tidy_flows: Build a tidy table with the flows for each iteration

In isotracer: Isotopic Tracer Analysis Using MCMC

Build a tidy table with the flows for each iteration

Description

If neither n_per_chain and n are provided, all iterations are used.

Usage

tidy_flows(
  nm,
  mcmc,
  n_per_chain = NULL,
  n = NULL,
  n_grid = 64,
  steady_state = FALSE,
  dt = NULL,
  grid_size = NULL,
  at = NULL,
  end = NULL,
  use_cache = TRUE,
  cores = NULL
)

Arguments

nm	A networkModel object.
mcmc	The corresponding output from run_mcmc.
n_per_chain	Integer, number of iterations randomly drawn per chain. Note that iterations are in sync across chains (in practice, random iterations are chosen, and then parameter values extracted for those same iterations from all chains).
n	Integer, number of iterations randomly drawn from mcmc. Note that iterations are *not* drawn in sync across chains in this case (use n_per_chain if you need to have the same iterations taken across all chains).
n_grid	Size of the time grid used to calculate trajectories
steady_state	Boolean (default: FALSE). If TRUE, then steady state compartment sizes are calculated for each iteration and steady state flows are calculated from those compartment sizes.
dt, grid_size	Time step size or grid points, respectively.
at	Timepoints at which the predictions should be returned.
end	Final timepoint used in the projections.
use_cache	Boolean, use cache for faster calculations?
cores	Number of cores to use for parallel calculations. Default is NULL, which means to use the value stored in options()[["mc.cores"]] (or 1 if this value is not set).

Details

Warning: This function is still maturing and its interface and output might change in the future.

Value

A tidy table containing the mcmc iterations (chain, iteration, parameters), the grouping variables from the network model and the flows. The returned flow values are the average flow per unit of time over the trajectory calculations (or steady state flows if steady_state is TRUE).

Examples

tf <- tidy_flows(aquarium_mod, aquarium_run, n_per_chain = 25, cores = 2)
tf
tfmcmc <- as.mcmc.list(tf)
plot(tfmcmc)

isotracer documentation built on Sept. 22, 2023, 1:07 a.m.