This function provides a unified interface to the various simulation algorithms for SPN, returning output sampled at a lattice of time points to the user, and handling various exogenous events that may occur during the simulation (such as release of adult mosquitoes).
Usage
sim_trajectory_CSV(
x0,
tmax,
dt = 1,
dt_stoch = 0.1,
folders = "./",
stage = c("M", "F"),
S,
hazards,
Sout = NULL,
sampler = "tau",
method = "lsoda",
events = NULL,
batch = NULL,
verbose = TRUE,
...
)
Arguments
- x0
the initial marking of the SPN (initial state, M0)
- tmax
the final time to end simulation
- dt
the time-step at which to return output (not the time-step of the sampling algorithm)
- dt_stoch
time-step used for approximation of hazards
- folders
vector of folders to write output
- stage
life-stages to print. Any combination of: "E", "L", "P"," M", "U", "F", "H"
- S
a stoichiometry
Matrix-class
object- hazards
list of hazard functions
- Sout
an optional matrix to track event firings
- sampler
determines sampling algorithm, one of; "ode", "tau", "cle", or "dm"
- method
if
sampler
is "ode", the solver to use, fromdeSolve
- events
a
data.frame
of events- batch
a
list
of batch migration events, created frombatch_migration
, may be set toNULL
if not used- verbose
print a progress bar?
- ...
further named arguments passed to the step function
Details
dt_stoch
is used by the Poisson Time-Step (step_PTS
) and
Chemical Langevin (step_CLE
) methods to approximate the hazards.
A smaller dt_stoch
provides a better approximation, but will take longer
to run.
The stoichiometry matrix (S
) is generated in spn_S
.
The list of hazards (hazards
) come from spn_hazards
.
Several samplers are provided. The default is a Poisson Time-Step
(step_PTS
) method. Other options are Gillespie's Direct Method
(step_DM
) and a Chemical Langevin sampler (step_CLE
).
Additionally, for convenience, an ODE "sampler" (step_ODE
) is
provided for compatibility with other samplers. This function uses methods from
deSolve
.
If using the ode
sampler, several methods
are provided in the deSolve
package, see ode
. For inhomogeneous systems, consider
using the "rk4" method to avoid excessive integration times.
Additionally, events
objects must follow the format required by
deSolve
. This was done for consistency, see events
for more information.
This function writes all output to .csv files. Each simulation is written to
a folder
element - the number of repetitions is the number of folders
provided. What life-stages get recorded is specified by the stage
parameter.
All life-stages can be stored, or any subset thereof. Females are split by
infection status, i.e. by "S", "E", or "I".
This function tracks state variables specified by argument stage
by default; an optional argument Sout
can be provided to track number of event firings each time step (for discrete stochastic simulations),
or cumulative intensity (for continuous stochastic simulations), or the rate function of
particular events for ODE simulation. The matrix must have number of columns equal to
number of events in the system (the number of hazard functions), and a row for each tracking
variable. If Sout
is provided, it outputs an additional csv, "Tracking.csv".
The function track_hinf
is provided, which builds a matrix to track
human infection events.
To return simulations to R for further processing, see sim_trajectory_R
.