daedalus 0.2.0

This is a minor version release of {daedalus} that adds real-time epidemic modelling functionality while removing the implementation of vaccination and vaccination-group infection pathways.
There are no intervening versions between this and v0.1.0.

1. Added new function daedalus_rtm() (for real-time modelling) which returns either a <daedalus_output> object or a list of these.

   • Has an Rcpp backed using RcppEigen and Boost Headers {BH} for Boost odeint solvers; added Rcpp, RcppEigen, and BH as dependencies;

   • Removes reactive intervention implementation and lifting; instead a single intervention on economic sectors can be passed for implementation in a user-specified time-frame ;

   • Allows NPI on social contacts (basic scaling of transmission rate $\beta$) when economic sector NPI is active (default is 1.0 for no distancing); see arg social_distancing_mandate;

   • Allows spontaneous social distancing mediated by daily deaths to be turned on (off by default); see arg auto_social_distancing;

   • Allows passing a 45-element numeric vector specifying sector-wise openness coefficients;

   • Allows passing a list of <daedalus_infection> objects to infection to accommodate parameter uncertainty (in this case it returns a list of <daedalus_output>);

   • Hosptial capacity only determines when excess mortality is activated;

   • Initial state asumes 1 in 10 million infected.

2. Added C++ code in src/daedalus.cpp to help with ODE RHS, observer for ODE system, looping over parameter combinations, and exposing C++ code to R.

3. Added functions to help with daedalus_rtm():

   • prepare_output_cpp() to handle output from Rcpp fn (returned as list of matrices);

   • make_conmat_large() prepares a 49 $\times$ 49 contact matrix for C++ ODE RHS;

   • make_work_contacts() and make_consumer_contacts() scale contacts by workers in economic sectors -- $N$ in $\beta SI \text{CM} / N$.

4. Package classes:

   • <daedalus_country> now returns life expectancy vector;

5. Package data:

   • Exporting economic sector names;

   • Exporting country-wise life-expectancy data;

   • Added C++-model compartment names as a constant.

6. Downstream functions:

   • get_costs() returns life-years lost; values of lives lost vector is renamed to life_value_lost

   • get_life_years_lost() calculates life-years lost from total deaths and life-expectancy.

7. Package infrastructure:

   • Updated .Rbuildignore, .gitignore, .lintr, _pkgdown.yml, WORDLIST for C++ code;

   • Updated Readmes to reflect package title and scope;

   • Added basic tests for daedalus_rtm().

daedalus 0.1.0

This is a minor version release of {daedalus} for use in the IDM conference in 2024. See the changelog on the package website, or read the NEWS.md file for more information on this release.