LoginSign Up
← Back to all sparks
S

susier

ANALYTICS
Velocity0.0

R package susier by stephenslab — release notes from GitHub.

github.com/stephenslab/susier ↗

Fine-mapping workhorse susieR spends its releases hunting null-effect trimming bugs

r-packagestatistical-geneticsfine-mappingcpp-bindingsbug-fixes
◆Current state
susieR implements the Sum of Single Effects regression model for variable selection and fine-mapping, widely used in statistical genetics. The recent releases are a tight run of correctness work concentrated in one area: null effect trimming. Version 0.15.55 fixed trimming under the Servin-Stephens residual variance method, 0.15.56 fixed it again for non-uniform prior weights fourteen minutes later, 0.15.57 corrected an ELBO null space term for RSS with X and a matrix symmetry check, and 0.15.58 addressed an alpha0/beta0 issue. Version 0.16.0 migrates the C++ bindings from Rcpp to cpp11 with cpp11armadillo.
◆Where it's heading
The version-number churn understates how narrow this work is — four consecutive releases touching the same trimming and residual-variance machinery suggests one area where the implementation and the intended behavior had drifted apart. The 0.16.0 binding migration is the only structural change, and it is invisible to users while mattering for build portability and long-term maintenance. Development is clearly active, with automated release tooling and dependency bumps flowing through the same stream.
◆Prediction
With the binding migration just landed, near-term releases are likely to address fallout from it alongside continued fixes in the same trimming and residual-variance code.

◆Recent moves

  1. 3mo ago

    Migrates C++ bindings from Rcpp to cpp11 and cpp11armadillo

    Moves the C++ bindings off Rcpp onto cpp11 with cpp11armadillo, reverts susie.ash to V0, and improves verbose output. The binding migration is user-invisible but the only structural change in this run of otherwise narrow bug-fix releases.

    View source ↗
  2. 3mo ago

    Fixes alpha0/beta0 handling under Servin-Stephens

    Fixes an alpha0/beta0 issue in the Servin-Stephens path alongside a dependency bump. The third release in a row touching this residual variance method.

    View source ↗
  3. 4mo ago

    Corrects the null space ELBO term for RSS with X

    Corrects the null space ELBO term for the RSS lambda computation using X, and fixes a matrix symmetry check that failed on mismatched row and column names. ELBO corrections matter because convergence and model comparison both key off it.

    View source ↗
  4. 5mo ago

    Fixes null effect trimming with non-uniform prior weights

    Fixes null effect trimming when prior weights are non-uniform, released fourteen minutes after 0.15.55 fixed a different trimming bug. The pair reads as one debugging session split across two version bumps.

    View source ↗
  5. 5mo ago

    Fixes null effect trimming under Servin-Stephens estimation

    Fixes null effect trimming when estimate_residual_method is set to Servin_Stephens. The first of four consecutive releases converging on the same area of the code.

    View source ↗