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Changelog

Source: NEWS.md

phylospatial (development version)

  • plot.phylospatial() gains a taxa argument for choosing which lineage ranges to plot when y = "comm", by name or by index, instead of a random sample. Also fixed the max_taxa documentation, which referred to the wrong y value.

  • moss() gains a data argument for loading companion layers on the same grid as the moss data set: "protection" (fraction of each cell in protected areas) and "popdens" (human population density), for use as init and cost in conservation prioritizations. Both are available in raster and polygon formats.

  • Fixed an error in ps_prioritize() and ps_prioritizr() when init or cost was supplied as an sf object, which the documentation already listed as supported.

phylospatial 1.5.0

CRAN release: 2026-10-01

  • New tree scaling functions modify a phylogeny’s branch lengths to focus analyses on particular parts of evolutionary history. slice_tree() keeps only the portions of branches within a specified depth window, enabling time-sliced diversity analyses. delta_tree() applies Pagel’s delta transformation while preserving total tree height, shifting emphasis toward deeper or more recent divergence. uniform_tree() sets all branch lengths to 1, so that phylogenetic diversity measures become clade richness. rescale_tree() is a unit conversion function that rescales branch lengths without changing their relative proportions. Transformed trees can be passed to phylospatial() or assigned to the tree element of an existing phylospatial object. See ?tree_scaling and vignette("phylospatial-data").

  • phylospatial() gains a rescale argument controlling how branch lengths are scaled during construction: "sum1" (the default, matching previous behavior) scales them to sum to 1, "tip1" scales the longest root-to-tip path to 1, and "raw" keeps the original units. The method used is recorded in the new ps$rescale element.

  • New function ps_performance() computes performance curves for ps_prioritize() results, tracking cumulative cost, protection added, conservation value, and the fraction of the tree meeting one or more range protection targets as sites are added in priority order. A plot() method is included. To support this, ps_prioritize() results now carry a "prioritization" attribute recording the settings, inputs, and raw rankings used.

  • Fixed a bug in ps_prioritize() where sites not selected before max_iter was reached were returned as NA rather than the lowest possible rank (as documented). With method = "probable" and summarize = TRUE, this also inflated summary statistics for sites selected in only a few reps, since the average rank, rank percentiles, and topX proportions were computed only across reps in which a site was selected. Unselected sites are now ranked last (i.e. equal to the number of occupied sites) in all outputs.

  • Fixed an error in ps_prioritize() when using method = "probable" and summarize = FALSE with spatial output. Rep layers are now named rep1, rep2, etc.

  • New function ps_prioritizr() converts a phylospatial object into a conservation planning problem for the prioritizr package, which finds optimal solutions using integer linear programming. Every branch of the phylogeny is treated as a conservation feature with a range protection target, and existing protection (init) counts toward targets. Three objectives are supported: minimum-cost target achievement ("min_set"), and maximum target coverage ("targets") or minimum target shortfall ("shortfall") within a budget. The returned problem can be extended with any of prioritizr’s solvers, constraints, and penalties. Requires prioritizr (>= 9.0.0).

phylospatial 1.4.0

CRAN release: 2026-04-16

  • 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.

phylospatial 1.3.0

CRAN release: 2026-04-03

New features

  • 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.

Breaking changes

  • 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.

phylospatial 1.2.1

CRAN release: 2025-12-23

phylospatial 1.2.0

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.

phylospatial 1.1.1

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.

phylospatial 1.1.0

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.

phylospatial 1.0.0

CRAN release: 2025-01-24

  • Initial release