paleobuddy
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Comparison · Analytics
deeptime vs treespace
A side-by-side editorial comparison of deeptime and treespace — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:phylogenetics
deeptime vs treespace: at a glance
What is deeptime?
A geologic-time plotting layer that outgrew time axes and became a geology rendering toolkit.
deeptime extends ggplot2 with geological time scales, radial deep-time coordinates and phylogeny-aware geoms, and since 2.0.0 it also renders standardized FGDC/USGS geologic patterns as ggplot2 fills. The current 2.4.0 release adds geom_text_clade() for labeling clades on radial phylogenies and repairs long-standing coord_trans_xy() and scale-placement edge cases.
What is treespace?
treespace ships once every year or two, and only when CRAN or a user forces it.
treespace explores and compares sets of phylogenetic and transmission trees, including the tree-distance measures used in outbreak reconstruction. Its release history is entirely reactive: five updates across five years, each triggered by a CRAN policy change, an upstream package removal, or a bug someone reported. The most recent is an Rd cross-reference format patch plus a maintainer email change.
deeptime vs treespace: editorial side-by-side
deeptime
0.0ANALYTICS
A geologic-time plotting layer that outgrew time axes and became a geology rendering toolkit.
◆ Current state
deeptime extends ggplot2 with geological time scales, radial deep-time coordinates and phylogeny-aware geoms, and since 2.0.0 it also renders standardized FGDC/USGS geologic patterns as ggplot2 fills. The current 2.4.0 release adds geom_text_clade() for labeling clades on radial phylogenies and repairs long-standing coord_trans_xy() and scale-placement edge cases.
◆ Where it's heading
The package is converging on two jobs: being the canonical R renderer for stratigraphic drawing conventions, and keeping pace with ggplot2's own churn. A sustained deprecation program — gggeo_scale(), coord_geo_polar(), getScaleData(), now disparity_through_time() — is trimming the surface down to coord_geo(), coord_geo_radial() and the pattern functions. Roughly half of each recent release is ggplot2 4.0 compatibility work.
◆ Prediction
Expect disparity_through_time() and coord_geo_polar() to be removed outright in the next major version, and further geoms aimed at annotating radial phylogenies.
treespace
0.0ANALYTICS
treespace ships once every year or two, and only when CRAN or a user forces it.
◆ Current state
treespace explores and compares sets of phylogenetic and transmission trees, including the tree-distance measures used in outbreak reconstruction. Its release history is entirely reactive: five updates across five years, each triggered by a CRAN policy change, an upstream package removal, or a bug someone reported. The most recent is an Rd cross-reference format patch plus a maintainer email change.
◆ Where it's heading
The package is stable and lightly staffed rather than abandoned — bugs that affect correctness do get fixed, and CRAN deadlines are met. But the 2023 update is the telling one: rather than vendor or replace adephylo when it faced removal, the maintainers disabled two tree-vector methods and marked the loss as hopefully temporary. Two years on, nothing in the feed indicates they came back.
◆ Prediction
The next entry will most likely be another CRAN-compliance patch, on the pattern of four of the last five releases. Whether the Abouheif and sumDD methods ever return is not something these entries give any signal on.
Alternatives to deeptime and treespace
Other Analytics products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either deeptime or treespace.
geodist
geodist stays dependency-free and fast, and warns you when 'cheap' distances stop being honest.
errors
errors keeps making uncertainty print the way each scientific field expects.
CMAQ
CMAQ went global in v5.5, and has been patching that surface ever since.
enpls
enpls has not changed its statistics since 2016 — only its website, twice.
grex
grex is a lookup table with a version number — it ships when the annotation moves.
See all deeptime alternatives → · See all treespace alternatives →
Recent activity from deeptime and treespace
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agodeeptimegeom_text_clade() labels clades on radial phylogenies
- 8mo agodeeptimeArgument renames for ggplot2 4.0 parity
- 8mo agodeeptimePattern code dictionary and time-scale theming
- 11mo agotreespacetreespace patches Rd cross-references for CRAN
- 1y agodeeptimegeom_text_phylo() arrives with ggplot2 4 compatibility
- 1y agodeeptimeContrast-aware label colors across the built-in scales
- 1y agodeeptimeFGDC geologic patterns become ggplot2 fills ⚡
- 2y agotreespacetreespace disables Abouheif and sumDD as adephylo exits CRAN
- 3y agotreespacetreespace fixes vignette build on NA tree names
- 5y agotreespacetreespace fixes dist indexing that broke its tests
- 5y agotreespacetreespace corrects tip label handling in transmission distances
Frequently asked questions
What is the difference between deeptime and treespace?
Both compete on the same themes — phylogenetics — within Analytics. deeptime and treespace are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is deeptime better than treespace?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. deeptime and treespace are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
What are the best alternatives to deeptime?
Top deeptime alternatives in Analytics are ranked by recent ship velocity. Browse the "deeptime alternatives" section above for the current picks, or visit /alternatives/deeptime-r for the full list with editorial commentary on each.
What are the best alternatives to treespace?
Top treespace alternatives in Analytics are ranked by recent ship velocity. Browse the "treespace alternatives" section above for the current picks, or visit /alternatives/treespace-r for the full list with editorial commentary on each.