bkmrhat
A parallel-chain helper for bkmr that has settled into pure upkeep.
Comparison · Infra & APIs
fdacluster vs pathfindR
A side-by-side editorial comparison of fdacluster and pathfindR — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-packagercpp
fdacluster vs pathfindR: at a glance
What is fdacluster?
Functional data clustering grew from one algorithm into a comparable suite
fdacluster clusters functional data while separating amplitude from phase variation, aligning curves as part of the clustering rather than before it. The algorithm set covers k-means, hierarchical clustering and DBSCAN, all producing a common caps result object so runs can be compared directly. Version 0.4.0 tightened the interface with is_domain_interval and transformation arguments describing the input data, added compatibility checking between incompatible option combinations, and split the L2 and normalized L2 distances into separate C++ classes to enforce that plain L2 cannot be combined with dilation or affine warping it is not invariant to.
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.
fdacluster vs pathfindR: editorial side-by-side
fdacluster
0.0INFRA · APIS
Functional data clustering grew from one algorithm into a comparable suite
◆ Current state
fdacluster clusters functional data while separating amplitude from phase variation, aligning curves as part of the clustering rather than before it. The algorithm set covers k-means, hierarchical clustering and DBSCAN, all producing a common caps result object so runs can be compared directly. Version 0.4.0 tightened the interface with is_domain_interval and transformation arguments describing the input data, added compatibility checking between incompatible option combinations, and split the L2 and normalized L2 distances into separate C++ classes to enforce that plain L2 cannot be combined with dilation or affine warping it is not invariant to.
◆ Where it's heading
The trajectory runs from method implementation toward guardrails and portability. Early releases added capability; recent ones prevent misuse and reduce weight - dplyr, forcats, tidyr and purrr removed in 0.4.0, furrr swapped for future.apply - while 0.4.2 is entirely C++ correctness, replacing Armadillo's whole-object finiteness check with scalar std::isfinite and fixing an integer overflow in linear index computation that broke large datasets. Cadence is roughly one release a year.
◆ Prediction
Given that the last two releases were dependency reduction and numerical correctness rather than method work, expect the next to continue in that vein unless a new clustering algorithm is contributed.
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 fdacluster 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 fdacluster or pathfindR.
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
profoc
A forecast combination package that spun its profiler out into its own project
adjustedCurves
A survival curve package spending release after release correcting its own estimates
See all fdacluster alternatives → · See all pathfindR alternatives →
Recent activity from fdacluster 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 ⚡
- 7mo agofdaclusterInteger overflow fixed for large datasets, C++ finiteness checks corrected
- 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 agofdaclusterParallel worker setup and an acronym correction
- 1y agofdaclusterInput description arguments and enforced distance-warping compatibility
- 3y agofdaclusterMedian centroids and centroids defined on unioned grids
- 3y agofdaclusterNamespace notation and optional dependency guards
- 3y agofdaclusterHierarchical clustering, DBSCAN and a shared result class arrive together ⚡
Frequently asked questions
What is the difference between fdacluster and pathfindR?
Both compete on the same themes — r-package, rcpp — within Infra & APIs. fdacluster 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 fdacluster better than pathfindR?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. fdacluster 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 fdacluster?
Top fdacluster alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "fdacluster alternatives" section above for the current picks, or visit /alternatives/fdacluster 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.