paleobuddy
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Comparison · Analytics
aedseo vs treespace
A side-by-side editorial comparison of aedseo and treespace — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:epidemiology
aedseo vs treespace: at a glance
What is aedseo?
An epidemic-onset detector that now brackets the whole season, not just its start
aedseo is a Statens Serum Institut R package for automated early detection of seasonal epidemic onsets, built around growth-rate estimation over consecutive time intervals. The 1.0.0 line moved it well past its original scope: observations are now modelled as cases or population-adjusted incidence, multiple waves can be estimated in one pass, and disease-specific thresholds are computed by a dedicated function. Version 1.1.0 adds an estimate of when a season has ended after the first onset.
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.
aedseo vs treespace: editorial side-by-side
aedseo
0.0ANALYTICS
An epidemic-onset detector that now brackets the whole season, not just its start
◆ Current state
aedseo is a Statens Serum Institut R package for automated early detection of seasonal epidemic onsets, built around growth-rate estimation over consecutive time intervals. The 1.0.0 line moved it well past its original scope: observations are now modelled as cases or population-adjusted incidence, multiple waves can be estimated in one pass, and disease-specific thresholds are computed by a dedicated function. Version 1.1.0 adds an estimate of when a season has ended after the first onset.
◆ Where it's heading
The arc runs from a single-purpose onset detector toward a full seasonal-surveillance toolkit. Each release since 1.0.0 has widened what the package can say about a season rather than improving how it says it: incidence denominators, background population, multi-wave detection, thresholds, and now season end. Fixes in between are narrow and numerical, such as confidence intervals under ATLAS BLAS.
◆ Prediction
The natural next step is symmetry with the onset machinery the package already has: turning the 1.1.0 seasonal offset into a first-class output alongside onset, with its own summary and plotting methods.
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 aedseo 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 aedseo 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 aedseo alternatives → · See all treespace alternatives →
Recent activity from aedseo and treespace
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agoaedseocombined_seasonal_output() now estimates when a season ends
- 8mo agoaedseoFix growth-rate confidence intervals under ATLAS BLAS
- 9mo agoaedseoIncidence, population adjustment and multi-wave detection land in 1.0.0 ⚡
- 11mo agotreespacetreespace patches Rd cross-references for CRAN
- 2y agoaedseoMaintainership transferred to Lasse Engbo Christiansen
- 2y agoaedseoepi_calendar() and richer autoplot displays
- 2y agoaedseoFirst CRAN release of the aeddo onset detector
- 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 aedseo and treespace?
Both compete on the same themes — epidemiology — within Analytics. aedseo 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 aedseo better than treespace?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. aedseo 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 aedseo?
Top aedseo alternatives in Analytics are ranked by recent ship velocity. Browse the "aedseo alternatives" section above for the current picks, or visit /alternatives/aedseo-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.