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[CALL] Making COVID-19 Data Computable

Posted 6 years ago
POSTED BY: Alan Joyce
9 Replies

Please check out my post where I processed Facebook population density map and make them computable datasets in Wolfram Language. It can be very useful for epidemic models using population densities.

POSTED BY: Mohammad Bahrami

I've wrangled the US county data of Cases and Deaths from JHU dataset.

CloudGet[CloudObject[
  "https://www.wolframcloud.com/obj/47230f9f-9bc0-4682-9aff-bdde93e98544"]]

The dataset has this structure: enter image description here

Example:

CloudGet[CloudObject[
    "https://www.wolframcloud.com/obj/47230f9f-9bc0-4682-9aff-bdde93e98544"]][
  SelectFirst[#USCounty == 
     Entity["AdministrativeDivision", {"LosAngelesCounty", 
       "California", "UnitedStates"}] &]][
 DateListPlot[
   Through[{Differences, 
      MovingAverage[Differences[#], Quantity[1, "Weeks"]] &}[#Cases]],
    PlotRange -> All, 
   PlotLegends -> {"Daily new cases", "Filtered over 1 week"}] &]

enter image description here

POSTED BY: Mohammad Bahrami
Posted 6 years ago

This note gave me a warm fuzzy for sure! I don't have an immediate need, but it speaks to practical purposes for useful ends. Thank you! Brian W

POSTED BY: Brian Whatcott
Posted 6 years ago
Posted 6 years ago

I have tracked accumulated Case and Death data for Oklahoma from Worldometers.info.

Because these data are somewhat noisy, I used an exponential low pass on the input with time constant ~ 3 days and fit the series to a sigmoid function of this kind: cases = k / (1 + exp( A - b*days)) like this: OK Sum of Reported CV-19 Cases

I continue by presenting the logistic function (with best-fit parameters) to Wolfram Alpha to plot the differential : which is cases per day like this: Oklahoma  CV-19 Cases per Day

In the same way I fit deaths to a logistic like this: Ok UNSMOOTHED CV-19 Deaths

and the resulting Alpha plot of death rate like this:  OK CV-19 Death Rate

Here is a plot of residual errors in the case fitting function: enter image description here I noticed a growing 7 day oscillation in reported cases. This may be a clerical artifact - or some intyernal dynamic.

DISCUSSION.
The logistic function is just two model steps away from the initial exponential function, and for later days the intermediate Straight Line fit. It provides high R^2 values for the largely pre-peak data. The logistic function has a short-coming to balance its simplicity: it uses the same exponential parameters before AND after the peak. This may become less realistic if the post-peak data decays on a LONGER time constant as it may well do. I hope that this approach may dissuade modelers starting from case/day data which is inevitably more noisy than the sigmoid case progression. It is perfectly possible to require the non-linear regression application to refit the exponential rate after an established peak rate day, but I do not yet have sufficient data to make this practical.

POSTED BY: Brian Whatcott
POSTED BY: Alan Joyce
Posted 6 years ago

POSTED BY: Robert Rimmer
POSTED BY: Bob Sandheinrich
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