CoSMic

Description

A calibration-microsimulation approach to reduce uncertainty for policy decisions on non-pharmacological interventions in the COVID-19 pandemic. The package implements an age-structured spatial microsimulation model that extends the Susceptible-Exposed-Infectious-Recovered (SEIR) framework. Using an optimization approach based on subnational trends in the number of intensive care patients, it is able to calibrate the model to the ongoing spread of the epidemic and tries to estimate how the NPIs have affected it. Based on these estimates the model can provide national and sub-national forecasts for trends in the number of ICU patients and other indicators under different scenarios regarding NPIs.

Installation

R-version

Since the CoSMic R-version is currently not developed up to the state of a proper R-package please install it using

library(devtools)
devtools::install_github("hpcralf/CoSMic",build_vignettes=TRUE)

Alternatively you can check out the code with

git clone https://github.com/hpcralf/CoSMic.git

or download the source code zip-file from https://github.com/hpcralf/CoSMic/archive/main.zip.

Once having checked out the code or extracted the source-package, change to the code directory (CoSMic in case of git-chekcout or CoSMic-main in case of zip-file download), start a R session and execute

library(devtools)
devtools::install(build_vignettes=TRUE)

Fortran-version

Even though the Fortran model version is usable as a stand alone program it is meaningfull to also install the R-version since the input files as well as the default set of input data can be generated automatically using the function convert.Rp.to.Fp included in the R-version of the model.

To build and install the the Fortran-version of the CoSMic model the GNU configure and build system is system is used. To build the Fortran-version a working MPI-Fortran-compiler is needed.

First checkout the current master branch from github

git clone https://github.com/hpcralf/CoSMic.git

Change into the CoSMic directory, create a build directory, save the CoSMic basepath to an environment variable and change into the build directory.

cd CoSMic
mkdir build
export COSMIC_PATH=$PWD
cd build

Set the FC and FCFLAGS environment variables to select the installed MPI-compiler and activate OpenMP support. In case you are using a standard MPI-installation like OpenMPI along with the GNU Fortran compiler gfortran on a Linux based system this will work like stated below.

export FC=mpif90
export FCFLAGS="-fopenmp -O3"
../Fortran/configure --prefix=${COSMIC_PATH}/install

Now build and install the Fortran-version and extend the PATH environment variable.

make
make install
export PATH=$COSMIC_PATH/install/bin:$PATH

Usage

Please see

• https://github.com/hpcralf/CoSMic/blob/main/aux/CoSMic_0.11.1.0000.pdf
• https://github.com/hpcralf/CoSMic/blob/main/aux/CoSMic-Basic-Usage.html