Package index • spacc

Core Functions

Main spatial accumulation functions

spacc(): Spatial Species Accumulation Curves
spaccDiversity(): Spatial Accumulation of a Custom Diversity Metric
spaccWavefront() wavefront(): Wavefront Expansion Accumulation
distanceDecay(): Distance-Decay Analysis
distances(): Compute Distance Matrix

Diversity

Alpha, beta, and gamma diversity partitioning

alphaDiversity(): Alpha Diversity (Per-Site)
gammaDiversity(): Gamma Diversity (Regional)
diversityPartition(): Alpha-Beta-Gamma Diversity Partitioning
diversityProfile() diversityProfilePhylo() diversityProfileFunc(): Diversity Profile
evenness(): Evenness Profiles

Hill Numbers

Diversity accumulation with Hill numbers (q=0,1,2)

spaccHill(): Spatial Accumulation with Hill Numbers
spaccHillCoverage(): Spatial Hill Numbers at Standardized Coverage
spaccHillBeta(): Spatial Hill Number Beta Diversity

Beta Diversity

Spatial beta diversity with turnover/nestedness partitioning

spaccBeta() spaccBetaFunc() spaccBetaPhylo(): Spatial Beta Diversity Accumulation

Community Turnover

Distance-decay, zeta diversity, and null models

betaDecay(): Beta Distance-Decay
zetaDiversity(): Zeta Diversity
ses(): Standardized Effect Size (SES) via Null Models

Phylogenetic & Functional Diversity

Accumulation of PD and FD metrics

spaccPhylo(): Spatial Phylogenetic Diversity Accumulation
spaccFunc(): Spatial Functional Diversity Accumulation

Coverage-Based Rarefaction

Standardize by sample completeness

spaccCoverage(): Coverage-Based Spatial Rarefaction
interpolateCoverage(): Interpolate Richness at Target Coverage Levels
extrapolateCoverage(): Extrapolate Richness Beyond Observed Coverage

Per-Site Metrics

Extract metrics per starting site for heatmap visualization

spaccMetrics(): Per-Site Accumulation Metrics
as_sf(): Convert spacc_metrics to sf

Richness Estimators

Non-parametric richness estimation

chao1(): Chao1 Richness Estimator
chao2(): Chao2 Richness Estimator
iChao1(): Improved Chao1 (iChao1) Richness Estimator
iChao2(): Improved Chao2 (iChao2) Richness Estimator
ace(): ACE Richness Estimator
jackknife(): Jackknife Richness Estimator
bootstrap_richness(): Bootstrap Richness Estimator
completenessProfile(): Sample Completeness Profile

Spatial Structure

Spatial eigenvectors and variance partitioning

spatialEigenvectors(): Spatial Eigenvectors (PCNM/dbMEM)
spatialPartition(): Spatial Variance Partitioning with MEMs

Analytical Methods

Expected curves without simulation

coleman(): Coleman Expected Accumulation
mao_tau(): Exact (Mao Tau) Expected Accumulation
collector(): Collector's Curve
spatialRarefaction(): Spatially-Constrained Rarefaction

Species-Area Relationships

Diversity-area relationships, endemism, fragmentation

dar(): Diversity-Area Relationship (DAR)
spaccEndemism(): Spatial Endemism Accumulation
sesars(): Sampling Effort Species-Area Relationship (SESARS)
sfar(): Species-Fragmented Area Relationship (SFAR)

Analysis

Post-hoc analysis of accumulation curves

extrapolate(): Extrapolate Total Species Richness
extrapolateArea(): Extrapolate Richness to a Larger Area (Ugland T-S Curve)
compare(): Compare Two Accumulation Curves
as_spacc(): Convert an Accumulation Curve from Another Package to a spacc Object
rarefy(): Individual-Based Rarefaction
subsample(): Spatial Subsampling

Internal

Internal functions (not for end users)

analytical: Analytical Accumulation Methods
c(<spacc>): Combine spacc Objects
c(<spacc_beta>): Combine spacc_beta Objects
c(<spacc_coverage>): Combine spacc_coverage Objects
c(<spacc_hill>): Combine spacc_hill Objects
compareModels(): Compare Multiple SAR Models
predict(<spacc>): Predict from Empirical Accumulation Curve
predict(<spacc_fit>): Predict richness at a given sampling effort
predict(<spacc_area>): Predict richness at a given area
confint(<spacc_fit>): Confidence interval for an extrapolated asymptote
plot(<spacc>): Plot Spatial SAC
plot(<spacc_metrics>): Plot spacc_metrics
autoplot.spacc: Autoplot Methods for spacc Objects