tidy_flows {isotracer} | R Documentation |
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 |
mcmc |
The corresponding output from |
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 |
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 |
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
|
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.
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)