README.md
In lorecatta/DENVfoiMap: Runs the analysis of the paper on global dengue FOI mapping and prediction of intervention impact
DENVfoiMap
The goal of DENVfoiMap is to provide a set of functions to run a
complete analysis similar to the one described in the following study:
A complete analysis includes:
- making global predictions of dengue force of infection at 1/6 degree
resolution (approximately 20 km),
- estimating baseline global dengue burden (number of annual
infections, mild febbrile cases and hospitalized cases), and
- predicting the effect of transmission-reducing type of interventions
and the Sanofi Pasteur dengue vaccine on burden.
As the analysis described in the aformentioned publication includes
uncertainty estimation and sensitivity analyses of model parameters,
which require considerable computing time, the original code was
tailored to run on the High Performance Computing Cluster at the
Department of Infectious Disease Epidemiology (Imperial College London).
DENVfoiMap does not aim to perform uncertainty estimation and
sensitivity analysis. It however provides a set of functions to run a
complete analysis using a single bootstrap sample of the original force
of infection dataset. To reduce computation time I provide an example
code which produces predictions only for the country of Brazil. Model
fitting and making global predictions, for different bootstrap samples,
do require some form of parallelization if you wish to run them fast.
Installation
Please install DENVfoiMap from github with
devtools::install_github("lorecatta/DENVfoiMap")
Load and attach it with
library(DENVfoiMap)
This
vignette
and the analysis.R script explain how to run a complete analysis.
Please do get in touch (l.cattarino@gmail.com) if you have any queries
or encounter issues when using DENVfoiMap.
lorecatta/DENVfoiMap documentation built on April 1, 2022, 4:05 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
DENVfoiMap
The goal of DENVfoiMap is to provide a set of functions to run a
complete analysis similar to the one described in the following study:
A complete analysis includes:
- making global predictions of dengue force of infection at 1/6 degree resolution (approximately 20 km),
- estimating baseline global dengue burden (number of annual infections, mild febbrile cases and hospitalized cases), and
- predicting the effect of transmission-reducing type of interventions and the Sanofi Pasteur dengue vaccine on burden.
As the analysis described in the aformentioned publication includes
uncertainty estimation and sensitivity analyses of model parameters,
which require considerable computing time, the original code was
tailored to run on the High Performance Computing Cluster at the
Department of Infectious Disease Epidemiology (Imperial College London).
DENVfoiMap does not aim to perform uncertainty estimation and
sensitivity analysis. It however provides a set of functions to run a
complete analysis using a single bootstrap sample of the original force
of infection dataset. To reduce computation time I provide an example
code which produces predictions only for the country of Brazil. Model
fitting and making global predictions, for different bootstrap samples,
do require some form of parallelization if you wish to run them fast.
Installation
Please install DENVfoiMap from github with
devtools::install_github("lorecatta/DENVfoiMap")
Load and attach it with
library(DENVfoiMap)
This
vignette
and the analysis.R script explain how to run a complete analysis.
Please do get in touch (l.cattarino@gmail.com) if you have any queries
or encounter issues when using DENVfoiMap.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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