High-Performance Open-Source Archive
New function ps_grid() converts point occurrence
data (e.g. GBIF records) into raster format suitable for use with
phylospatial functions.
New functions ps_suggest_n_iter() and
ps_trace() provide convergence diagnostics for null model
randomizations, wrapping nullcat::suggest_n_iter() and
nullcat::trace_cat() on the occupied-site tip community
matrix.
ps_rand() and ps_quantize() now expose
wt_row and wt_col as named parameters for
spatially or functionally constrained null models. These accept weight
matrices (e.g., a geographic distance decay matrix from
ps_geodist()) that bias which pairs of sites or species
exchange values during randomization.
ps_rand() gains a new fun = "nullcat"
path for binary data. This is the recommended path for binary data when
convergence diagnostics or spatial weights are desired.
ps_rand() now exposes n_iter as a named
parameter controlling the number of swap iterations per null matrix.
This is routed to nullcat::nullcat(),
nullcat::quantize_prep(), or
vegan::simulate.nullmodel() (as burnin)
depending on the selected fun. The default of 1000 fixes a
pre-existing issue where the vegan sequential path used only 1 iteration
per matrix by default.
ps_dissim() now computes distances much faster via
parallelDist for relevant metrics, while falling back to
vegan as needed. It also adds support for traditional
non-phylogenetic species turnover metrics via a new
tips_only option.
New helper function ps_geodist() computes pairwise
geographic distances between sites.
The community matrix (ps$comm) now stores only
occupied sites, improving speed and memory usage for datasets with many
unoccupied cells. Speedups are proportional to the fraction of empty
sites and affect all major functions, with ps_dissim()
seeing the largest gains (~4x with 50% unoccupied cells) due to its
quadratic scaling.
New fields ps$occupied and ps$n_sites
track which rows in the original data are occupied and the total site
count, respectively.
New exported function ps_expand() expands
occupied-only results back to the full spatial extent with
NA for unoccupied sites.
nrow(ps$comm) now equals the number of occupied
sites, not total cells. Use ps$n_sites for the
total.
ps$dissim is now dimensioned to occupied sites
only.
to_spatial(ps$comm, ps$spatial) no longer works
directly. Use ps_expand(ps, ps$comm, spatial = TRUE) or
ps_get_comm(ps) instead.
ps_get_comm() with spatial = FALSE
returns an occupied-only matrix.
ps_diversity(), ps_rand(),
ps_dissim(), and ps_prioritize() have been
refactored to optimize compute speed (~2x to 20x speedup).
ps_ordinate() now defaults to
method = "cmds", and has a bug fixed in its
"pca" method.
CRAN compliance: fixed vignette builds to conditionally load suggested package ‘tmap’.
ps_diversity() now computes a smaller set of metrics
by default, in order to reduce default run times.
ps_rand() includes a new choice of summary
statistic: in addition to the default “quantile” function, a new
“z-score” option is available.
quantize() and ps_rand() now use
nullcat::quantize() internally, addressing a flaw in the
earlier implementation.
phylospatial() and other functions that call it now
use a compute-optimized internal range constructor.
ps_diversity() now computes a smaller set of metrics
by default, in order to reduce runtimes.
ps_rand() includes a new choice of summary
statistic: in addition to the default “quantile” function, a new
“z-score” option is available.
ps_diversity() now includes several new divergence
and regularity measures, including terminal- and node-based versions of
mean pairwise distance (MPD) and variance in pairwise distance
(VPD).
ps_rand() now includes an explicit
"tip_shuffle" algorithm; previously this method could only
be implemented by supplying a custom randomization function.
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