Changelog • PEcAn.uncertainty

PEcAn.uncertainty 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".

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

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).

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).

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

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).