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exploreringbp's Introduction

Explore the feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

This application allows interactive exploration of individual contact tracing and isolation scenarios for the 2019-nCoV outbreak using the branching process model developed in “Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts” by Hellewell et al. For more details on the model used or the scenarios considered please see the paper.

Running the app

Install the application and required dependencies with the following:

remotes::install_github("epiforecasts/exploreringbp", dependencies = TRUE)

Run the app locally.

exploreringbp::run_app()

Usage

The results tab contains a summary of a single outbreak scenario.

The settings tab contains sliders which can be used to vary the outbreak scenario.

The details tab contains a brief overview of the model used in the app and links to resources for further information.

Docker

This app was developed in a docker container based on the tidyverse docker image.

To build the docker image run (from the exploreringbp directory):

docker build . -t exploreringbp

To run the docker image run:

docker run -d -p 8787:8787 --name exploreringbp -e USER=exploreringbp -e PASSWORD=exploreringbp exploreringbp

The rstudio client can be found on port :8787 at your local machines ip. The default username:password is exploreringbp:exploreringbp, set the user with -e USER=username, and the password with - e PASSWORD=newpasswordhere.

exploreringbp's People

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exploreringbp's Issues

Scale of outbreak trajectories

the scale of the outbreak trajectories is often huge, even though the interesting part may be down at the bottom.

  • Roz's feedback

Cases for outbreak generation updates

suggestions:

  • find a different way to represent the "simulations that reach this generation", proportional sizes are difficult to discern
  • group controlled and uncontrolled outbreaks

update text on settings page

  • add padding between dispersion and theta input elements
  • change "asymptomatic" to "subclinical"
  • add units for max simulation time
  • decimal place error on one slider
  • % outbreak controlled - potentially round to 1 dec place?
  • fix short and long label spacing - add explanatoin

Parameter summary

In the box on the results pane, would be good to show list of all of the values that they have set for each parameter on the previous pane.

update slider UI - add current value or parameter table

The current value only shows if you click and hold the slider handle - so it's difficult to review all of the settings.

Potential solutions:

  • Add a value label within each element
  • Add a parameters table, either to the settings or results tab (or both)

Outbreak trajectory length

We define control as 0 cases within 12-16 weeks so either:
a) no need to show cumulative cases beyond that are they are already considered controlled/uncontrolled.
b) update the bit where % controlled is stated to highlight what the definition of control is that we use

Greyscale

I would really prefer some colour somewhere. Maybe blue lines on the cumulative trajectories and light blue intervals on the right-hand plot.

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