"Workflow" version of run.meta.analysis.pft #' Run Bayesian meta-analysis for a single PFT (file-based wrapper)

Usage

run.meta.analysis.pft(
  pft,
  iterations,
  random = TRUE,
  threshold = 1.2,
  dbfiles,
  dbcon,
  use_ghs = TRUE,
  update = FALSE
)

Arguments

pft: (list) PFT list object, as defined in settings. Must include the following: outdir, name, posteriorid
iterations: (integer) Number of sampler iterations for MCMC analysis
random: (boolean; default = TRUE) Should random effects be used?
threshold: Gelman-Rubin convergence diagnostic (MGPRF) default = 1.2 following Bolker 2008 Ecological Models and Data in R
dbfiles: (character) directory where previous results are found
dbcon: (DBI connection object) BETY database connection object
use_ghs: (boolean; default = TRUE) If TRUE, do not exclude greenhouse data
update: (boolean; default = FALSE) If TRUE, replace existing posteriors with new ones

Value

The pft list (invisibly), or NA if no trait data are available. The returned pft list is a named list with the following elements:

name: (character) PFT name, e.g. "temperate.deciduous".
outdir: (character) Path to directory where output files are stored (trait data, priors, posteriors, MCMC samples).
posteriorid: (integer) Row ID of the posterior record in BETYdb's posteriors table.
constants: (named list, optional) Trait values to treat as fixed constants, bypassing the meta-analysis.

The function's primary outputs are communicated through files saved in pft$outdir.

Details

Upstream contract (reads from pft$outdir):

trait.data.Rdata: Named list of data frames produced by get.trait.data.pft. Loaded into trait_env$trait.data.
prior.distns.Rdata: Data frame of prior distributions produced by get.trait.data.pft. Loaded into prior_env$prior.distns.

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

trait.mcmc.Rdata: Contains trait.mcmc: a named list of mcmc.list objects (one per trait) with posterior MCMC samples from JAGS. Each element has columns beta.o (overall mean) and optionally sd.o (overall SD).
post.distns.MA.Rdata: Contains post.distns: a data frame with one row per trait and columns distn, parama, paramb, n summarizing the fitted posterior distribution.
post.distns.Rdata: Symlink to post.distns.MA.Rdata.
jagged.data.Rdata: Contains jagged.data: a named list of data frames (one per trait) formatted for use in the JAGS meta-analysis model (see jagify).

Downstream contract: The files trait.mcmc.Rdata and post.distns.Rdata are expected by get.parameter.samples (in PEcAn.uncertainty), which loads them to generate ensemble and sensitivity analysis samples.

Note: The core computation is performed by meta_analysis_standalone, which accepts and returns R objects directly — see its documentation for the pure-function interface.