Package: spacc
Title: Fast Spatial Species Accumulation Curves
Version: 0.11.0
Authors@R: c(
    person("Gilles", "Colling", , "gilles.colling051@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0003-3070-6066")),
    person("Marius", "Muja", role = c("ctb", "cph"),
           comment = "nanoflann library (inst/include/nanoflann.hpp, BSD license)"),
    person("David G.", "Lowe", role = c("ctb", "cph"),
           comment = "nanoflann library (inst/include/nanoflann.hpp, BSD license)"),
    person("Jose Luis", "Blanco", role = c("ctb", "cph"),
           comment = "nanoflann library (inst/include/nanoflann.hpp, BSD license)")
    )
Copyright: See inst/COPYRIGHTS for the copyright holders of the bundled
        nanoflann library.
Description: 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>.
License: MIT + file LICENSE
Language: en-US
Encoding: UTF-8
Depends: R (>= 3.5)
LinkingTo: Rcpp, RcppParallel
Imports: Rcpp, RcppParallel, stats, parallel
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, svglite, ggplot2, cli,
        sf, areaOfEffect, ape, iNEXT, iNEXT.3D, iNEXT.beta3D, betapart,
        cluster, vegan
Config/testthat/edition: 3
VignetteBuilder: knitr
SystemRequirements: GNU make
URL: https://gillescolling.com/spacc/, https://github.com/gcol33/spacc
BugReports: https://github.com/gcol33/spacc/issues
Config/roxygen2/version: 8.1.0
NeedsCompilation: yes
Packaged: 2026-10-10 20:27:46 UTC; Gilles Colling
Author: Gilles Colling [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-3070-6066>),
  Marius Muja [ctb, cph] (nanoflann library (inst/include/nanoflann.hpp,
    BSD license)),
  David G. Lowe [ctb, cph] (nanoflann library
    (inst/include/nanoflann.hpp, BSD license)),
  Jose Luis Blanco [ctb, cph] (nanoflann library
    (inst/include/nanoflann.hpp, BSD license))
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Repository: CRAN
Date/Publication: 2026-10-11 13:40:12 UTC
