spacc
High-performance spatial species accumulation curves using fixed-focus spatially constrained rarefaction, nearest-centroid expansion, and nearest-neighbor walks with a C++ backend for speed. Supports Hill numbers (q=0,1,2), beta diversity partitioning (turnover/nestedness) at site and pooled resolution, coverage-based rarefaction and extrapolation of alpha and beta diversity, phylogenetic diversity (PD; Faith's PD, EvoHeritage, mean pairwise distance, mean nearest taxon distance), functional diversity accumulation including aggregated functional diversity and intraspecific trait variation, phylogenetic and functional redundancy, interaction network accumulation, diversity-area relationships (DAR), endemism-area curves, sampling-effort correction and fragmentation analysis, species-area relationship (SAR) models based on extreme value theory (EVT), and area-based richness extrapolation via the total-species curve. Total richness is also estimated from frequency counts, including the accumulation rate curve estimator and an estimator for sites sampled without replacement, and shift-and-rotate null models test the position of a sampling design. 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/ece3.4425>, Borda-de-Agua et al. (2025) <doi:10.1038/s41467-025-59239-7>, Hanski et al. (2013) <doi:10.1073/pnas.1311190110>, Jost (2007) <doi:10.1890/06-1736.1>, Ugland et al. (2003) <doi:10.1046/j.1365-2656.2003.00748.x>, Chao et al. (2023) <doi:10.1002/ecm.1588>, Chiu (2023) <doi:10.1111/2041-210X.14146>, Chiu et al. (2023) <doi:10.1098/rstb.2022.0183>, Rosindell et al. (2024) <doi:10.1093/sysbio/syad072>, Wojcik et al. (2024) <doi:10.1111/2041-210X.14470>, Ridder et al. (2024) <doi:10.1111/2041-210X.14443>, Jones et al. (2025) <doi:10.1111/ddi.70080>, and Shestopaloff (2025) <doi:10.1007/s10651-025-00644-y>.
- A species richness estimator for sample‐based incidence data sampled without replacement
- An accumulation rate curve estimator for total species
- Conservation evaluation and phylogenetic diversity
- Coverage‐based rarefaction and extrapolation: standardizing samples by completeness rather than size
- DAR (diversity–area relationship): Extending classic SAR (species–area relationship) for biodiversity and biogeography analyses
- Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling
- Measuring overall functional diversity by aggregating its multiple facets: Functional richness, biomass evenness, trait evenness and dispersion
- Microclimate moderates plant responses to macroclimate warming
- Modelling the species-area relationship using extreme value theory
- Partitioning Beta Diversity at Two Spatial Resolutions Reveals Biotic Homogenisation With Habitat Degradation
- PARTITIONING DIVERSITY INTO INDEPENDENT ALPHA AND BETA COMPONENTS
- Partitioning the turnover and nestedness components of beta diversity
- Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage
- Quantifying and estimating ecological network diversity based on incomplete sampling data
- Rarefaction and extrapolation with beta diversity under a framework of Hill numbers: The iNEXT.beta3D standardization
- Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies
- The species–accumulation curve and estimation of species richness
This page was built for software: spacc
