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DICE

An R package for modeling and forecasting direct-contact and vector-borne infectious diseases.

DICE Installation Instructions

Using 'devtools' in an R console

> library(devtools)
> install_git(url="https://github.com/predsci/DICE4", subdir="dice")

NOTE: This method is convenient, but it may still be worthwhile to download the repository (see next subsection) to a user directory. The scripts in examples/ directory and the manual (dice/vignettes/dice.pdf) are quite useful.

Manually from command line

Navigate to your preferred directory

$ cd mydir

Download the repository from GitHub (requires git command line tools)

$ git clone https://github.com/predsci/DICE4.git

Navigate into the local repo directory

$ cd DICE4

Use python script to compile from source

$ ./compile.py

NOTE: If you do not wish to or cannot install DICE globally, it can also be installed to a local R-library using 'R CMD build dice' and 'R CMD INSTALL -l /my_lib_loc dice'

Installation notes

Installation of sf

Some users report trouble installing the package 'sf' from source code. Installation from binaries is generally sufficient for DICE. The package 'sf' is a sub-dependency of DICE (DICE->cdcfluview->sf). Installation of 'sf' from source requires proper installation and configuration of GDAL(https://gdal.org/). The GDAL capabilities of sf are not utilized for cdcfluview/DICE.

Getting Started

In general, the scripts in examples/ are a good way to get started and the manual dice/vignettes/dice.pdf contains much more detailed information along with some walk-throughs. Help pages for DICE and runDICE are also good starting points:

> library(DICE)
> ?DICE
> ?runDICE

About

Arbitrary scale SIR model for studying transmission dynamics of influenza and other novel pathogens

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