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ss3diags

ANALYTICS
Velocity0.0

Stock Synthesis Model Diagnostics for Intergated Stock Assessments

github.com/PIFSCstockassessments/ss3diags ↗

A fisheries diagnostics package that lives and dies by one upstream dependency.

fisheries-stock-assessmentmodel-diagnosticsr-packagenoaadependency-management
◆Current state
ss3diags provides residual, retrospective and hindcast cross-validation diagnostics for Stock Synthesis models, sitting directly on top of r4ss. Its recent history is dominated by that dependency: when r4ss 1.50.0 renamed columns across its read and write functions, ss3diags pinned itself to 1.49.3 only, then spent the following release adapting. It now requires r4ss 1.50.0 and above and has moved to native R pipes.
◆Where it's heading
The package is a downstream consumer whose release schedule is largely dictated by NOAA's r4ss. Between compatibility passes it has been shifting documentation from loose cookbook scripts into proper vignettes and shedding bundled Rdata in favour of objects generated at build time. Note that 2.0.3 and 2.1.0 were published the same day, so version order in this feed does not track chronology.
◆Prediction
The next release most likely follows the next breaking r4ss change; between those, expect continued vignette and parameter-validation work.

◆Recent moves

  1. 1y ago

    Adapts to r4ss 1.50.0 and drops the local binary fetcher

    Completes the r4ss 1.50.0 adaptation: the dependency floor moves up, the local get_ss3_exe workaround is dropped in favour of the upstream function, references follow r4ss's new naming, and magrittr pipes give way to native ones. This closes the compatibility break the previous release could only pin around.

    View source ↗
  2. 1y ago

    Pins r4ss to 1.49.3 after upstream breaking changes

    Pins the dependency to r4ss 1.49.3 only, because 1.50.0's read/write changes break existing functions, and adds a local get_ss3_exe with a token fix for SAML errors downloading SS3 binaries. A defensive release that freezes users in place until the adaptation lands.

    View source ↗
  3. 2y ago

    Vignette tutorials replace cookbook scripts

    Replaces the cookbook recipe scripts with vignette tutorials for running and interpreting the diagnostics, and removes bundled Rdata objects now produced in the vignettes themselves. Documentation as the deliverable rather than an afterthought.

    View source ↗
  4. 3y ago

    SSdeltaMVLN gains variance-covariance and bias options

    Adds variance-covariance approximation and bias correction options to SSdeltaMVLN, and resolves r4ss function name conflicts with dplyr and kableExtra by removing NAMESPACE imports. Namespace hygiene that recurs whenever the r4ss surface shifts.

    View source ↗
  5. 3y ago

    Aligns with CRAN r4ss 1.44.0 and shared CI workflows

    Aligns the dependency with the CRAN r4ss 1.44.0, adopts shared NOAA GitHub Actions workflows and fixes ensemble quantile shading. Mostly infrastructure, published the same day as 2.1.0.

    View source ↗
  6. 3y ago

    SSrmse() split out as a standalone calculation

    Pulls RMSE calculation out of SSplotJABBAres into a standalone SSrmse(), adds y-axis limit control to two plots and a median-trajectory toggle to SSplotKobe. Separating a statistic from the plot that produced it makes it usable in reports.

    View source ↗