Changelog • phylospatial

phylospatial (development version)

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.

CRAN release: 2025-12-23

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 release: 2025-12-20

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.

CRAN release: 2025-05-02

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.

CRAN release: 2025-04-09

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.

CRAN release: 2025-01-24