AllomAve

allometery wrapper function that handles loading and subsetting the data, fitting the Bayesian models, and generating diagnostic figures. Set up to loop over multiple PFTs and components. Writes raw MCMC and PDF of diagnositcs to file and returns table of summary stats.

AllomAve(pfts, components = 6, outdir = NULL, con = NULL,
  field = NULL, parm = system.file("data/Table3_GTR-NE-319.v2.csv",
  package = "PEcAn.allometry"), ngibbs = 5000, nchain = 3,
  dmin = 0.1, dmax = 500)

Arguments

pfts	pft list from PEcAn settings (if con) OR list of pft spcd's If the latter, the names within the list are used to identify PFTs 'acronym' - USDA species acronyms (see plants.usda.gov), used with FIELD data (vector) 'spcd' - USFS species codes, use with PARM data (vector)
components	IDs for allometry components from Jenkins et al 2004 Table 5. Default is stem biomass (6). See data(allom.components)
outdir	output directory files are written to. Default is getwd()
con	database connection
field	path(s) to raw data files
parm	path to allometry equation file (NULL default loads Jenkins Table 3)
ngibbs	number of MCMC iterations (per chain) to run
nchain	number of MCMC chains
dmin	minimum dbh of interest
dmax	maximum dbh of interest

Value

nested list of parameter summary statistics

Details

There are two usages of this function. When running 'online' (connected to the PEcAn database), pass the database connection, con, and the pfts subsection of the PEcAn settings. When running 'stand alone' pass the pft list mapping species to species codes and the file paths to the allometry table and field data (optional)

Examples

# NOT RUN {
if(FALSE){
  pfts = list(FAGR = data.frame(spcd=531,acronym='FAGR'))
  allom.stats = AllomAve(pfts,ngibbs=500)

  ## example of a PFT with multiple species (late hardwood)
  ## note that if you're just using Jenkins the acronym column is optional
  pfts = list(LH = data.frame(spcd = c(531,318),acronym=c('FAGR','ACSA3')))
}

# }