Categories

## Building Covid 19 tool to help forecast hospital beds

What a frilling week. Market turmoil, oil crashes, and Covid arrived to come kick our asses. I chose to not sit idly by as a spectator, and instead forge a weapon (web app) that will help hospitals around the world predict the wave IN THEIR AREA and tell them how many beds they need and if they will be swamped.

It needs to predict when the wave arrives, and how many of each type of beds will be needed. Standard, ICU, and Critical. Plus, as the data for Covid gets better, the user can change the inputs easily on the webpage.

I haven’t named it officially yet, maybe call it COBE Tool – COvid Bed Estimator Tool. I will put in in Shiny at shiny.io hosted.

Early results show what will happen if Covid19 burns without social distancing. 72% of America catches it.

Tools used : R, with packages Epimdr, Desolve, Shiny. The core code for generating the S E I R table is below.

``````require(deSolve)
times = seq(0, 450, by=1)
#paras = c(mu = 0, N = 1, beta = 1000, sigma = 365/15, gamma = 365/5)
sigma<- 1/5 # this is     The rate at which an exposed person becomes infective. Inverse of
gamma<-1/15 #  The rate at which an exposed person becomes resistant (recovers)
paras = c(mu = 0, N = 1, beta = .1173, sigma = sigma, gamma = gamma)
start = c(S=(.999) , E=0, I=.001, R = 0.0)
#start = c(S=0.06, E=0, I=0.001, R = 0.939)
out=ode(y=start, times=times, func=seirmod, parms=paras)
#init       <- c(S = 1-1e-6, I = 1e-6, R = 0.0)
#parameters <- c(beta = 1.4247, gamma = 0.14286)
#out <- ode(y = init, times = times, func = sir, parms = parameters)
out <- as.data.frame(out)
tail(out)
plot(out\$time,out\$R)
plot(out\$time,out\$I)
``````
Categories

## CoVid19 forecasting cumulative cases

I do a bit of competition forecasting. Almanis, Good Judgement Open, and the Hybrid Forecasting Challenge. Some are open, some you must be invited. I’ve found that I’m good at battlefield casualties and epidemiology. Here are my thoughts on CoVid19, and the chances of having greater than 100k cumulative cases by 20MAR20

Finally the Markets are realizing CoVid19 will affect the economy.

Instantaneous forecast from yesterdays increase is 20 days left *1753 new yesterday +85403=~ 120,000 cases.

The instantaneous estimate is no longer trending down, Containment is generally working in China, but CoVid19 has now gone into the wild in other countries. I think there will be no hope of <100k by 20MAR20
But the numbers are increasing more linearly than geometrically.

The real numbers for WHO cases over the last 4 weeks are:

85403 (SitRep Day 40) – not a full week
80239 (SitRep Day 36),
73332 (SitRep Day 29)
43103 (SitRep 22),
20630 (SitRep 15)

Extrapolated weekly estimate is 85403-77794 * 3 weeks left = ~108,000
This shows signs of slowing that the Chinese fight to drop Ro is working. From the model below, I show Ro to be ~1.1 to 1.2 where last week I thought it to be 1.7 roughly.

However, now that is is wild in other countries who aren’t prepared for the Draconian methods China executed. I expect the Ro to begin to rise again.

There is a slim chance to think CoVid-19 will stay below 100k cases as I’m beginning to believe the virus is currently ‘contained’ in China. Also possible is if you believe other countries will systemically under report for political ends. Iran clearly is not reporting real numbers at this time.

Of new concern is the finding previously unknown clusters, even in the USA. Of note is this is a secondary infection not primary from travelers from China. That reinforces my thinking that many second and third world countries have wild clusters established and will begin to spread fast. They may not detect them in time to add to 20MAR WHO report.

I recommend folks follow Dr Campbell on Youtube to get his input, as he has foreign health workers with first hand accounts in Iran emailing him. Those accounts reveal hundreds to thousands infected.

Another great resource is https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 or their mobile friendly version https://www.arcgis.com/apps/opsdashboard/index.html#/85320e2ea5424dfaaa75ae62e5c06e61

The quarantine’s goal is to drop the Ro number from ~2.3 down to less than 1 hopefully, but more likely 1.2 IMHO so we need to adapt that to our numbers.

My assumptions are :
1) too late for containment
2) Wild clusters are undetected in many other countries
3) Iran’s clusters are far worse than feared.
4) The reported cases will increase quasi-geometrically perhaps linearly but not exponential until 20MAR20
5) The new post quarantine Ro is still above 1.1 and below 1.5

Raw data collected via Tencent on the official numbers is https://news.qq.com/zt2020/page/feiyan.htm
yea, its in Simplified Chinese.