simul: Simulate ssm

Description Usage Arguments Value

View source: R/wrap.r

Description

Function to simulate a ssm.

Usage

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simul(
  ssm,
  approx = c("ode", "sde", "psr"),
  dt = NULL,
  id = 0,
  root = NULL,
  n_thread = 1,
  n_parts = NULL,
  start = NULL,
  end = NULL,
  eps_abs_integ = NULL,
  eps_rel_integ = NULL,
  freeze_forcing = NULL,
  freq = NULL,
  interpolator = NULL,
  verbose = FALSE,
  warning = FALSE,
  no_dem_sto = FALSE,
  no_white_noise = FALSE,
  no_diff = FALSE,
  traj = TRUE,
  hat = FALSE,
  seed_time = TRUE
)

Arguments

ssm

a ssm object, returned by new_ssm.

approx

character, approximation used to simulate ssm:

  • "ode" deterministic approximation, based on Ordinary Differential Equations.

  • "sde" diffusion approximation, based on Stochastic Differential Equations.

  • "psr" Euler-multinomial approximation, based on Poisson process with Stochastic Rates.

dt

numeric, integration time step.

id

integer, unique integer identifier that will be appended to the output.

root

character, root path for output files (if any) (no trailing slash). If NULL (default), outputs are written in "your_model_path/the_name_of_the_wrapper".

n_thread

numeric, number of threads to be used. Default to 1. Use "max" to set it automatically to the number of cores available on the machine using detectCores.

n_parts

numeric, number of particles.

start, end

character, starting and ending date of model simulation (in YYYY-MM-DD format). Default to data range.

eps_abs_integ

numeric, absolute error for adaptive step-size control.

eps_rel_integ

numeric, relative error for adaptive step-size control.

freeze_forcing

character, freeze covariates to their value at specified date (in YYYY-MM-DD format).

freq

numeric, for simulations outside the data range, print the outputs (and reset incidences to 0 if any) every specified days.

interpolator

character, gsl interpolator for covariates

verbose

logical, print logs (verbose). Default to FALSE.

warning

logical, print warnings. Default to FALSE.

no_dem_sto

logical, turn off demographic stochasticity (if any). Default to FALSE.

no_white_noise

logical, turn off white noises (if any). Default to FALSE.

no_diff

logical, turn off diffusions (if any). Default to FALSE.

traj

logical, print the trajectories. Default to TRUE.

hat

logical, print the state estimates. Default to FALSE.

seed_time

logical, seed the random number generator with the current time. Default to TRUE.

Value

a ssm object updated with latest SSM output and ready to be piped into another SSM block.


StateSpaceModels/ssminr documentation built on Feb. 7, 2020, 8:20 p.m.