SI Example

The si_example_object function efficiently generates objects associated with the example SI model. It either creates these objects or extracts them from a pre-computed cache if they have already been created in the current session. This function is predominantly used to simplify examples in the package documentation – it allows package developers to efficiently get these basic example objects to illustrate many different concepts, without having to spend time computing them over and over again when generating the documentation. The si_example_code function displays code that could be used to generate these objects, and clarifies what these functions do.

Usage

si_example_object(
  object = c("specification", "simulator", "data", "calibrator", "optimized_calibrator")
)

si_example_code(
  object = c("specification", "simulator", "data", "calibrator", "optimized_calibrator")
)

Arguments

object

Type of object associated with the example SI model. Can be one of the following: "specification", "simulator", "data", "calibrator", "optimized_calibrator". The functions used to produce each of these objects, respectively, are mp_tmb_library, mp_simulator, mp_trajectory, mp_tmb_calibrator, and mp_tmb_calibrator.

Functions

• si_example_object(): Return an object associated with the example SI model.

• si_example_code(): Show code that could be used to generate an object associated with the example SI model.

Examples

# Get SI calibrator in two different states
cal1 = si_example_object("calibrator")
cal2 = si_example_object("optimized_calibrator")

# Optimize cal1 so that it is equal to cal2
mp_optimize(cal1)
#> outer mgc:  1441.015 
#> outer mgc:  821.4155 
#> outer mgc:  156.7428 
#> outer mgc:  125.3782 
#> outer mgc:  34.31059 
#> outer mgc:  1.723101 
#> outer mgc:  0.003634738 
#> outer mgc:  1.52728e-08 
#> $par
#> params params 
#>    0.2    0.1 
#> 
#> $objective
#> [1] 49.74796
#> 
#> $convergence
#> [1] 0
#> 
#> $iterations
#> [1] 7
#> 
#> $evaluations
#> function gradient 
#>       11        8 
#> 
#> $message
#> [1] "relative convergence (4)"
#> 
mp_tmb_coef(cal1)
#> outer mgc:  1.52728e-08 
#> outer mgc:  11.74622 
#> outer mgc:  12.05664 
#> outer mgc:  11.71903 
#> outer mgc:  11.46633 
#> outer mgc:  31.49728 
#>       term   mat row col default  type estimate  std.error
#> 1   params  beta   0   0    0.25 fixed      0.2 0.03608530
#> 2 params.1 gamma   0   0    0.25 fixed      0.1 0.03656268
mp_tmb_coef(cal2)
#> outer mgc:  1.52728e-08 
#> outer mgc:  11.74622 
#> outer mgc:  12.05664 
#> outer mgc:  11.71903 
#> outer mgc:  11.46633 
#> outer mgc:  31.49728 
#>       term   mat row col default  type estimate  std.error
#> 1   params  beta   0   0    0.25 fixed      0.2 0.03608530
#> 2 params.1 gamma   0   0    0.25 fixed      0.1 0.03656268

# Inspect the code used to produce all objects in this example SI model.
si_example_code("specification")
#> mp_tmb_library("starter_models", "sir", package = "macpan2")
si_example_code("simulator")
#> mp_simulator(specification, 50, "infection")
si_example_code("data")
#> mp_trajectory(simulator)
si_example_code("calibrator")
#> mp_tmb_calibrator(specification, data, traj = "infection", par = c("beta", 
#>     "gamma"), default = list(beta = 0.25, gamma = 0.25))
si_example_code("optimized_calibrator")
#> mp_tmb_calibrator(specification, data, traj = "infection", par = c("beta", 
#>     "gamma"), default = list(beta = 0.25, gamma = 0.25), optimize = TRUE)