InstituteforDiseaseModeling/covasim

"Time for disease recovery" parameters

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Describe the bug

  1. "Time for disease recovery" parameters in "covasim/covasim/README.rst" is not up to date.
  2. Not sure if this is a bug but I don't understand why crit2rec == sev2rec == 18.1
  3. And for crit2die, I think 9.7 days would be a better number

Expected behavior

  1. The README should match the code in covasim/covasim/parameters.py
  2. I think crit2rec should be this: 16.6 days = 24.7 onset-to-recovery - 6.6 sym2sev - 1.5 sev2crit
  3. In the calculation provided in the code, 18.8 days total was used instead of 17.8, which is a more precise number.
    In the study cited in the code (Verity et al.), the authors said that: "In the subset of 24 deaths...early in the epidemic...we estimated the mean time from onset to death to be 18·8 days [15·7–49·7]" "However...our posterior estimate...informed by the analysis of aggregated data from China, is MORE PRECISE (mean 17·8 days [16·9–19·2])"

Additional context

  1. The code parameters were updated to use more accurate numbers from recent research but the README was not updated.