Changes in version 1.9.0.9000                      

  - Multiple bugfixes in input.ens.gen() handling of parent ids (#3783):
      - No longer skips inputs that have a parent but no sampling
        method.
      - Argument parent_ids now accepts integer vectors even if not
        wrapped in a list.
      - New argument bad_parent_action chooses how to handle parent ids
        that do not match an input path: default "error" to stop with an
        error, "resample" to replace invalid indices from the input
        paths that do exist.
  - run.ensemble.analysis() now respects settings$modeloutdir rather
    than assuming an out/ folder inside settings$outdir (@Akash-paluvai,
    #3722).
  - Added generate_OAT_SA_design() for creating input design matrices
    for sensitivity analysis. This function ensures non-parameter inputs
    (met, IC, soil) are held constant, which is required for valid
    variance decomposition in one-at-a-time (OAT) sensitivity analysis
    (#3729)
  - get.parameter.samples() now consistently accepts PFTs with no outdir
    specified. These previously failed when no database connection was
    available.
  - Improved row alignment and text scaling in
    plot_variance_decomposition().
  - plot_variance_decomposition() gains argument order_by, sorting
    highest variance to the top by default. To reproduce old behavior,
    use order_by = "none".

                        Changes in version 1.9.0                        

License change

PEcAn.uncertainty is now distributed under the BSD 3-clause license
instead of the NCSA Open Source license.

Added

  - Added the shared input_design matrix, generated via new funtion
    generate_joint_ensemble_design(), keeps parameter draws and sampled
    inputs aligned across run.write.configs(), write.ensemble.configs(),
    and write.sa.configs(). (@blesson-07, #3535, #3677).
  - New function compute_sobol_indices for use in global sensitivity
    analyses (@blesson-07, #3612).

Changed

  - Breaking: write.ensemble.configs gains new mandatory arguments
    input_design and ensemble.size, and removes argument samples. Note
    that input_design and ensemble.size are added to the beginning of
    the argument list, so calls passing defaults unnamed as the first
    arg will break (#3612, #3634).
  - Breaking: input.ens.gen gains new mandatory argument ensemble_size,
    added between the existing settings and input args.
  - Plotting sensitivity now makes less noise in the console and once
    again produces a one-page PDF as intended (#3560).
  - write.ensemble.configs and write.sa.configs now generate an ensemble
    id if one is not provided in a DB-free run (#3654). Runs with DB
    continue to always generate a new id. Note that multi-site runs with
    no id provided will now get a separate ensemble ID (and thus
    generate separate analyses) for each site.
  - Documented that runModule.run.sensitivity.analysis does not yet work
    with multisite settings. This will be fixed in a future release.
  - The default sampling method of get.ensemble.samples has changed from
    "uniform" to "random" (#3535).

                        Changes in version 1.8.1                        

  - write.ensemble.configs now respects argument write.to.db when
    settings$database$bety$write is NULL (but if
    settings$database$bety$write is set, it still overrides
    write.to.db).
  - Roxygen fixes

                        Changes in version 1.8.0                        

  - Added an optional pfts argument to run.sensitivity.analysis() so
    that sensitivity analysis and variance decomposition can be run on a
    subset of PFTs defined in settings if desired (#3155).

                        Changes in version 1.7.2                        

  - Added a NEWS.md file to track changes to the package.