Package: spacc 0.8.3

Gilles Colling

spacc: Fast Spatial Species Accumulation Curves

High-performance spatial species accumulation curves using nearest-neighbor algorithms. Implements 'kNN' and 'kNCN' sampling methods with a 'C++' backend for speed. Supports Hill numbers (q=0,1,2), beta diversity partitioning (turnover/nestedness), coverage-based rarefaction and extrapolation, phylogenetic diversity (Faith's PD, mean pairwise distance, mean nearest taxon distance), functional diversity accumulation, diversity-area relationships (DAR), endemism-area curves, sampling-effort correction and fragmentation analysis, and species-area relationship (SAR) models based on extreme value theory (EVT). Multiple starting points (seeds) provide uncertainty quantification. Methods are described in 'Chao' et al. (2014) <doi:10.1890/13-0133.1>, 'Baselga' (2010) <doi:10.1111/j.1466-8238.2009.00490.x>, 'Chao' and 'Jost' (2012) <doi:10.1890/11-1952.1>, 'Faith' (1992) <doi:10.1016/0006-3207(92)91201-3>, 'Ma' (2018) <doi:10.1002/ece3.4526>, 'Borda-de-Agua' et al. (2025) <doi:10.1038/s41467-025-59239-7>, 'Hanski' et al. (2013) <doi:10.1073/pnas.1311190110>, and 'Jost' (2007) <doi:10.1890/06-1736.1>.

Authors:Gilles Colling [aut, cre, cph]

spacc_0.8.3.tar.gz
spacc_0.8.3.tar.gz(r-4.7-arm64)spacc_0.8.3.tar.gz(r-4.7-x86_64)spacc_0.8.3.tar.gz(r-4.6-arm64)spacc_0.8.3.tar.gz(r-4.6-x86_64)
spacc_0.8.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
spacc/json (API)
NEWS

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

Bug tracker:https://github.com/gcol33/spacc/issues

Pkgdown/docs site:https://gillescolling.com

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

3.99 score 28 scripts 51 exports 2 dependencies

Last updated from:075fd1c458. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK202
linux-devel-x86_64OK221
source / vignettesOK312
linux-release-arm64OK198
linux-release-x86_64OK213
wasm-releaseOK157

Exports:acealphaDiversityas_sfbetaDecaybootstrap_richnesschao1chao2colemancollectorcomparecompareModelscompletenessProfiledardistanceDecaydistancesdiversityPartitiondiversityProfilediversityProfileFuncdiversityProfilePhyloevennessextrapolateextrapolateCoveragegammaDiversityiChao1iChao2interpolateCoveragejackknifemao_taurarefysessesarssfarspaccspaccBetaspaccBetaFuncspaccBetaPhylospaccCoveragespaccDiversityspaccEndemismspaccFuncspaccHillspaccHillBetaspaccHillCoveragespaccMetricsspaccPhylospatialEigenvectorsspatialPartitionspatialRarefactionsubsamplewavefrontzetaDiversity

Dependencies:RcppRcppParallel

Community Assembly and Turnover

Rendered fromcommunity-assembly.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2026-06-20
Started: 2026-06-20

Diversity Accumulation

Rendered fromdiversity.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2026-06-20
Started: 2026-06-20

Extrapolation and Species-Area Models

Rendered fromextrapolation.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2026-06-20
Started: 2026-06-20

Getting Started with spacc

Rendered fromquickstart.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2026-06-20
Started: 2026-06-20

Rarefaction and Standardization

Rendered fromrarefaction-standardization.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2026-06-20
Started: 2026-06-20

Richness Estimation and Completeness

Rendered fromrichness-estimation.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2026-06-20
Started: 2026-06-20

Spatial Analysis: Endemism, Fragmentation, and SAR

Rendered fromspatial-analysis.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2026-06-20
Started: 2026-06-20

Readme and manuals

Help Manual

Help pageTopics
ACE Richness Estimatorace
Alpha Diversity (Per-Site)alphaDiversity
Analytical Accumulation Methodsanalytical
Convert spacc_metrics to sfas_sf
Autoplot Methods for spacc Objectsautoplot.spacc
Beta Distance-DecaybetaDecay
Bootstrap Richness Estimatorbootstrap_richness
Combine spacc Objectsc.spacc
Combine spacc_beta Objectsc.spacc_beta
Combine spacc_coverage Objectsc.spacc_coverage
Combine spacc_hill Objectsc.spacc_hill
Chao1 Richness Estimatorchao1
Chao2 Richness Estimatorchao2
Coleman Expected Accumulationcoleman
Collector's Curvecollector
Compare Two Accumulation Curvescompare
Compare Multiple SAR ModelscompareModels
Sample Completeness ProfilecompletenessProfile
Diversity-Area Relationship (DAR)dar
Distance-Decay AnalysisdistanceDecay
Compute Distance Matrixdistances
Alpha-Beta-Gamma Diversity PartitioningdiversityPartition
Diversity ProfilediversityProfile
Functional Diversity ProfilediversityProfileFunc
Phylogenetic Diversity ProfilediversityProfilePhylo
Evenness Profilesevenness
Extrapolate Total Species Richnessextrapolate
Extrapolate Richness Beyond Observed CoverageextrapolateCoverage
Gamma Diversity (Regional)gammaDiversity
Improved Chao1 (iChao1) Richness EstimatoriChao1
Improved Chao2 (iChao2) Richness EstimatoriChao2
Interpolate Richness at Target Coverage LevelsinterpolateCoverage
Jackknife Richness Estimatorjackknife
Exact (Mao Tau) Expected Accumulationmao_tau
Plot Spatial SACplot.spacc
Plot spacc_metricsplot.spacc_metrics
Predict from Empirical Accumulation Curvepredict.spacc
Individual-Based Rarefactionrarefy
Standardized Effect Size (SES) via Null Modelsses
Sampling Effort Species-Area Relationship (SESARS)sesars
Species-Fragmented Area Relationship (SFAR)sfar
Spatial Species Accumulation Curvesspacc
Spatial Beta Diversity AccumulationspaccBeta
Functional Beta Diversity AccumulationspaccBetaFunc
Phylogenetic Beta Diversity AccumulationspaccBetaPhylo
Coverage-Based Spatial RarefactionspaccCoverage
Spatial Accumulation of a Custom Diversity MetricspaccDiversity
Spatial Endemism AccumulationspaccEndemism
Spatial Functional Diversity AccumulationspaccFunc
Spatial Accumulation with Hill NumbersspaccHill
Spatial Hill Number Beta DiversityspaccHillBeta
Spatial Hill Numbers at Standardized CoveragespaccHillCoverage
Per-Site Accumulation MetricsspaccMetrics
Spatial Phylogenetic Diversity AccumulationspaccPhylo
Spatial Eigenvectors (PCNM/dbMEM)spatialEigenvectors
Spatial Variance Partitioning with MEMsspatialPartition
Spatially-Constrained RarefactionspatialRarefaction
Spatial Subsamplingsubsample
Wavefront Expansion Accumulationwavefront
Zeta DiversityzetaDiversity