Maintainer is changing to @rozeggo (#212).
-
Updated all GitHub Actions workflows in line with {epiverse-trace/packagetemplate} (#212).
-
Updated DESCRIPTION and license files with new maintainer and new copyright year (#212).
-
Added
R/dev-utils.R
for extra release issue bullet points, and addedtools/check.env
for global environment checks (#212). -
Corrected internal article links in vignettes (#212).
-
Added continuous benchmarking workflows using {touchstone} following the pattern of {epiforecasts/EpiNow2} (#212).
This patch adds:
-
Default values for the contact matrix, susceptibility matrix, and susceptibility distribution matrix to allow quick estimates of final size for a given
$R_0$ in a population with homogeneous mixing and full susceptibility (#180); -
Combines the documentation for the functions
r_eff()
,r0_to_lambda()
, andlambda_to_r0()
under the name 'r0_conversions'; -
Adds vignettes on the theoretical background and on projecting re-emergence of a disease due to demographic turnover (#193, #194 by @adamkucharski);
-
Streamlines the examples in the Readme;
-
Replaces the PNG logo in the Readme with an SVG version;
-
Updates the GitHub Actions workflow YAMLs, the
.lintr
config file,_pkgdown.yml
,.Rbuildignore
,CITATION.cff
andCRAN-SUBMISSION
; workflows and configuration files bring the package in line with {packagetemplate} (#181, #186, #188). -
Standardises the
DESCRIPTION
file. -
Adds package-level documentation.
-
Adds spellchecking and the
WORDLIST
file. -
Adds tools to check that the package does not modify the global state, code to flag any partial matching of function arguments,.
-
Updates references cited in the vignettes.
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 underinst/include/
- The package includes a package header under
inst/include
calledfinalsize.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
$R_{eff}$ in a population with heterogeneous social contacts and susceptibility to infection - Convert from the basic reproductive number provided by the user
$R_0$ to the transmission rate (denoted by$\lambda$ ), 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
- Calculate the effective basic reproductive number
- 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
- The
Readme.Rmd
uses auto-rendering of the package and repository name toReadme.md
via an updatedrender-readme
Github Actions workflow - The Cpplint workflow now includes linting and checking using Cppcheck for header files
- Updated
NEWS.md
file to track changes to the package.
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:
- A choice of equation solver functions.
- 100% code coverage,
- A basic usage vignette, and two advanced vignettes,
- Example data from the POLYMOD dataset obtained using the socialmixr R package,
- Workflows to render the vignettes and README as a website.