outbreak! (ebola, sars, coronavirus, etc)

We are going to see about 300k dead of this by years end aren’t we?

seems very likely. hard to say what would intervene to prevent that.

I often struggle with statistics and probability. Could someone please explain PPV/positive predictive value to me? As in this:

Additionally, with antibody testing, the chance of getting a false-positive test result is high. In an area where very few people have had Covid-19, for example, a higher percentage of positive antibody results may be false-positives, according to the CDC.

“In a population where the prevalence is 5%, a test with 90% sensitivity and 95% specificity will yield a positive predictive value of 49%,” according to the CDC. (Sensitivity refers to a test’s ability to correctly generate a positive test, while specificity refers to a test’s ability to correctly generate a negative result.) “In other words, less than half of those testing positive will truly have antibodies.”

“A positive test result is more likely a false-positive result than a true positive result,” according to the Infectious Disease Society of America.

I don't get it. Is it saying that a certain (big?) number of positive results can be discounted just because ... they're statistically unlikely?

5% of the population has the antibody. The test has a false positive rate of 5% (that's what 95% specificity means). For simplicity, assume a false negative rate of 0% (i.e. assume sensitivity is 100%). It doesn't change the numbers very much and makes the argument easier to follow.

Suppose you test 100 people. On average there are 5 people among the 100 who has the antibodies. But you'll get 10 positive results. That's the 5 real cases (we assume our test catches everyone who has it) plus the 5 false positives.

In other words, given these numbers, a person who tests positive has a 50% chance of actually having the antibodies (5 people among the 10 who test positive actually have it). That's the "positive predictive value".

If you add in the fact that the test has false negatives too, you actually get a positive predictive value a bit below 50%, i.e. if you get a positive test, it's still more likely that you don't have the antibodies than you do.

The simplest way to think about this is: tests are most useful if the true prevalance of the antibodies (5% in this case) is greater than the false positive rate of the test (happens to be 5% too in this case). Otherwise a given positive test is more likely to be a false positive.

Of course if you take the test lots of times and keep getting positive, you can rule out false positives. And a person who has tested positive is *much* more likely to have the disease than a randomly chosen person who hasn't taken a test.

But the basic point is sound: antibody testing is of dubious utility as long as the antibodies are rare and the false positive rate is high.

Awesome break down imo

(FPR >> prevalance is one of the reasons we don't screen healthy young people for diseases of old age btw.)

Thank you! That helps a lot. A follow up: those numbers seem to hinge mathematically/scientifically on a survey of the broader, general population where the vast majority of people have likely not had or even been exposed to Covid. But if you just tested people who had or suspected they had Covid, a sort of self-selecting (if not statistically sound, scientifically speaking) pool, wouldn't the PPV be higher? Maybe it isn't useful in terms of applicable data that can then be extrapolated across populations, but it seems that it could be useful for that specific demographic. That is, you don't screen young people for diseases associated with old age, but if you limited screenings *exclusively* to old people, then would the PPV for Old Age Illness X be higher? Does it/can it work that way?

Or put another way, maybe, does this mean that generally speaking the more prevalent the illness, the higher the PPV, even if the specificity/sensitivity is relatively high?

For example, I was looking at strep throat numbers, because strep is so common in kids, and I think I saw that the rapid test is .... well, this is what I saw:

The clinical issue is that rapid strep tests have very high specificity – in the range of 98 percent to 99 percent – so there are very few false positives. However, the sensitivity of most current rapid strep tests ranges from 90 percent to 95 percent, so there is a greater chance of false negatives.

So in the case of the strep rapid test, it's hitting 98-99% specificity, which is good, but does't seem *that* much better than the 95% specificity of the Covid antibody test, and the sensitivity of both tests seem relatively similar (around 90%). Which may be why I'd heard that the Covid test, like strep, is more likely to yield false negatives than false positives, even if the false positive rate is still statistically something to be aware of.

Here we go: Texas reintroducing some restrictions on businesses. Bars close today, restaurant dining to 50% pic.twitter.com/y6Ok8kLPoE

— Christopher Hooks (@cd_hooks) June 26, 2020

Wow, they haven’t even closed bars yet, til now? This whole country is in denial

It's a step, but the resistance to a mask mandate is absurd.

Bars and restaurants had been closed, but were steadily reopening bit by bit since May

2020 headlines:

On Facebook, she denounced a Starbucks worker who asked her to wear a mask. It backfired — he got 32,000 dollars in tips.

"she" then started a gofundme for Turning Point USA, which got $96,500 as of last night.

not really, but that's how this fucking country works these days

i didn't know the medical center in houston that is almost full is billed as the largest in the world!

I'm so fucking upset about all this right now, 3 fucking months of staying inside and not doing shit all for nothing because our idiot leaders cannot do the bare fucking minimum, fuck FUCK!!!!!

PHOENIX — A drive-up testing site equipped for several hundred people in West Phoenix was swarmed on Saturday by about 1,000 people, leaving some baking in their cars for hours.

A nearby testing station has already reached capacity for this weekend, appointments vanishing within minutes. Hospitals are filling up. Restaurants are again shutting down, more than a month after Arizona reopened its economy under the mantra “Return Stronger.”

Arizona has emerged as an epicenter of the early summer coronavirus crisis as the outbreak has expanded, flaring across new parts of the country and, notably, infecting more young people.

Maricopa County, which includes Phoenix, is recording as many as 2,000 cases a day, “eclipsing the New York City boroughs even on their worst days,” warned a Wednesday brief by disease trackers at Children’s Hospital of Philadelphia, which observed, “Arizona has lost control of the epidemic.”

But physicians, public health experts, advocates and local officials say the crisis was predictable in Arizona, where local ordinances requiring masks were forbidden until Gov. Doug Ducey (R) reversed course last week. State leaders did not take the necessary precautions or model safe behavior, these observers maintain, even in the face of compelling evidence and repeated pleas from authoritative voices.

“We have failed on so many levels,” said Dana Marie Kennedy, the Arizona director of AARP, who said her organization has yet to receive a response to four letters outlining concerns to the governor. She is working on a fifth.

Neither the governor’s office nor the state health department responded to requests for comment.

At critical junctures, blunders by top officials undermined faith in the data purportedly driving decision-making, according to experts monitoring Arizona’s response. And when forbearance was most required, as the state began to reopen despite continued community transmission, an abrupt and uniform approach — without transparent benchmarks or latitude for stricken areas to hold back — led large parts of the public to believe the pandemic was over.

And now, Arizona is facing more per capita cases than recorded by any country in Europe or even by hard-hit Brazil. Among states with at least 20 people hospitalized for covid-19, the disease caused by the coronavirus, no state has seen its rate of hospitalizations increase more rapidly since Memorial Day.

How Arizona ‘lost control of the epidemic’

doesn't even need to mention that the president decided to hold a campaign rally with hitler youth in an indoor 3,000 church just a few days, even though all of the above was already exceedingly clear, and few of the hitler youth wore masks, in deference to the notoriously non-tacky and tasteful aesthetics and non-vanity of the president, and no one ever asked them to, either, at least not from the stage

they should be scared, they all deserve to fucking die

― time is running out to pitch in $5 (Karl Malone)

I just don't want this post to vanish under the fold without a resounding "KARL OTM"

heh, thanks sleeve

i immediately wanted to rescind it. i am a bad place, generally, and am going to cut myself off before i get really fucking annoying

self-care is revolutionary, man, practice it <3

No they deserve to die and I hope they burn in hell

http://www.activeresponsetraining.net/wp-content/uploads/2016/06/let-the-hate-flow-through-you2-768x498-620x402.jpg

i meant "i am in a bad place", but "i am a bad place" is better, and i request that you send all the dead assholes to my place when they're done here

get in my fucking lodge, republicans

caek do you teach medical students? in my experience our stats training was woeful and I had to basically self-teach what I didn't remember from undergrad

does this mean that generally speaking the more prevalent the illness, the higher the PPV, even if the specificity/sensitivity is relatively high?

yes

you can fill out this table with some simple round numbers and see how changing the prevalence, sens/spec, etc, one at a time changes the PPVs and NPVs

whoops https://www.medcalc.org/calc/diagnostic_test.php

So that would just have to shake out over time the more prevalent covid becomes, right? That is, the PPV is lower than 50% because it's not that widespread yet, so statistically, on paper, it's likely that a lot of those positives are false positives. But that's based on projection, right? It's also possible, if less statistically likely, that in practice all of those positives are in fact true positives?

FL has once again temporarily shutdown standalone bars, suspending alcohol service statewide (restaurants that serve food and alcohol can continue)

Meanwhile, Illinois continues to cautiously open up, encouraged by great numbers. The question in my mind is not will the states/places that half-assed it at best run into problems - duh - it's will the states/places that took things seriously and got good results be able to sustain those results as things open up again.

Florida supposedly had "good numbers" before re-opening, which is usually easy when you game the data like Desantis did/is doing.

speaking of,

"Florida is reporting 8,942 new covid-19 cases on Friday, blowing past its single-day high of 5,511 set on Wednesday. It is the 19th day in a row the state has hit a new average high. Average cases are now up about 77 percent from a week ago, and 526 percent since Memorial Day."

fuck.

Yeah, it's hard to hide that kind of data.

Rep. Mark Green, R-Tenn., is furious because, earlier today, he saw a jogger wearing a face mask. pic.twitter.com/OVyvP1v41k

— Alexander Nazaryan (@alexnazaryan) June 26, 2020

"Don't look back, you can never look back"

I've given up with Florida. we have a Governor who doesn't give a shit, we have a populace who doesn't give a shit.

you should maybe get out of there?

if I didn't have folks living here that might need me for emergencies, that ship woulda sailed a while ago.

course, all of my usual destinations are places that also aren't doing well with COVID, so it might be "midwestern state with 50 miles between houses"

will the states/places that took things seriously and got good results be able to sustain those results as things open up again.

I think the widely agreed answer among epidemiologists is 'no'. An increase in cases is unavoidable, along with an increase in hospitalizations and deaths. The opening up of businesses and small social gatherings is a solution to a different problem than "how do we keep the virus from spreading"; instead it is in answer to the profound social costs incurred by the indefinite extension of the shutdown, not just in terms of the economy and plummeting tax revenues, but also the massive mental stress on the whole population and the resulting social unrest and desperation that was emerging.

Some form of reopening was always bound to happen. What's most disheartening is that the time that should have been spent strengthening the public health infrastructure and preparing the nation to unify in the face of a dire necessity, was spent dithering, wallowing in incompetence, then sowing discord in search of political (and financial) gain. Now we just have chaos and confusion, and the people who are saying the right things about maintaining caution, distancing and wearing masks are drowned out or talked over by idiots and nonsense.

https://www.cnn.com/2020/06/26/politics/maskwearing-coronavirus-analysis/index.html

I've given up with Florida. we have a Governor who doesn't give a shit, we have a populace who doesn't give a shit.

― I hear that sometimes Satan wants to defund police (Neanderthal), Friday, June 26, 2020 10:37 AM (seventeen minutes ago) bookmarkflaglink

cmon over to arizona...

Also, come on, can we not to do the whole "just move" thing? It's rarely that easy.

not to mention moving from a place of high incidence to a place of low incidence is potentially a really good way to spread a disease

tbf it WOULD be easy for me compared to other people (if not for the aforementioned folks) in that I have an assload of savings, live alone, and a job that I can do in any state.

but yeah, I would definitely not do so unless I had a clean test first and self-quarantined for 14 days upon arrival.

truth be told though I'm thinking of moving into the ocean

No Covid in the ocean, afaict.

I agree that the "why don't you just move" schtick is always a lame reply but i would maybe suggest an exception for florida

there's also the "everybody I have ever known in my life sans about four people live in Florida" dilemma, but maybe we can all move and form a commune somewhere.

i should note that i lived in sarasota for nine months at one point, speaking from some experience

No Covid in the ocean, afaict.

― Josh in Chicago, Friday, June 26, 2020 2:08 PM (seven minutes ago)

very high mask use iirc

wait til the first person tries to fuck a whale

the arizona of the ocean

https://i.imgur.com/sHDCpfE.jpg

wtf are you all doing! where a mask! fuck