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Case/Death Tracking Figure (Currently Figure 1) #736

Open rando2 opened 3 years ago

rando2 commented 3 years ago

Is your feature request related to a problem? Please describe. There had been some previous feedback that the figure showing the accumulation of deaths over time wasn't super closely tied to the content of the manuscript in that section. I'm wondering if instead we'd want to try to modify it to show cases over time (from the same data source) alongside the SARS cases from 2002-03

Describe the solution you'd like The same data source has case information for COVID-19, so it should not be a huge switch to use a different data source there. It's a little harder to find data for SARS (and I had also considered MERS, but couldn't find anything usable). The best resource I've found is this one: https://www.kaggle.com/imdevskp/sars-outbreak-2003-complete-dataset?select=sars_2003_complete_dataset_clean.csv

It scrapes the WHO website to pull the updates case numbers for every day from March to July 2003 (WHO started releasing SARS reports in March, the pandemic was classified as under control in July). It would be better to have data going back further, but I haven't found where that would be.

For MERS, there are some graphs circulating online (e.g., this one that seem to show time series data, but it's not clear where their data sources are.

Describe alternatives you've considered A clear and concise description of any alternative solutions or features you've considered. We definitely do not need to make this switch! I will open a PR soon that provides some additional context but I wanted to create this while I had everything fresh in my mind. The gist is that these three pandemics followed very different trajectories despite all being coronaviruses with fairly high death rates (COVID-19 has the lowest death rate).

Additional context Another possible issue is scale -- the SARS pandemic just didn't get out of control like this one did.

rando2 commented 3 years ago

See #962 -- let's do the following as soon as we're able:

  1. Smooth out the SARS data (not published every day)
  2. Include the daily cases (in the dataframe loaded for SARS, can be obtained from CSSE here
  3. Possibly add in vaccination data from OWID to contextualize what will hopefully be declining deaths soon?