COVID-19 Epi Dashboard


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About

The goal of this dashboard is to provide an epidemiological overview of the COVID-19 pandemic, incorporating data from multiple sources.

It is being actively developed by the data science team at Epicentre MSF.

The tool is built using the R programming language and the shiny web framework. Packages used include the tidyverse, leaflet and highcharter.

If you are part of the MSF network, you can access further Epicentre COVID-19 content on our Sharepoint site.

Current data sources

European Centre for Disease Prevention and Control

Data on the geographic distribution of COVID-19 cases worldwide

Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)

Data imported from the Our World in Data github repository

ACAPS COVID-19: Government Measures Dataset

Data available on HDX

Shapefiles

Natural Earth

How we estimated the trends

Trends are estimated daily on the daily number of cases and deaths in JHU CSSE data observed over a period of 12 days. The most recent 2 days of data are not considered, as counts may not yet be complete due to reporting delays. For example, if data is available as of the 14th of a given month, trends will be calculated on the period from 1st-12th of that month.

On the 12-day time-series we first carry a smoothing using a 3-day moving average. As a result, we obtain 10-day smoothed values for which we run a linear regression of the values in the natural logarithm scale using the following formula:

lm(ln(smoothed values) ~ 10 days)

The standard error of the model was used to calculate the confidence intervals.

Trends presented in the report were defined using the coefficients of the linear regression as follows:

  • Increasing trend: an upward trend that was statistically significant; this means a positive coefficient and the confidence intervals do not include 0.
  • Declining trend: a downward trend that was statistically significant; this means a negative coefficient and the confidence intervals do not include 0.
  • Stable trend: an upward or downward trend that was not statistically significant; this means an either positive or negative coefficient, but the confidence intervals include 0.

To ensure reliable estimates we estimate the trend only if the cumulative number cases (or deaths) during the 12-day period was higher than 50.

We opted to model the slope on window of 12 days because it includes 3 generation time of 4 days.