Release v0.9.0 · gcol33/spacc

API Changes

wavefront() was renamed spaccWavefront() so that every spatial-accumulation
curve front door shares the spacc prefix. The old name is a deprecated thin
wrapper and still works. The distance- and area-relationship functions keep
their established names: distanceDecay(), betaDecay(), zetaDiversity(),
and dar().
spaccBeta() gains traits and tree arguments and now computes taxonomic,
functional, or phylogenetic beta diversity from a single front door. Supplying
traits gives the trait-weighted Baselga partition; supplying tree gives the
branch-length-weighted (PhyloSor) partition. spaccBetaFunc() and
spaccBetaPhylo() are deprecated thin wrappers and still work.
diversityProfile() gains traits and tree arguments and now computes
taxonomic, functional (Leinster-Cobbold), or phylogenetic (Chao et al.) Hill
profiles from a single front door. diversityProfileFunc() and
diversityProfilePhylo() are deprecated thin wrappers and still work.

extrapolateArea() extrapolates richness to a spatial extent larger than the
one sampled, using the total-species (T-S) curve of Ugland, Gray & Ellingsen
(2003): sites are partitioned into spatial subareas, the expected total
richness of random subarea combinations is plotted against their convex-hull
area, and an asymptotic model is fitted and extended to a target area with a
median-bias-corrected site-bootstrap interval. New spacc_area class with
print()/summary()/plot()/predict()/as.data.frame() methods.
extrapolate() gains a calibrated interval = "bootstrap" (now the default)
that refits the chosen model across resampled seed curves and returns
percentile bounds, replacing the over-confident nls profile interval as the
default. predict(fit, interval = "bootstrap") returns a prediction band, and
plot() draws it. interval = "profile" recovers the old behaviour.
extrapolate() now reports goodness of fit (residual RMSE over the observed
range), an extrapolation-range note, and the nonparametric chao2()/iChao2()
estimates alongside the asymptote. It warns when the asymptote exceeds the
observed richness by more than warn_ratio (default 2), when it disagrees with
chao2() by more than 50%, and when predict() is evaluated beyond ~2.5x the
sampled effort.

plot() on a spacc_endemism object no longer lists "Endemic species" twice
in the legend. The confidence-band fill was drawn as its own guide because the
ribbon covered only the endemism series; that fill guide is now suppressed so a
single line-colour legend remains.
Removed a stray blank line beneath the y-axis title in plot() for
spacc_beta objects.
extrapolate() asymptote confidence intervals are no longer over-confident.
The previous confint() used an nls profile interval on the (ultra-smooth)
mean curve, ignoring across-seed variability; it could exclude the truth in
every replicate of a recovery simulation. confint() now returns the
calibrated bootstrap interval by default (method = "profile" is still
available). The documentation notes that the parametric asymptote can be
biased high on clustered or under-sampled data and points to the nonparametric
estimators for calibrated total-richness intervals (#1, #3, #5).