run_nimble_model: Run Nimble Model in Parallel Function will run a Nimble model...

In trashbirdecology/bbsebird: Unifying BBS and eBird Data for Integrating Modeling

Run Nimble Model in Parallel Function will run a Nimble model for 'nc' indepdendent chains

Description

Run Nimble Model in Parallel Function will run a Nimble model for 'nc' indepdendent chains

Usage

run_nimble_model(
  code,
  data,
  fn.samps = NULL,
  constants = NULL,
  inits,
  monitors = NULL,
  monitors2 = NULL,
  ncores = NULL,
  ni = 10000,
  nb = 100,
  nt = 1,
  nc = 1,
  aI = 200,
  seed = NULL,
  ntries = NULL,
  calculate = FALSE,
  block.name = "alpha+b",
  block.samp.type = "AF_slice",
  parallel = TRUE,
  mod.name = NULL,
  dir.out = NULL,
  fn.times = "runtimes.csv",
  save.output = TRUE
)

Arguments

code	nimble model code
data	data as a list
fn.samps	filepath for .rds file where sample monitors will be saved.
constants	constants as list
inits	list of initial values
monitors	optional Character vector of parameters to monitor.
monitors2	optional Character vector of parameters to monitor.
ncores	maximum number of cores to employ. Actual number used is the minimum of nc and ncores
ni	number iterations to run
nb	number of burn-in iterations to discard (I think it's PRE-THINNING burnin discard...)
nt	thinning rate (every Nth iteration will be saved)
nc	number of chains to run (in parallel)
aI	adapt interval, used in nimble::addSamplers
seed	seed number
ntries	optional If using parameter block sampler, specify the maximum number of tries. Defaults to ~50% of the number of GAM basis functions.
calculate	logical if TRUE will calculate the model logprob. Used as argument 'calculate' in function nimble::nimbleModel()
block.name	optional one of c("alpha+b", "all"). If "alpha+b" will block each alpha and b across all T. If "all" will block all alpha and b for each Ts.
block.samp.type	optional one of c("AF_slice", "RW_block").
parallel	logical if TRUE will run chains in parallel (using foreach).
mod.name	a shorthand name for saving outputs.
dir.out	path where samps and runtimes wll be saved
fn.times	filename of runtimes output. Optional. Defaults to runtimes.csv
save.output	Logical. If TRUE will attempt to save MCMC results output as .rds to file.

trashbirdecology/bbsebird documentation built on June 30, 2022, 12:18 a.m.