Example: EpiEstimApp

Analyses can be conducted using the EpiEstim App, rather than using R directly. For a description as to how to access the App, please see https://github.com/jstockwin/EpiEstimApp/wiki.

Here we demonstrate how the App can be used to reproduce the analysis underlying Figure 2 of our paper, which is cited at the bottom of this page.

Data

First save the files 'DataS1.csv' and 'DataS2.csv' - both available with our paper - on your computer.

The App

Once you have opened the App, you should see the following:

Since we wish to upload incidence data, select "Own data" and then click next. You will then see this:

Click "Browse..." and navigate to the file 'DataS1.csv' on your computer. Change the slider that sets the sliding time window to "6", and then click next. This then leads to:

Ensure that "No" is selected, and click next again, leading to:

Since we wish to upload data from patients in known chains of transmission, click "Patient Data" and then click next. You arrive at

We will upload our own file, so click "Own Data" and then next:

The data are from patients in known transmission chains, so click "Patient data" followed by next.

Now click "Browse..." and navigate to 'DataS2.csv' on your computer. Click next.

Choose to conduct the analysis using an Offset Gamma distribution by selecting 'Offset Gamma', and then click "Go". EpiEstim is now running, which could take a couple of minutes. After that, the results of the analysis should appear, which will look something like this:

You have now produced results using the EpiEstim App!