This is the second release of finalsize, and includes:
- The package’s C++ code for the solver algorithms has been moved from source files under
src/into headers under
- The package includes a package header under
finalsize.h, which allows other Rcpp packages to link to finalsize and reuse the solver algorithms provided here.
- Three helper functions have been added to:
- Calculate the effective basic reproductive number Reff in a population with heterogeneous social contacts and susceptibility to infection
- Convert from the basic reproductive number provided by the user R0 to the transmission rate (denoted by λ), given the population’s social contacts and susceptibility structure
- Convert from a user-provided transmission rate to the basic reproductive number given the population’s social contacts and susceptibility structure
- Two new vignettes have been added which are intended to serve as contextual background information for users:
- A guide to constructing susceptibility matrices
- A comparison with a simple susceptible-infectious-recovered epidemic model
- Package infrastructure has been modified:
- The package now specifies C++17 as standard
Readme.Rmduses auto-rendering of the package and repository name to
Readme.mdvia an updated
render-readmeGithub Actions workflow
- The Cpplint workflow now includes linting and checking using Cppcheck for header files
NEWS.mdfile to track changes to the package.
CRAN release: 2022-12-05
Initial release of finalsize, an R package to calculate the final size of an epidemic in a population with demographic variation in social contacts and in susceptibility to infection.
This release includes: 1. A choice of equation solver functions. 2. 100% code coverage, 3. A basic usage vignette, and two advanced vignettes, 4. Example data from the POLYMOD dataset obtained using the socialmixr R package, 5. Workflows to render the vignettes and README as a website.