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)
head(out)
tail(out)
plot(out$time,out$R)
plot(out$time,out$I)

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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.
https://www.youtube.com/watch?v=IL7oGRKETZM

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.
-edit- English translate https://translate.google.com/translate?hl=en&sl=auto&tl=en&u=https%3A%2F%2Fnews.qq.com%2Fzt2020%2Fpage%2Ffeiyan.htm

An excellent model that lets you adjust inputs is here:
https://art-bd.shinyapps.io/nCov_control/
(using Ro ~ 1.2 ‘ Effective reproductive number with control’ fits the data best)

I encourage all to play with that model, as it shows the case load with default Ro vs post quarantine Ro and the real cases reported. More on that model here: https://annals.org/aim/fullarticle/2760912/reporting-epidemic-growth-reproduction-numbers-2019-novel-coronavirus-2019-ncov

In all, the infections are showing to grow steadily. If CoVid-19 establishes in South America we may get to 200k quickly, not so sure if it is just the Middle East. The model now shows we’ll hit 100k, but it looks like more likely end at 120k by 20MAR.

I still think we’ll hit 100k cases by March 10.

Probability of <100k by 20MAR20 is 5%. Probability of 100k-200k by 20MAR20 is 92%, Over 200k is 3%


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An Atlatl

So I’m an archer not an Atlatl guy. But since it is just a stick that throws a stick, I cut a branch, carved it up, then promptly obsessed about finding good dart material. For Texas, broad leaf ligustrum is the solution. It grows straight after copicing. I have a mott of Ligustrum in my yard so I harvested some 1/2″ poles 5 feet long and made the darts.

Atlatl v1.0

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Alaskan Native American Archery

Having traveled a bit this year thru Alaska, I’ve taken note to photograph all archery equipment I see in the museums. I release these photos under Creative Commons 3.0 license.


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Best Practices creating PAO number system for memory training

So it has been a few weeks since finishing my PAO, many hours later I’ve got it up and running well. Speed is coming along. But now that I’m using it effectively, here are few things I’d wish I’d done differently.

To those coming behind me, who want to build their PAO, here is my advice:

  1. It is normal to struggle to build your 2 digit PAO. I had real trouble finding 100 people who were memorable and I had connection too. In the end when I was about 10 short, I just crammed 10 people that I kinda knew about into the PAO. That was a bad idea, connection seems to be key. You will be using this the rest of your life, take time to build out your PAO people.
  2. Using the Major system to pick the people was just…a waste. Now that I’m using it, I don’t pronounce anything in my head, I just image the PAO. The Major system did nothing for me but handicap the order that I put in people to the PAO. (I even saw someone using Major system for actions and object, which is an aweful idea, adding another burden to remember WHAT the P does and what O it does with with. Go with logical AO for the P) It does nothing for speed or recall. It kinda helped on memorizing it, but that was slow and ultimately overridden but another method, and I’ll address that in #3.
  3. I struggled for days memorizing it. But an hour after I read someone recommended putting it into a dedicated memory palace I did. But I had to make a big palace, 100 loci. I used a video game map, Once I walked thru it, BAM! They they all were, settled into their places within the hour. I’ll address optimizing this in #5.
  4. But I get ahead of myself. The P of PAO are going to be key for speed. I now wish I’d grouped them by decade. 0-10 should have been generics, ie. Astronaut, Doctor, Baker, Butler, Soldier. 10-19 Sports figures, 20-29 Ex girlfriends, 30-39 Star Wars people, 40-49 Harry Potter folks, 50-59 old college professors, etc… This should increase speed in using it. And also make it easier to use 1-40 for Cards, with 4 suits, Clubs, Diamonds, Hearts, Spades (by alpha) all clubs are generics, Diamonds sports figures, ex girlfriends are Hearts, etc. To make it extra fast take care on your memory palace layout.
  5. So when I’m recalling cards now, it is sometimes faster to pull by location. So if you make sure your first 41 locations (remember there is a 00 that goes before 01 where the card deck starts at Ace of Clubs) are grouped with each decade (suit) in a common area. Like 1 big room or 2 rooms with 5. Don’t put 21-23 in the same room with 18-20. Keep the breaks clean, isolate the decades (1-10, 11-20, 21-30, 31-40) cleanly in their own areas. Speed is key on cards and helps with numbers.
  6. Dedicate this memory palace to your PAO. Never reuse it. That will keep it clear of interference.
  7. Be logical on the AO. If you have a P of a Juggler (06), and you are remembering Bill Gates (King of Diamonds) juggling Han Solo’s Blaster, then you quickly remember the ‘A’ is the Juggler 06 and the ‘O’ is Han Solo. Don’t do something weird and have Juggler flying spaceship and Han solo tunneling in minecraft. You will have to do extra cross-tabling recall if you abandon logical actions.

And with that I’m done. I wish someone had given me this advice a month ago.

-mt


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Improved Celeste ripening. Jujube’s has fruit set.

July 4th – All the figs are doing well but the Violette de Bordeaux which is barely growing. At last count, I have 5 fig trees in the front, 4 in the backyard, 2 in pots, and 2 at work.

The Honey Jar Jujube finally set fruit this year, it has been in ground 2 winters. The Shanx Li and the Chico did not set fruit although they bloomed.

Violette de Bordeaux has been a slow grower for 3 years, even with irrigation.

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Honey shed coming along

The shed keeps moving along.

Shed coming along

asdf

Ingenious use of string and weights (outside of shed) that pull up the form. It made it so I could lift up the form slowly without a 2nd persons help.

You can see the form I use to guide to build out the curve of the catalan arch roof.

I’ve also tried making Texas persimmon jam.

Texas Persimmon Jelly


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Modifications to my Downtube 9FS bike

So I got a Downtube 9FS in 2015, with the intent to modify it to a eBike with a Bafang BBS02 motor. Then take it on an epic tour through the Carribean islands.

A bike out to the festival and camped.

A bike out to the festival and camped.

The Downtube is a folding bike, permitting multi-modal travel. Take it on a bus, no problem, train, no problem, trunk of my wifes Honda Civic… tight fit, but no problem. So it has some big pluses. After I’ve put 2000 ebike miles on it, I understand its utility a lot better.

The bike

First, with the Bafang ebike motor, you get to use the gears. And the 9FS has 9 gears. Big plus as I live in a hilly area of Austin. I chose the 44T chainring model as I wanted more torque over speed.  Wow, does it climb hills,  up 20% grade hills at 9mph in bottom gear pulling only 16amps.

Second, I put on big apple tires, 2.15″ tires. Gives more cushion, steering feels less twitchy, but the big tires caused some derailour problems and I lose my lowest gear due to clearance to the tire. I’m thinking these maybe too big for the back wheel._1320029

_1320031Third, the battery is heavy, like 15# and now the bike is very back heavy and prone to accidental wheelies.  Part of that is I chose a handlebar throttle and not a thumb throttle. So I accidentally can throttle sometimes. And part of that is the handlebar throttle is not very linear. Turn it 1/2 way and nothing, 3/4 and you are at full throttle. Somewhere at 11/16th you start to feather into the throttle. Not a good throttle and I should get another, but I’m cheap.

Fourth, my pattern is using under 5 amp-hours for 95% of my trips. The bike normally can do 2.5 miles per amp-hour of battery. So 5 ah= 12.5 miles of range.  But I’m lugging either a 20ah battery or a 26 ah battery around when i should have a 5-8ah battery. Preferably one mounted in a bottle rack.  For instramentaion, I went with a WattsUp wattmeter to tell me how many amp-hourss I have left, because

The blue WattsUp meter will tell me how many amp-hours I've used. Not as good as a Cycle Analyst, but more appropriate and low profile.

The blue WattsUp meter will tell me how many amp-hours I’ve used. Not as good as a Cycle Analyst, but more appropriate and low profile.

the Bafang has no useful power readings.  Bear in mind the only measurement you really want to worry about is amp hours. You run outta those and you have to pedal home.

Sixth, speaking of racks, putting a rack on this bike was a pain to research what would work. I eventually went with a Biologic rear rack (https://www.amazon.com/gp/product/B006OSYSUA) and a Axiom Journey Lowrider rack

Biologic back rack

Biologic back rack

for the front fork (https://www.amazon.com/gp/product/B0081FQW4E)

Axiom front rack for suspension bikes.

Axiom front rack for suspension bikes.

Then I bought Axiom panniers for front and back.

Seventh, after all that I realized that most carribean islands I want to tour are so damn small I should just take a light folding bike with no motor. Even Aruba can be toured in a day. So I need to buy a Nova and put on a rack and I’m good to go.

 

Ultimately, I’ve discovered that this ebike excels at letting me ride around town, out of town, and all around, and then I can take other modes of transportation back. It is a keeper.


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Notes on Authorship lecture

I’ve uploaded the notes Fast Track to Writing Books.


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Green Pumpkin Wonderness for Holloween

Halloween fun!

The Green Ruby Pumpkin from miguel ortega on Vimeo.


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