INTRODUCTION
The continual threat of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has ground the world to a metaphysical stop. Economies appear to be under threat of a long recession, political debates have delayed needed relief to citizens, lack of N95 masks for healthcare workers place them at greater risk for doing their jobs, and mortality has increased world-wide. We are undoubtedly experiencing an seminal period in the 21st Century and data analysts have rushed to develop stunning visuals and dashboards such as the ones developed by Johns Hopkins University, “Our World in Data”,1 and the Centers for Disease Control and Prevention to feature the impact the SARS-CoV-2 is having on our world.
MOTIVATING EXAMPLE
In this article, we will replicate the total deaths due to SARS-CoV-2 using data from the European Centre for Disease Control and Prevention (ECDC)2 or from the Our World in Data’s GitHub site.3 Due to the changing nature of SARS-CoV-2 data, this exercise will have used data that would ultimately be updated in the future. Please visit the ECDC site to download the most recent SARS-CoV-2 data.
The figure we will replicate is one posted on the “Our World in Data” website and looks like the following:
Source: Our World in Data. Total confirmed COVID-19 deaths: How rapidly are they increasing? URL: https://ourworldindata.org/grapher/covid-confirmed-deaths-since-5th-death [last accessed: 17 April 2020].
We will download data from the ECDC and then use Excel to recreate this plot for several countries (we won’t create plots for all the countries, but you can feel free to do so by taking advantage of the available data).
Step 1. Download data from the ECDC.
You can download the raw data from the ECDC’s site here. Alternatively, you can also download the cleaned data for this article here (I cleaned the data and prepared them for use in Excel).
The data has the following format:
Each column represents a country and the rows represents the total number of deaths for each day after the 5th confirmed death.
Step 2. Select all of the data and insert a line chart.
Once all the data have been downloaded, select all of them. Insert a line chart and Excel will automatically generate a figure for you. This figure will need to be edited further, but Excel does a good job of plotting the total number of deaths along the X-axis (time).
Right-click in the chart region and click on the Select Data option. You want to de-select the “Days since the 5th total confirmed death” because this is not the value of interest. Rather, this represents the values for the X-axis (time).
Once you de-select the “Days since the 5th total confirmed death,” your line chart should look like the following figure.
Step 3. Changing the scale on the Y-axis.
In the figure from the Our World in Data, the values for total deaths are plotted using a log-scale. When Excel generates the line chart, it automatically uses the continuous scale on the Y-axis. To change this, you need to right-click on the Y-axis and then select Format Axis...
Once you make the changes to the Y-axis scale, the line chart should now look similar to the one from Our World in Data.
Step 4. Adding the axes labels and formatting the lines.
Once the line chart’s Y-axis has been transformed into a log-scale, you can make changes to the axes labels and the line formatting. Select the Design tab to made changes to the Y-axis label. Select the Add Chart Element to open the drop-down menu, then select the Axis Title followed by the Primary Vertical option. This will allow you to make changes to the Y-axis label.
Change the Y-axis label to read, “Log number of COVID-19 deaths.” Do the same thing for the X-axis label, but change it to read “Days since 5th death occurred.” Your figure should look like the following.
You can make the lines thinner by right-clicking on one of them (e.g., China), opening up the options. Select Format Data Series… and then adjusting the Width to be 1.5 points. This will make the line easier to see without having to take up space with the thicker lines.
Repeat this process for all the lines in the chart. Once you have completed that, the line chart should look like the following.
Step 5. Now all that’s left is changing some of the aesthetics.
The final line chart replicates the figure from Our World in Data and provides the references line for a doubling in the number of deaths for each country. The reference line (“Doubling every 5 days”) was creating using a base of 10 on a log-scale to replicate a doubling of that value every 5 days. The reference line was also placed on a secondary axis to create a continuous line (since creating a line on the same scale as the other countries would have yielded gaps because we’re doubling deaths every 5 days). In the Design tab, you can add the secondary horizontal axis to match that of the primary horizontal axis (time). The secondary vertical and horizontal axes had their font color changed to white to hide them from view and to clean the final figure.
Gridlines were added along with the label for the reference line, which indicates to point where the total confirmed SARS-CoV-2 deaths are doubling every five days.
Here is the final chart after some formatting changes were made.
Conclusions
Although we plotted total deaths from SARS-CoV-19 from existing data, these were limited to five countries. More countries can be added using the available data, and it is encouraged that you try to plot all the other countries as an exercise. The reference line provides us with the doubling of deaths on a log-scale and carefully provides the readers with a threshold where certain doubling of deaths would be reported. China seems to have controlled their total number of deaths, but there is a spike at the end of day 87 that shows an increase in deaths. This may be due to reporting error or a change in the definitions of death. The US, including the other European countries, are trailing the rest of the world in containing the SARA-CoV-2 pandemic. Hopefully, this type of data visualization will help inform decision makers to develop policies that would mitigate the impact of SARS-CoV-19 on mortality any parts of the world.
You can download the data and complete exercise here.
References
Roser M, Ritchie H, Ortiz-Ospina E, Hasell J. Coronavirus Disease (COVID-19) – Statistics and Research. Our World Data. March 2020. https://ourworldindata.org/coronavirus. Accessed April 17, 2020.
European Centre for Disease Control and Prevention. Download today’s data on the geographic distribution of COVID-19 cases worldwide. European Centre for Disease Prevention and Control. https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide. Published April 18, 2020. Accessed April 18, 2020.
Our World in Data. GitHub: Owid/Covid-19-Data. Our World in Data; 2020. https://github.com/owid/covid-19-data. Accessed April 18, 2020.