imuGAP Model Options

Configures model-side options for imuGAP estimation.

Usage

imugap_options(
  df = 5L,
  dose_schedule = c(1, 4),
  compute_log_lik = FALSE,
  time = c("bspline"),
  offsets = c("static"),
  link = c("logit", "probit"),
  solver = c("halley2", "direct", "newton2", "builtin", "halley10")
)

Arguments

df

single positive integer; degrees of freedom to use for the cohort B-spline basis expansion (default: 5L).

dose_schedule

ascending integer vector of ages at which each dose 1..n becomes eligible (default: c(1, 4) for 2-dose vaccines).

compute_log_lik

logical scalar; compute pointwise log-likelihood during sampling? (default: FALSE).

time

character string specifying the temporal model component (default: "bspline"). Options include "bspline".

offsets

character string specifying the spatial offset model component (default: "static"). Options include "static".

link

character string specifying the link function formulation (default: "logit"). Options include "logit" and "probit".

solver

character string specifying the rootfinder solver method (default: "halley2"). Options include "halley2", "direct", "newton2", "builtin", and "halley10".

Value

an object of class imugap_options, wrapping a named list of model options.

Examples

imugap_options()
#> $df
#> [1] 5
#> 
#> $dose_schedule
#> [1] 1 4
#> 
#> $compute_log_lik
#> [1] FALSE
#> 
#> $time
#> [1] "bspline"
#> 
#> $offsets
#> [1] "static"
#> 
#> $link
#> [1] "logit"
#> 
#> $model
#> [1] "bspline_static_zero_halley2_logit"
#> 
#> $solver
#> [1] "halley2"
#> 
#> $solver_type
#> [1] 2
#> 
#> attr(,"class")
#> [1] "imugap_options"
imugap_options(dose_schedule = c(1, 3))
#> $df
#> [1] 5
#> 
#> $dose_schedule
#> [1] 1 3
#> 
#> $compute_log_lik
#> [1] FALSE
#> 
#> $time
#> [1] "bspline"
#> 
#> $offsets
#> [1] "static"
#> 
#> $link
#> [1] "logit"
#> 
#> $model
#> [1] "bspline_static_zero_halley2_logit"
#> 
#> $solver
#> [1] "halley2"
#> 
#> $solver_type
#> [1] 2
#> 
#> attr(,"class")
#> [1] "imugap_options"
imugap_options(link = "probit", solver = "halley2")
#> $df
#> [1] 5
#> 
#> $dose_schedule
#> [1] 1 4
#> 
#> $compute_log_lik
#> [1] FALSE
#> 
#> $time
#> [1] "bspline"
#> 
#> $offsets
#> [1] "static"
#> 
#> $link
#> [1] "probit"
#> 
#> $model
#> [1] "bspline_static_zero_halley2_probit"
#> 
#> $solver
#> [1] "halley2"
#> 
#> $solver_type
#> [1] 2
#> 
#> attr(,"class")
#> [1] "imugap_options"