Run sensitivity analysis on finished model runs

Usage

run.sensitivity.analysis(
  settings,
  plot = TRUE,
  ensemble.id = NULL,
  variable = NULL,
  start.year = NULL,
  end.year = NULL,
  pfts = NULL,
  ...
)

Arguments

settings: a PEcAn settings object
plot: logical. Option to generate sensitivity analysis and variance decomposition plots (plot = TRUE) or to turn these plots off (plot = FALSE).
ensemble.id: ensemble ID
variable: which variable(s) to do sensitivity analysis for. Defaults to all specified in settings
start.year: defaults to what is specified in settings
end.year: defaults to what is specified in settings
pfts: a vector of PFT names found in settings to run sensitivity analysis on
...: currently unused

Value

Nothing (called for side effects). Saves sensitivity.results as sensitivity.results.*.Rdata and optional PDF plots.

Details

Upstream contract (reads from settings$outdir):

samples.Rdata: Produced by get.parameter.samples. Loaded to obtain trait.samples, trait.names, pft.names, and sa.run.ids.
sensitivity.samples.<id>.Rdata: Produced by run.write.configs. If present, overrides sa.run.ids and sa.samples from samples.Rdata.
sensitivity.output.<var>.<years>.<id>.Rdata: Produced by get.results. Contains sensitivity.output: a named list (PFT -> matrix) of model outputs for each SA run.

File-based side effects (saved to settings$outdir):

sensitivity.results.<var>.<years>.<id>.Rdata: Contains sensitivity.results: a named list (PFT -> list) with elements sensitivity.output (partial derivatives) and variance.decomposition.output (elasticities and partial variances).
sensitivityanalysis.<pft>.<var>.<years>.<id>.pdf: Sensitivity analysis diagnostic plots (one per PFT). Generated when plot = TRUE.
variance.decomposition.<pft>.<var>.<years>.<id>.pdf: Variance decomposition "popsicle" plots (one per PFT). Generated when plot = TRUE.

Note: This is a terminal step in the workflow — nothing downstream loads sensitivity.results.*.Rdata programmatically. The results are consumed by visualization or user inspection.

Author

David LeBauer, Shawn Serbin, Ryan Kelly

Examples

if (FALSE) { # \dontrun{
library(PEcAn.settings)
library(PEcAn.uncertainty)
settings <- read.settings("path/to/pecan.xml")
run.sensitivity.analysis(settings)
} # }