vat is an interactive R package used with the Atlantis ecosystem model.
An example of vat from the Icelandic Atlantis model can be seen here. Note, that the Atlantis model in that example is a work-in-progress.
To install:
library(devtools)
install_github(repo = "mareframe/vat")If you have installed Atlantis on the machine where you want to run vadt, you should have all necessary tools.
Windows users that are getting errors installing ncdf4, please see this page on the wiki.
If you are a Mac user and are getting installation errors, please make sure that the command line tools for Xcode are installed.
To run the interactive Shiny application for vat, named vadt for visualizing Atlantis diagnostic tool. You need to running the following sequence of functions.
-
create_vadt(). This creates an object of classvadtcontaining all the data needed forvadt(). -
animate_vadt(). This function creates optional animated plots forvadt(). -
vadt(). This is the function that launches the actual Shiny application.
Please see each functions respective manpage for details on its usage. For example, ?create_vadt and ?vadt in R.
At present vat is a moving target. We welcome all feedback on it's UI as well as any additional features, you would like to see added. Please report issues and feature requests. Once the vadt UI is frozen and when work in the Icelandic Atlantis model moves onto data presentation for stakeholders, then a new function(s) will be added to this package for data presentation.
Please note if you if you are interested in running vat in the manner shown in the example (i.e. on a locally hosted web server), you must install shiny-server and you need to modify vat. If there is interest in this from other Atlantis modelers, please open an issue and I will start maintaining a seperate repository for that code.
Atlantis users may also be interested in the rlantis package. This package contains helper files for Atlantis as well as creating static graphs.