This application is described in Getz, et. al, A runtime alterable epidemic model with genetic drift, waning immunity, and vaccinations. https://doi.org/10.1101/2021.06.07.21258504 The current version is 1.073 beta. It installs with its own Java runtime (JRE 8_202).
See the User Guide here
Download slides from Adaptive vaccination may be needed to extirpate COVID-19: Results from a runtime-alterable strain-drift and waning-immunity model, presentation by Wayne Getz and Richard Salter to MIDAS: Covid-19 Modeling: Impact of Interventions, June 14, 2021.
To install and run under MacOSX
- Download and unzip this zip file. The unzipped file will create a folder called SEIVAgentv1.073macosx.
- Create or choose a folder as your working folder for this project.
- Double-click on SEIVAGENT-1.073.dmg to mount and open the disk image containing the application. You must first accept the end user license agreement.
- Drag the SEIVAgent icon to the working folder.
- Drag the rest of the contents of the SEIVAgentv1.073macosx folder to the working folder.
- Launch the SEIVAgent application. The first time you launch do so by right-clicking the icon and select Open and select the Open override. Subsequent launches will only require a double-click.
- You may see a warning message with an Open override.
- Open System Preferences / Security & Privacy and click on General.
- Click on "Allow Anyway" to unblock the launch. This package contains a Java runtime and has been verified as malware free.
- Any security queries regarding keystrokes can be denied.
- When the simulation starts you may need to adjust the display resolution in order for the dashboard to fit on the screen. Use System Preferences / Displays to make this adjustment
To install and run under Windows
- Download and unzip this zip file.
- Double-click the installer SEIVAgent-1.073.exe and follow instructions. This will install SEIVAgent and its required Java runtime.
- Launch the application using the shortcut, and bypass any security warnings.
- Make any display resolution adustments to accomodate the dashboard, as with MacOSX.
Running SEIVAgent
- Before inititating a simulation either select the various parameter values for the run or do the following:
- Press the "Open settings" button at the top left-hand side of the application and in the downloaded "SEIVagent_version" folder select the file "BasicParameters.xml."
- Now go to the bottom right-hand corner next to the "Run" button, insert the number of steps for the simulation, and press the "Run" button to initiate the run.
- If you want to run our JavaScript adaptive vaccination driver, then go to the "JS" button, second from the left at the bottom of the app and press it to open the JS window. Now press the "Open Script" button at the top (in the middle) of this window and select the "vaccadjust.js" file to open this script. Then press the "Load Script" button at the bottom right-hand corner of the JS window, then press the "Go" button at the bottom middle of this window. Pressing the "Stop" button will act to stop the run and reset it to the starting point at step (time) 0.
Using the R example
- In R or R Studio, install the package contained in seiv_0.2.0.tar.gz as a source package into your R platform from Tools -> Install packages. Otherwise, install from the console by typing install.packages("[PATH_TO_DIR]/seiv_0.2.0.tar.gz", repos = NULL, type = "source") providing the right path to the working folder.
- Install any uninstalled packages (ggplot2, reshape).
- Open and load the program Rdemo.R.
- Invoke the program from the console using go(run=10, sampleSize=165)