isotracer (version 1.1.8)

tidy_flows: 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
)

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).

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. Note that any pulse that might be specified in the input model nm is ignored in this case.

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.

Note about how steady state sizes for split compartments are calculated: the steady size of the active portion is calculated divide it is divided by the active fraction (portion.act parameter) to get the total size including the refractory portion. In this case we get a "steady-state" refractory portion, consistent with steady state size of active fraction and with portion.act parameter.

Examples

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