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.