Simulates an epidemic outbreak with a stochastic branching process from a number of initial seed cases.
Every simulated case has disease and intervention parameters stochastically drawn from user-provided distributions. These parameters determine which secondary cases occur, which in turn create the next generation of cases. This simulation implements modelling of interventions such as: * manual/conventional contact tracing, * app-based contact tracing usage and compliance, * reduction of contacts through physical distancing, * self-isolation of cases after certain conditions are met, and * quarantine/isolation of new arrivals.
This simulation also includes the option of adding new cases via importation, which may have different contact tracing and self-isolation conditions. The simulation itself outputs a dataframe that summarizes every case generated during the course of the simulation. This can be used to generate metrics or other statistics across a large number of runs. Some example driver functions to do this are provided in the package and as vignettes.
This package is inspired by Hellewell et al. “Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.” The Lancet Global Health 2020; 8: E488–E496. DOI: 10.1016/S2214-109X(20)30074-7.
To install this package along with the vignettes, use
remotes::install_github("bcgov/epi.branch.sim", ref="main", build_vignettes=TRUE)A very simple example of setting up and running a scenario for 30 days.
# Set up simulation objects
sim_params <- epi.branch.sim::initialize_sim_params(
R0=3.0, infect_dur=999, vary_trace=FALSE, p_trace=0.8,
p_trace_app=0, p_trace_app_comp=0, p_symp=0.9, dt=1,
incub_params=list(dist='weibull', shape=2.322737, scale=6.492272),
generation_int_params=list(dist='skew_norm', omega=2, alpha=1.95),
iso_delay_params=list(dist='Hellewell', shape=1.651524, scale=4.287786),
sec_infect_params=list(type='Hellewell', disp=0.16),
import_params=list(type="None"),
phys_dist_params=list(
pd_pop_frac = 0,
pd_contact_rate1 = 1.0,
pd_contact_rate2 = 1.0,
pd_change_t = 0)
)
start_time <- 0
n_initial <- 20
sim_status <- epi.branch.sim::initialize_sim_status(start_time,n_initial)
state_df <- epi.branch.sim::create_state_df(n_initial,sim_params, sim_status, initialize=TRUE)
record_df <- epi.branch.sim::create_record_df(state_df, sim_status, initialize=TRUE)
# Run for 30 steps
for (t in 1:30){
out <- epi.branch.sim::step_simulation(sim_status, state_df, record_df, sim_params)
sim_status <- out$status # update sim_status
state_df <- out$state # update state_df
record_df <- out$record # update record_df
}
# Output products are the state_df and record_df data framesDetailed documentation on the simulation algorithm, input parameters,
output data frames and examples are provided as vignettes. Once the
package is installed with the build_vignette=TRUE option as above,
these vignettes can be viewed with:
browseVignettes('epi.branch.sim')For help on all documented functions and objects, use:
help(package='epi.branch.sim')This package is stable. This is a public release of a tool regularly used within our team in order to share the tool more widely. At release, the package is functional, all of the intended features are working and documented. More features may be added based on usage and demand, but there are no current plans to continue development at this time.
To report bugs/issues/feature requests, please file an issue.
If you would like to contribute to the package, please see our CONTRIBUTING guidelines.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
Copyright 2020 Province of British Columbia
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
This project was created using the bcgovr package.