daedalus - daedalus 0.2.24

This release is the last version to work with daedalus.data v0.01, and is provided primarily as a convenience. All future versions require later versions of daedalus.data. See the package changelog for more details on changes between daedalus v0.2.0 and this version.

- R
Published by pratikunterwegs 7 months ago

daedalus - 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.

1. 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.

2. 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 $\beta SI \text{CM} / N$.

1. Package classes:

- `<daedalus_country>` now returns life expectancy vector;

1. Package data:

- Exporting economic sector names;

- Exporting country-wise life-expectancy data;

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

1. 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.

1. 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()`.

- R
Published by pratikunterwegs about 1 year ago

daedalus - 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.

- R
Published by pratikunterwegs over 1 year ago