EcoHealth Alliance’s ongoing OpenRVFcast project is developing a generalizable, open-source modeling framework for predicting Rift Valley Fever (RVF) outbreaks in Africa, funded by the Wellcome Trust’s climate-sensitive infectious disease modeling initiative. We aim to integrate open data sets of climatic and vegetation data with internationally-reported outbreak data to build an modeling pipeline that can be adapted to varying local conditions in RVF-prone regions across the continent.
data/
contains downloaded and transformed data sources. These data
are .gitignored and non-EHA users will need to download the data.R/
contains functions used in this analysis.reports/
contains literate code for R Markdown reports generated in
the analysisoutputs/
contains compiled reports and figures.renv.lock
and code used to manage
dependencies is in renv/
and other files in the root project
directory. On starting an R session in the working directory, run
renv::restore()
to install R package dependencies.mermaid.js
syntax and should display as a graph on GitHub. It can also be viewed
by pasting the code into https://mermaid.live.)graph LR
subgraph Project Workflow
direction LR
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end
linkStyle 0 stroke-width:0px;
To run the pipeline, the user will need to adapt the _targets.R
file
to use their own object storage repository (we use AWS) and will need to
supply keys in an .env
file.
EHA users: see the stripts/
repository to be able to directly download
data from AWS outside of the targets workflow.
Follow the links for more information about: