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Comparison · Infra & APIs
adjustedCurves vs pathfindR
A side-by-side editorial comparison of adjustedCurves and pathfindR — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
adjustedCurves vs pathfindR: at a glance
What is adjustedCurves?
A survival curve package spending release after release correcting its own estimates
adjustedCurves computes confounder-adjusted survival and cumulative incidence curves across a range of estimators - IPTW, AIPTW, Aalen-Johansen, direct standardisation - with support for multiple imputation and bootstrapping. The recent releases are dominated by corrections to numbers the package already reported. Version 0.11.4 fixed cumulative incidence estimates under method="aalen_johansen" that were being read one time step early, which the maintainer notes could differ substantially when events are few, and added risk and event counts to the ggsurvplot conversion including correctly pooled values under multiple imputation.
What is pathfindR?
pathfindR dropped Java from its subnetwork search and rebuilt it in C++
pathfindR runs active-subnetwork-oriented pathway enrichment on gene expression results. Version 3.0.0 re-implemented the greedy, simulated-annealing and genetic search algorithms in R and C++ through Rcpp, removing the Java dependency the package had carried since its early releases, and renamed three exported functions in the process. The two patches since have been consolidation: 3.0.1 fixed signed integer overflow in the new C++ hash function flagged by gcc-UBSAN and clang-UBSAN on CRAN, and 3.0.2 repaired tests after a companion data package changed a dataset structure.
adjustedCurves vs pathfindR: editorial side-by-side
adjustedCurves
0.0INFRA · APIS
A survival curve package spending release after release correcting its own estimates
◆ Current state
adjustedCurves computes confounder-adjusted survival and cumulative incidence curves across a range of estimators - IPTW, AIPTW, Aalen-Johansen, direct standardisation - with support for multiple imputation and bootstrapping. The recent releases are dominated by corrections to numbers the package already reported. Version 0.11.4 fixed cumulative incidence estimates under method="aalen_johansen" that were being read one time step early, which the maintainer notes could differ substantially when events are few, and added risk and event counts to the ggsurvplot conversion including correctly pooled values under multiple imputation.
◆ Where it's heading
Multiple imputation is the recurring fault line. The standard error pooling formula was implemented incorrectly until 0.11.2, then fixed again in 0.11.3 for the bootstrapping-plus-imputation combination, and 0.11.4 added the pooled risk table values that had previously been omitted entirely. A separate thread quietly removed capability: tmle and ostmle methods went in 0.10.0, and tmle support was pulled again in 0.11.1 after the concrete package left CRAN. Feature work does happen - risk tables, contrast arguments, the extend_to_last control on IPTW curves - but it is outweighed by correction.
◆ Prediction
Expect continued estimator-level corrections rather than new methods, and a possible return of tmle support if its upstream dependency returns to CRAN, since the removal was described as temporary.
pathfindR
0.0INFRA · APIS
pathfindR dropped Java from its subnetwork search and rebuilt it in C++
◆ Current state
pathfindR runs active-subnetwork-oriented pathway enrichment on gene expression results. Version 3.0.0 re-implemented the greedy, simulated-annealing and genetic search algorithms in R and C++ through Rcpp, removing the Java dependency the package had carried since its early releases, and renamed three exported functions in the process. The two patches since have been consolidation: 3.0.1 fixed signed integer overflow in the new C++ hash function flagged by gcc-UBSAN and clang-UBSAN on CRAN, and 3.0.2 repaired tests after a companion data package changed a dataset structure.
◆ Where it's heading
The dependency surface has been shrinking for two years and Java was the last heavy one. 2.4.0 removed magick, KEGGgraph and KEGGREST by moving KEGG visualization onto ggkegg; 2.7.0 pushed org.Hs.eg.db from Imports to Suggests under CRAN policy, with functions degrading to defaults when it is absent; 3.0.0 finished the job on the search engine itself. The corresponding cost is now visible in 3.0.1: owning the algorithms in C++ means owning their undefined-behaviour reports too.
◆ Prediction
Expect the near-term releases to keep hardening the Rcpp search code against sanitizer findings and to verify GA parity with the legacy JAR, since 3.0.0 claimed numerically identical results only for the greedy and simulated-annealing methods.
Alternatives to adjustedCurves and pathfindR
Other Infra & APIs 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 adjustedCurves or pathfindR.
daedalus
An epidemic-economic model teaching its interventions to react to the outbreak itself.
bkmrhat
A parallel-chain helper for bkmr that has settled into pure upkeep.
driveR
A cancer driver prioritization package that ships rarely and mostly to stay installable
metR
A meteorology ggplot2 extension where the netCDF reader became the main event
IsoriX
An isotope geolocation package still recovering from the r-spatial retirement
See all adjustedCurves alternatives → · See all pathfindR alternatives →
Recent activity from adjustedCurves and pathfindR
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agopathfindRTest fixes after a companion data package changed a dataset
- 1mo agopathfindRUndefined-behaviour fixes harden the new C++ search engine
- 1mo agopathfindRActive subnetwork search re-implemented in C++, Java dependency removed ⚡
- 6mo agoadjustedCurvesOff-by-one-step error corrected in cumulative incidence estimates
- 7mo agopathfindRHuman annotation database moves from Imports to Suggests
- 7mo agopathfindRGraceful handling for gene-set URL failures
- 1y agopathfindRKappa matrix fix for the igraph update
- 1y agoadjustedCurvesIPTW curves can now extend to the last observed time
- 2y agoadjustedCurvesDropped arguments and a wrong multiple-imputation pooling formula
- 2y agoadjustedCurvesRisk tables, contrast consolidation and faster bootstrapping
- 3y agoadjustedCurvestmle and ostmle methods dropped
- 3y agoadjustedCurvesDependency compatibility and installation documentation
Frequently asked questions
What is the difference between adjustedCurves and pathfindR?
Both compete on the same themes — r-package — within Infra & APIs. adjustedCurves and pathfindR 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 adjustedCurves better than pathfindR?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. adjustedCurves and pathfindR 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 Infra & APIs products to evaluate alongside.
What are the best alternatives to adjustedCurves?
Top adjustedCurves alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "adjustedCurves alternatives" section above for the current picks, or visit /alternatives/adjustedcurves for the full list with editorial commentary on each.
What are the best alternatives to pathfindR?
Top pathfindR alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "pathfindR alternatives" section above for the current picks, or visit /alternatives/pathfindr for the full list with editorial commentary on each.