm_calculate_it_metrics
Classify predictions based on an optimal thresholdh3sdm_classify
Compare multiple H3SDM species distribution modelsh3sdm_compare_models
Generate species richness or abundance count dataset from recordsh3sdm_count_from_records
Combine species and environmental data for SDMs using H3 gridsh3sdm_data
Evaluate performance metrics for a fitted H3SDM modelh3sdm_eval_metrics
Create a DALEX explainer for h3sdm workflowsh3sdm_explain
Calculate Area Proportions for Categorical Raster Classesh3sdm_extract_cat
Extract Area-Weighted Mean from Numeric Raster Stackh3sdm_extract_num
Filter environmental outliers from presence records using Mahalanobis distanceh3sdm_filter_outliers
Fits an SDM workflow to data using resampling and prepares it for stacking.h3sdm_fit_model
Fit and evaluate multiple H3SDM species distribution modelsh3sdm_fit_models
Generar cuadrícula H3 para un área de interésh3sdm_get_grid
Query Species Occurrence Records within an H3 Area of Interest (AOI)h3sdm_get_records
Download Species Records and Count Occurrences per H3 Hexagonh3sdm_get_records_by_hexagon
Generate presence/pseudo-absence dataset stratified in environmental spaceh3sdm_pa
Generate presence/pseudo-absence dataset from user-provided recordsh3sdm_pa_from_records
Predict species presence probability or counts using H3 hexagonsh3sdm_predict
Combine Predictor Data from Multiple sf Objectsh3sdm_predictors
Assign species presence records to H3 hexagonsh3sdm_pres
Create a tidymodels recipe for H3-based SDMsh3sdm_recipe
Creates a 'recipe' object for Generalized Additive Models (GAM) in SDMh3sdm_recipe_gam
Create a spatial-aware cross-validation split for H3 datah3sdm_spatial_cv
Creates and fully fits an ensemble model (Stack).h3sdm_stack_fit
Create a tidymodels workflow for H3-based SDMsh3sdm_workflow
Creates a tidymodels workflow for Generalized Additive Models (GAM).h3sdm_workflow_gam
Create multiple tidymodels workflows for H3-based SDMsh3sdm_workflows
Presence/pseudo-absence records for Silverstoneia flotatorrecords