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Arbovirus Modeling and Prediction to Forecast Mosquito-Borne Disease Outbreaks
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case matrix with estimates
graphical outputs
human case data
mosquito data
mosquito matrix with estimates
pictures for setup document
shapefile
strata
weather data
.gitignore
ArboMAP Main Code.Rmd
ArboMAP User's Guide.Rmd
ArboMAP Variable Selection.Rmd
ArboMAP.Rproj
ArboMAP_Main_Code.pdf
ArboMAP_User_s_Guide.pdf
ArboMAP_Variable_Selection.pdf
GRIDMET_downloader_v1_0.js
README.md

README.md

Arbovirus Modeling and Prediction to Forecast Mosquito-Borne Disease Outbreaks (ArboMAP)

ArboMAP is a set of software to be used in the RStudio envionment to model and predict vector-borne diseases, especially arboviruses transmitted by mosquitoes.

ArboMAP_User_s_Guide.pdf contains information on installation and use of ArboMAP. New users should begin by reading through the file completely.
ArboMAP Main Code.Rmd contains code for generating weekly forecasting reports.
ArboMAP Variable Selection contains code for selecting the best subset of climate variables to use with the arbovirus prediction model.
ArboMAP User's Guide.Rmd contains code for generating the user guide.
GRIDMET_dowmloader_v1_0.js contains code for the Google Earth Engine application for environmental data access.
ArboMAP.Rproj is an RStudio project that can be used to run the code and will allow the programs to find all the necessary data.

The various directories contain either example input data or example outputs from ArboMAP.

Important Note: the human and mosquito data that come packaged with ArboMAP are synthetic data, created by first fitting the model on West Nile virus in South Dakota, and then generating human cases and mosquito pools according to that model. Hence, while they are consistent with the overall trends of actual data, they are not the actual data, and must not be used as a basis for scientific inference. Rather, they are provided so that the user can see an example of the code working well with realistic data.

ArboMAP was developed by the EcoGRAPH research group at the University of Oklahoma with support from NASA. We are happy to answer your questions, and we would appreciate feedback on how these tools could be improved. Please contact justinkdavis@ou.edu for technical issues about the code, or mcwimberly@ou.edu for questions about the arbovirus modeling project.

Copyright (C) 2019, J. Davis and M. Wimberly

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

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