finalsize provides calculations for the final size of an epidemic in a population with demographic variation in contact patterns, and variation within and between age groups in their susceptibility to disease.
finalsize implements methods outlined in Andreasen (2011), Miller (2012), Kucharski et al. (2014), and Bidari et al. (2016).
finalsize can help provide rough estimates of the effectiveness of pharmaceutical interventions in the form of immunisation programmes, or the effect of naturally acquired immunity through previous infection (see the vignette).
finalsize relies on Eigen via RcppEigen for fast matrix algebra, and is developed at the Centre for the Mathematical Modelling of Infectious Diseases at the London School of Hygiene and Tropical Medicine as part of the Epiverse Initiative.
The package can be installed using
install.packages("finalsize")The current development version of finalsize can be
installed from Github using the
remotes package.
# install.packages("devtools")
devtools::install_github("epiverse-trace/finalsize")finalsize provides the single function
final_size(), to calculate the final size of an
epidemic.
Here, an example using social contact data from the socialmixr package investigates the final size of an epidemic when the disease has an R0 of 1.5, and given three age groups of interest — 0-19, 20-39 and 40+. The under-20 age group is assumed to be fully susceptible to the disease, whereas individuals aged over 20 are only half as susceptible as those under 20.
# load finalsize
library(finalsize)
# Load example POLYMOD data included with the package
data(polymod_uk)
# Define contact matrix (entry {ij} is contacts in group i reported by group j)
contact_matrix <- polymod_uk$contact_matrix
# Define population in each age group
demography_vector <- polymod_uk$demography_vector
# Define susceptibility of each group
susceptibility <- matrix(
data = c(1.0, 0.5, 0.5),
nrow = length(demography_vector),
ncol = 1
)
# Assume uniform susceptibility within age groups
p_susceptibility <- matrix(
data = 1.0,
nrow = length(demography_vector),
ncol = 1
)
# R0 of the disease
r0 <- 1.5 # assumed for pandemic influenza
# Calculate the proportion of individuals infected
final_size(
r0,
contact_matrix,
demography_vector,
p_susceptibility,
susceptibility
)
#> demo_grp susc_grp susceptibility p_infected
#> 1 [0,20) susc_grp_1 1.0 0.32849966
#> 2 [20,40) susc_grp_1 0.5 0.10532481
#> 3 40+ susc_grp_1 0.5 0.06995193More details on how to use finalsize can be found in the online documentation as package vignettes, under “Articles”.
To report a bug please open an issue.
Contributions to finalsize are welcomed. Please follow the package contributing guide.
Please note that the finalsize project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
citation("finalsize")
#>
#> To cite package 'finalsize' in publications use:
#>
#> Gupte P, Van Leeuwen E, Kucharski A (2022). _finalsize: Calculate the
#> Final Size of an Epidemic_.
#> https://epiverse-trace.github.io/finalsize/,
#> https://github.com/epiverse-trace/finalsize.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {finalsize: Calculate the Final Size of an Epidemic},
#> author = {Pratik Gupte and Edwin {Van Leeuwen} and Adam Kucharski},
#> year = {2022},
#> note = {https://epiverse-trace.github.io/finalsize/,
#> https://github.com/epiverse-trace/finalsize},
#> }