This repository contains code for an in-development R package recreating the mosquito model of - Niebuhr, 2016. Avian malaria transmission dynamics in New Zealand: investigating host and vector relationships along an elevational gradient. PhD Thesis, University of Otago.
The model is updated to use climate station data accessed from NIWA's CliFlo climate information database. Currently only one location, Musselburgh, Dunedin (CliFlo station ID - 15752), is accessed and all models are run for that station.
CliFlo requests require a user login (see https://cliflo.niwa.co.nz) and users need to add these as cliflo_usrid and cliflo_pwd environment variables on their local machine (see this page).
Install the appropriate version of Rtools and install the 'devtools' R package.
To install directly from the github repository run devtools::install_github(repo = "sihoward/mossiemodel-dev", ref = "master") in the R console.
The model is structured as an R package.
R package dependencies are flagged during install, and are deSolve, clifro, shiny, dplyr, ggplot2, tidyr, rlang.
After installation run example(mosqmod::runModel) to see a worked example.
To run the included shiny app locally run mosqmod::runMosqModApp().
Users on networks with restrictions may have to edit the permissions file 'cacert.pem' at 'C:/Program Files/R/R-X.0.0/library/RCurl/CurlSSL/cacert.pem' to send CliFlo requests. Alternatively, use runMosqModApp(cliflo_requests = FALSE) to supress requests when running locally.
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Add documentation to functions
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Vignette?
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Add datasets?
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Additional climate stations
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Manual upload of temperature time series
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Usage tracking?
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Drop M from UI