COVID19 - a quick look at the numbers as of April 27, 2020

It is day 40 in California as the lockdown was declared on March 19.

Where are we now?

Here is a screen capture of the death per 1 million over at Real Clear Politics.

The first screen grab is a partial list of nations. Italy was hit hard very early and then Spain followed. Since Belgium is a rather small country it hasn't made the news, but relative to population, it has been hit very hard. The USA number though terrible indicate it could have been much worse. There undoubtedly will be many studies as to why some countries got struck so severely while others fared better. From media reports, the sense is that Italy was the "perfect storm" of the high density of the cities in northern Italy, the age of the population, and the slow initial response. Whether this set of circumstances will account for some of the other hard hit countries remains to be seen.


Meanwhile, in the USA, the states in the northeast had death rates comparable to Italy/Spain/Belgium with New York exceeding the worst of Europe. There will be many studies and second guessing as to what resulted in the calamitous march of COVID19 in the northeast USA in particular New York and New York City. Most pundits have cited the high density of New York City and the large numbers of international passenger travel.


The fatality rate of COVID19 remains a moving target. The number often cited for flu is 0.1% of people who get the flu die from the flu. Thus, in the USA, a nation of about 330 million, if 30 million catch the flu during a typical season, 30,000 may die of it. If you look at the CDC estimates, from 2010-2017, the range was 12,000 to 51,000. Flu viruses are constantly mutating and some years it is more dangerous than others. Additionally, in some years the mixture of strains put into the flu vaccine design is more effective and sometimes less so.

But what is the fatality rate for COVID19?

We don't know.

According to John Hopkins COVID19 dashboard as of April 27, there were 3 million cases worldwide with about 211 thousand deaths. That is a 7% fatality rate. However, it is generally acknowledged that testing is not robust enough at this time to really get a fix on the fatality rate. What happens is that the tests are generally given to people who have some symptoms or are at risk (medical personnel). Thus, the figure is very likely to be overstated.

Also, likely to lower the fatality rate is the hypothesis that a certain percentage (currently unknown) of the population got COVID19 but they either had no symptoms or the symptoms were mild such that they never got tested. This could explain how the disease spread so rapidly as people unwittingly passed it onto others.

As a government official setting public health policy, the fatality rate estimate - really a guess back in March - drove the decision making. If you need to decide for Los Angeles County, a region with 10 million people, what do you do?

If you think 10% of the population is going to catch COVID19; then, 1 million people could get sick. If you think the fatality rate is 1% (10x worse than the flu), then 10,000 people will die. If you are working with numbers in this range, you are going to lock everything down and hope for the best.

But if your public health team thinks that only 4% will get COVID19 as this very small study shows (1). Thus, 400,000 gets COVID19. And what if the fatality rate in your projection is only 0.2%, worse than the flu but not astronomical? This scenario yields 800 dead. If you think these are the "facts" on the ground back in March, you probably don't go for a total lock down (2)?

As of this writing, the LA County reports 942 deaths attributed to COVID19. LA County death per day is declining so the number will go up but not dramatically so. Thus, perhaps COVID19 infection rate might be a bit higher than 4% and the fatality rate might be a bit higher than 0.2% yielding a situation that is akin to a bad flu. But the government officials didn't know this back in March when the orders to lock down were issued. How much worse it would have been if there was no lock down is unknowable.

But what about New York City, I don't think anyone imaged it was going to get that bad!

New York City is currently estimating death at 17,000. New York City population is about 8.4 million. What happened there? How do you get that many fatalities? The population infection rate must be much higher in NYC? Perhaps, for some reason the fatality rate is higher?

Some scenarios:
40% infection + 0.4% fatality = 13,440 deaths
30% infection + 0.6% fatality = 15,120 deaths
50% infection + 0.4% fatality = 16,800 deaths
60% infection + 0.3% fatality = 15,120 deaths

It will take many more months of investigating to piece together what happened in New York City and places where the COVID19 swept in with such deadly force.

Given the limited information at hand, if I had to guess the fatality rate of SARS-Cov2/COVID19 will turn out to be higher than the typical flu, perhaps around 0.3 to 0.6% (3), and what will turn out to be the driver of fatalities is a high infection rate due to unique features of the locality in question.

UPDATES:
Decided to add a few things after thinking more about what I posted last evening.
(1) Some scientists have called into question the antibody kit used in the study as not fully validated and await better characterized kits and larger numbers in the test population. Will better test kits reveal higher or low percent infection in the general population?
(2) The "what if" we don't know is what the infection rate would have been without the total lock down? In Los Angeles County, if the number rises to 8% infection with 0.2% fatality, then you have 1600 deaths. If you are on the board of supervisors and that is what your public health people tell you, what do you do? It all comes down to the "best guess" at the time about infection rates and fatality rates and how many people is it "tolerable" to lose to the virus. Scale the infection percent and fatality percent to higher numbers and the impetus to lock down becomes very strong.
(3) One could also suspect specific vulnerable populations will be looked at. The fatality rate might turn out to be quite "low" for the population as a whole. But what is the fatality rate when it hits a nursing home? Or an apartment building with a higher percentage of senior citizens? And there will definitely be studies on health disparities in poorer communities that may have a much higher fatality rate. Populations aren't homogeneous. There will be more to the data than just simple density of people in a community.

TBO = The Big One 3/3 Super Tuesday

There is not a lot of polling data out there according to Real Clear Politics.

What is the polling data saying?

California - Sanders is set to win, the question is whether anyone else will clear the 15% needed to snag some delegates. Biden needs to get over 15% and better yet 20%.

Texas - Sanders has a slim lead but it is within the margin of error and will be a key state to watch. Hence, Biden is getting Senator Amy and Mayor Pete to appear with him in a rally in Texas tonight. If this works, Biden gets the first down to keep the drive going.

North Carolina - Biden has a slim lead but it is within the margin of error and another key state to watch.

Virginia - the polling report at RCP is a bit out dated so it is hard to say what is going on there and another key state to watch

States Biden should win
  1. Alabama (52) - no polling data but a southern state where Biden should do well
  2. Arkansas (31) - no polling data but a southern state where Biden should do well
  3. Tennessee (64) - no polling data but a southern state where Biden should do well
States Sanders should win
  1. California (415) - polling data in favor of Sanders
  2. Colorado (67) - no polling data but Sanders won easily in 2016
  3. Maine (24) - no polling data but Sanders from nearby Vermont
  4. Massachusetts (91) - Warren's home state but will she beat out Sanders?
  5. Minnesota (75) - Klobuchar home state but will she beat out Sanders?
  6. Oklahoma (37) - no polling data but Sanders won easily in 2016
  7. Vermont (16) - no polling data but Sander's home state
  8. Utah (29) - no polling data but Sanders won easily in 2016
As you can see, there are six states where Sanders is likely to win and two where he will probably finish a strong second.

Unknown
  1. American Samoa (6) - Is it controlled by the Democratic establishment? If yes, Biden should win
  2. North Carolina (110) - close in the polls
  3. Texas (228) - close in the polls
  4. Virginia (99) - close in the polls
Biden will need to win these four to keep the race close. 

Bloomberg is a wild card. It would be terribly ironic if a multi-billionaire is the reason the Democrats win up with Sanders as the nominee an potential POTUS!


Round 4, South Carolina

Round 4 in the Democratic nomination battle.

In the first three rounds, the story has been Sanders.

By the numbers:

Iowa Caucus (the procedure adjusts for the voters second choice candidates)
Sanders won with 24.7% in the first round
But when adjusted for the caucus procedures Buttigieg got a slim delegate lead (13 vs. 12) because caucus takes into account voter's second choice candidates.

New Hampshire (straight up primary so one vote for one candidate)
Sanders won with 25.7% just beating out Buttigieg

Nevada Caucus (the procedure adjusts for the voters second choice candidates)
Sanders won with 34% and when adjusted for the caucus procedures he won easily (24 delegates to Biden’s 9).

South Carolina is up next and a primary state (straight up primary so one vote for one candidate)
Key questions: 
Will Biden win and by how much if he does? 
I think Biden needs a pretty large win to right the ship.
A +10% points would solidify his claim to be the comeback kid!
Clearing 40% would be even better
UPDATE: Biden cleared 40% with 48.4% and won by almost 30%

How many percent will Sanders get?
Sanders has a hard-core base of support that is around 25-30%. In 2016, he had his hard-core supporters AND the anybody but Clinton voter thus the reason for the hotly contested 2016 nomination race. Nevada was the first indication this season that maybe he is starting to break beyond his core voters. South Carolina will be another test. 
If his numbers drop back to Iowa and New Hampshire levels then he may really have a glass ceiling of support. 
UPDATE: Sanders came in at 19.9% the lowest of the first four races. IN states not known for left politics, Sanders appears to have a glass ceiling.

Will South Carolina voters decide it is a two-person race? 
If the third-place finisher is around 10% or less that means people are abandoning the lower tier candidates. Biden has the name ID and Sanders has the cash to compete widely in Super Tuesday. However, Buttigieg/Warren/Klobuchar are running out of money and won’t be able to run nation-wide in super Tuesday so they need to have a strong third and weaker than expected Biden/Sanders numbers in order to really remain viable. Steyer and Bloomberg are billionaires so they can stay as long as they want. But at some point they are businessmen and will eventually get out when they feel they have satisfied their egos enough.
UPDATE: Steyer came in at 11.3%, Buttigieg 8.2%, and Klobuchar 3.1% and all three have suspended their campaigns. 

Star Trek Short Treks and Picard

Saw all the live action Short Treks for season 2.

Very much enjoyed the Spock-Number One focused "Q&A."

Thought "The Trouble with Edward" was over the top. Don't mind playing some story lines for laughs but that was too much to take.

The Pike and Cadet test of character in "Ask Not" was wonderful in such a short package.

"Children of Mars" was a very moving story within the story of the Synth attack of Mars that is part of the backstory for Picard.

Will eventually get around to seeing the two animated ones.

Meanwhile, have seen episodes 1-2-3 of Picard.

Very different approach than Discovery. Discovery's non-stop action is in contrast to the slower paced Picard. It is true to Picard in his near the end of his days situation. He is not doing action hero stunts at his age! But his conviction to stand up and do something remains strong: the spirit is willing but the flesh is weak...

We have been treated to some short dream sequence bits with Brent Spiner's Data. Wonderful stuff.

Jonathan Del Arco appears as Hugh in episode 3 and will be seeing more of him in the episode ahead I'm sure!

Of the new cast members, too bad we probably won't be seeing much more of Picard's fiercely loyal Romulan winery-house-body guard staffers Laris and Zhaban. Really enjoyed them and their humor and drama.

Bit by bit, we have been introduced to Picard's new team. Jurati was first up as the expert on synthetic life forms. Musiker is Picard's estranged top aide from his days as an admiral. Loved the call back to Vasquez Rock. They even simply call the place by its real name! In episode 3, we meet the pilot Rios. Each character has been sketched out with their "issues" and strengths that will be filled out in the episodes to come. Thus, far they are well acted and will be interested to see how they develop in the remaining episodes.

Meanwhile, we have met the deliciously (perhaps a bit over the top) wicked bad guys: Narek, Rizzo, and Oh. You would think Star Fleet would be better at counter-intelligence! On the other hand, maybe the more things change the more they stay the same. Check out Malcolm Gladwell's podcast episode of how a Cuban spy operated in Washington DC for years! Rooting out the mole isn't always so easy.

And of course, at the center of the story is Dahj/Soji. It is unfolding out as a mystery: what is she looking for? are there more of her kind? why is it that both don't seem to know their true origins?

One plot nitpick: Jurati explains that Maddox had the idea that one could clone a neuron from Data's positronic brain to make the organic android Dahj/Soji and presumably others. However, I don't seem to recall that Data had any biological components? Cloning, in the sense we know it today, involves taking something biological (cells or DNA) and replicating it. I was under the impression that Data was entirely mechanical and wouldn't have any biological cells or DNA chromosomes to clone!

I suppose the closest thing to what Dahj/Soji are in other science fiction are the Blade Runner replicants. They were biological constructs and by implanting memories they can behave more human like and by genetic engineering they could have incredible physical strength.

LA Galaxy off season

The curtain fell on the LA Galaxy season in El Traffico VI. LAFC had been favored to win every match in the derby and finally broke through with a solid if messy 5-3 win.

Thus, LAFC march on in what is expected to be an MLS Cup. However, in the way is Seattle a past MLS Cup winner (2016) in the Western conference finals. If they win, they face the winner of the Eastern conference finals pitting Toronto (2017 MLS Cup winner) against Atlanta (2018 MLS Cup winner). All in all, the teams that have shown themselves to be top class the last few years.

LA Galaxy continue to retool after returning to the playoffs after missing the playoffs in 2017 and 2018. The defense really let them down on the semi-final match as it did many times during the season.

What is ahead for the front office?

DP decisions
1. Zlatan - He will be out of contract and rumors are for a return to Italy. However, the question is would Zlatan be willing to accept a smaller role on a contender or more playing time in a team less likely to to be a champion? He has expressed his displeasure at various aspects of MLS life (the referees, the lower quality supporting cast, the artificial turf at some venues, etc). On the other hand, he will get minutes on the LA Galaxy and the club provides him the kind of media exposure he clearly enjoys. Unless the front office has some other "big name" in mind to bring in as a DP, they will try to make a good faith offer to Zlatan and hope he declines so they can move on. 60:40 that Zlatan moves on.
News: Italy club interest might be less than expected. Rejoins AC Milan
2. JDS - He is still on contract and has been a key player and should continue to be central to plans for 2020.
News: JDS says he wants to finish his career with LAG
3. Alessandrini - He will be out of contract. However, he is a fan favorite, enjoys Los Angeles, and has contributed when healthy. Given his injury history, another DP contract is unlikely but some kind of deal could be made to keep him at a more modest salary level. 70:30 he stays on a reduced contract.
News: Out of contract, will he get a new deal? I think so at reduced salary

Defensive woes
4. Steres - Arguable the best value defender on the club. Good stats on a modest salary and a domestic player. The kind of player any MLS club would want to have around either as a starter or frequently rotated in player. 80:20 that he stays with a raise.
News: Out of contract, will he get a new deal? I think so at increased salary
News: He has a new contract.
5. Polenta - He was voted best defender of the year for the club but he has had some games where he was in the spotlight for what went wrong. Am guessing he is under contract and will be staying.
News: CoG MLS experts say Polenta might be a question mark about returning.
Option declined.
6. Feltscher - Had some good moments but not enough. He will probably be gone.
News: Option exercised.
7. Skjelvik - Had too many bad moments and saw minutes slashed over time. He will probably be gone.
News: Under contract! Unexpected that his original contract was 3-years. Perhaps, he will be traded to Europe.
8. Gonzalez - Am guessing he is under contract and will be staying. He has struggled in many games and maybe rated at this point as the poorest signing by the new front office. However, in fairness to him, he was played out of position on a number of occasions.
News: CoG MLS experts say Gonzales might be returning because his contract situation might be more secure than Polenta.
9.  Romney - A solid defender who can play multiple positions and a domestic player and won't break the salary bank. Romney has value on LAG as well as any other MLS club who need to have some domestic players to fill out the roster. The problem for Steres and Romney is that they are better at center-back than wide back positions. Wide back is a position of need for LAG with the likely departures of Feltscher and Skjelvik. Polenta and Gonzalez are center-backs and under contract thus making Steres and Romney as rotation players though Steres wound up starting quite a bit; thus, am thinking Romney moves on.
News: Romney to Nashville.  
10. Bingham - decent goalkeeper, not top of the line but solid

News: Under contract.

Latin American connections
10. Antuna - He had enough success that he will almost certainly be seeking greener pastures.
News: He is going to Chivas Guadalajara.
11. Favio Alvarez - Didn't have as much impact as Antuna so am figuring there might not be as much interest to draw him away from LAG. Probably will stay.
News: He was on loan and LAG may decline the option to renew. Option declined.
12. Pavon - He was a hit and will mostly likely get a DP level contract. Don't think he has done enough over a long enough period of time to draw big dollar interest from higher level leagues. A huge 2020 season could make his price go up and he will move on in 2021.
News: He is back at DP level as expected. 

The role players
13. Joe Corona - Probably under contract so should be staying.
News: Remains on contract.
14. Sebastian Lletget - Good to see him recovered from injury and have a good season. Don't know contract status but a solid non-DP level player with USMNT possibilities so LAG probably will want to keep around.
News: New contract with a raise.
15. Chris Pontius - solid veteran player for the bench and squad rotation but may want more playing time elsewhere.
News: Pontius has announced he will retire.
16. Perry Kitchen - Don't know contact status. Didn't get a lot of minutes due to injury. May want more playing time elsewhere.
News: Remains on contract.
17. Servando Carrasco - Good role player at a budget but at his age he might want to call it a career.
News: Option not exercised.
18, Matt Lampson - solid backup goalkeeper
News: Option not exercised.
19.  Justin Vom Steeg - solid young goalkeeper with possible future
News: Option exercised.

The youngsters
20. Julian Araujo - He is a wide back with lots of upside but not ready to be a routine starter at right back.
21. Efrain Alvarez - Mid-fielder with lots of upside but not not ready to be a routine starter.
22. Diedie Traore - Wide back back with lots of upside but not ready to be a routine starter at left back.
23. Emil Cuello - Mid-fielder with some upside but not not ready to be a routine bench player and occasional starter.
News: Option exercised.

Your best one-stop shop for the latest rumors and moves by LA Galaxy is Corner of the Galaxy Rumor Tracker.

The team sheet on the final match of the season (Conference semi-final against LAFC:
Bold face are players on the roster 
Italics are players in negotiation where it is anticipated they will return  
Regular typeface indicates that are gone for sure or very likely not returning 
  1. Ibrahimovic = out of contract, at AC Milan
  2. Pavon = re-signed at DP level
  3. Lletget = re-signed at TAM level
  4. Antuna = off to Chivas Guadalajara 
  5. dos Santos = remains on contract
  6. Kitchen = remains on contract
  7. Romney = traded to Nashville 
  8. Polenta = out of contract, option declined
  9. Steres = out of contract in negotiation new contract
  10. Gonzalez = remains on contract
  11. Bingham = remains on contract 
  12. Lampson = option declined
  13. Feltscher = option exercised
  14. Alessandrini = out of contract in negotiation
  15. Carrasco =  option declined
  16. Corona = remains on contract
  17. Alvarez = loan expired, option declined
  18. Pontius = retired
As you can see, of the final team sheet of 18 players, only 8 are back with 2 probably back if deals can be negotiated, and 8 not returning. It is going to be yet another rebuilding year for the LA Galaxy in 2020!

NEWS: Additions to the team
Sacha Kljestan - the 34 year old midfielder will add some depth to the squad 
Emilian Insua - 30 year old defender from Argentina recently playing in Germany
Aleksandar Katai - 28 year old Serbian midfielder recently at Chicago Fire




Short post on Short Treks Season 2

Enjoyed "Q & A" and "Ask Not."

Those two were delightful little character sketches that fit nicely into Star Trek lore. Will see if the fans are able to lobby for an Anson Mount, Rebecca Romijn, and Ethan Peck centered show. They have been wonderful.

I think Discovery might have been better served building around Sonequa Martin-Green, Doug Jones, and Michelle Yeoh. Instead, they wrote themselves into a corner with massive story arcs in the two seasons that were resolved in not entirely satisfying ways.

But back to the Short Treks, season two; though, I like the idea of a lighter touch and plots involving "origin stories," I thought "The Trouble with Edward" was over-the-top.

Monocle 3 install on Mac

Was attempting to install Monocle 3 onto a iMac.

Got stuck trying to install the leidenbase package.

Found a solution here at https://github.com/cole-trapnell-lab/leidenbase/issues/6

The program needs gfortran so went ahead and installed it from https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg

Was then able to proceed to the next step in the installation and am now trying out the various Monocle 3 tutorials!

COVID19 - a quick look at the numbers as of April 27, 2020

It is day 40 in California as the lockdown was declared on March 19. Where are we now? Here is a screen capture of the death per 1 milli...