parameter_sweep.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/parameter_sweep.R
\name{parameter_sweep}
\alias{parameter_sweep}
\title{Sweep across parameters}
\usage{
parameter_sweep(scenarios = NULL, samples = 1, sim_fn = NULL)
}
\arguments{
\item{scenarios}{A dataframe containing all gridded  scenarios - see the examples for the required structure.
Defaults to NULL.}

\item{samples}{Numeric, defaults to 1. The number of samples to take.}

\item{sim_fn}{Function, defaults to NULL. The vectorised model simulation function - see the examples
for usage.}
}
\value{
A nested \code{data.table} containing the parameters for each scenario and a nested list of output
from \code{wuhan_sim}.
}
\description{
Explore scenarios using gridding with sampling for parameters not in the grid. Parameters that
are included in the grid are currently hard coded. Use the \code{future} package to control parallisation
outside of the function.
}
\examples{


\dontrun{
library(data.table)

scenarios <- data.table(expand.grid(
delay_group = list(data.table(
 delay = c("SARS","Wuhan"),
 delay_shape = c(1.651524,2.305172),
 delay_scale = c(4.287786,9.483875)
)),
k_group = list(data.table(
 theta = c("<1\%","15\%","30\%"),
 k = c(1,0.88,0.47)
)),
index_R0 = c(1.5,2.5,3.5),
prop.asym = c(0,  0.1),
control_effectiveness = seq(0,1,0.2),
num.initial.cases = c(5,20,40))

list_cols <- grep("_group", colnames(scenarios), value = TRUE)
non_list_cols <- setdiff(colnames(scenarios), list_cols)

expanded_groups <- scenarios[, rbindlist(delay_group), by = c(non_list_cols)]
expanded_k <- scenarios[, rbindlist(k_group), by = c(non_list_cols)]

scenarios <- merge(
  expanded_groups, expanded_k, by = non_list_cols, allow.cartesian = TRUE
)
scenarios[, scenario :=  1:.N]

## Parameterise fixed paramters
sim_with_params <- purrr::partial(ringbp::scenario_sim,
                                 cap_max_days = 365,
                                 cap_cases = 5000,
                                 r0isolated = 0,
                                 disp.iso= 1,
                                 disp.subclin = 0.16,
                                 disp.com = 0.16,
                                 quarantine = FALSE)


## Default is to run sequntially on a single core
future::plan("sequential")
## Set up multicore if using see ?future::plan for details
## Use the workers argument to control the number of cores used.
future::plan("multiprocess")


## Run paramter sweep
sweep_results <- ringbp::parameter_sweep(scenarios, sim_fn = sim_with_params, samples = 1)


sweep_results
}
}