Ebolavirus 2014: the r0 from shitposting is 6.9

The Something Awful Forums > Discussion > Debate & Discussion > Ebolavirus 2014: the r0 from shitposting is 6.9

Charlz Guybon: Nov 16, 2010

I assumed it was something like this but it's depressing to get it confirmed. There's at least another thousand dead out there.

Also, "May their souls rest in perfect peace" seems like the traditional phrase of choice in Liberia when talking of the dead.
http://news.sl/drwebsite/publish/article_200526287.shtml

quote:

Sierra Leone News : Over 1,000 of 2,000 Lab-Confirmed Ebola Cases are not Accounted For!
By Awareness Times
Sep 29, 2014, 12:14

An article in the internationally acclaimed NEW YORK TIMES newspaper has openly mocked the Government of Sierra Leone�s announced numbers concerning Ebola patients by quoting a Western diplomat who said of the numbers:-

�Even a 2-year-old child can look at them and see they don�t add up!�

The NYTIMES article which was published on September 25th 2014 reported thus:
The numbers for Sierra Leone come from the Ministry of Health, and diplomats and international health officials say they are largely inaccurate, substantially underplaying the gravity of the situation on the ground. �Even a 2-year-old child can look at them and see they don�t add up,� the Western diplomat here said.

Many other internationally credible articles had revealed of greater number of burials of Ebola patients than was announced. These articles sparked widespread debates on social media with strong accusations amongst citizens that the Government was being deliberately dishonest.

However, it is a fact that the Government had very honestly informed in a Published Statement as far back as 24th September 2014 that the STAY AT HOME campaign which took place from 19th to 21st September, had revealed, "The true picture portrays a situation that is worse than what was being reflected in reports".

Despite this, many questions continued to be posed around especially at Dr. Sylvia Blyden, the Special Executive Assistant to the President who regularly engages citizens on social media. In response to the numerous queries, Dr. Blyden past Saturday September 27th took time to write the following which instantly went viral as it, for the first time, comprehensively showed cause of under-estimates.

UPDATE BY DR. SYLVIA BLYDEN

Let me thank all who have posed observations and questions to me about the incomprehensible difference in totals of announced lab-confirmed cases versus number of survivors & number of deaths. You are all quite right that the difference is currently like one thousand and clearly, such a large number of over 1,000 Ebola patients, are not to be found in health centers around the country. You are quite correct! So, where are these compatriots?

The fact is that a few of these unaccounted-for numbers are currently admitted in Ebola centers but I can categorically state today that the vast majority of the [over] 1,000 patients are already DEAD and lying in their graves. Yes, they are dead and buried! Hundreds of them! :-( May their souls rest in peace.

As some have repeatedly stated for months now, the numbers we are being given from Health Ministry as official Ebola death figures are absolutely incorrect. Before going further, let me state that the initial appearance of the hitherto unknown Ebola disease was a strange situation for us to handle and as can be perfectly understood, we had a tough learning curve during which we, as a country, made a series of blunders. One such blunder is the reason behind the erroneous death figures.

Let me explain.

The erroneous death figures within the laboratory-confirmed category, are NOT caused by deliberate massaging but a flight of common sense; probably caused by the stress of what was unfolding on us. What am I saying here? Please read the following explanation carefully...

Now, most of the missing patients not currently accounted for, have resulted from a policy where sick patients blood samples are collected from them in their villages and towns and these samples taken to the lab in Kenema, Kailahun or Freetown for testing whilst the patients were left behind in their communities, waiting for their results. By the time, the results were available as confirmed positive and health officials prepared and went back to the villages/towns with ambulances to collect the patients, only a few were met still alive. Many of these patients (most of whom had been seriously ill), had already died in their communities and been buried. May their souls rest in perfect peace.

Now here comes the 'interesting' part.

Former Health Minister Miatta Kargbo and former World Health Organisation Representative Dr. Jacob Mufunda, had ordered that ONLY DEATHS INSIDE CLINICAL FACILITIES were to be recognised as "confirmed deaths" to be announced. So, all those laboratory positive patients who died in their towns and villages before they could be collected in ambulances for treatment at Ebola Centers, were never announced as deaths though already announced amongst number of laboratory positive cases. These unannounced deaths of our compatriots, ran up to HUNDREDS of deaths of laboratory confirmed cases! May their souls rest in perfect peace.

This, is the simple reason behind the incorrect (fake) death figures in the laboratory confirmed categories. Sierra Leone was not counting our compatriots who died outside of health facilities. May their souls rest in perfect peace.

This grave error that resulted in skewed death figures, was immediately picked up by the new Health Minister, Dr. Abubakarr Fofanah, on assuming office and, in a poignant presentation to the Presidential Task Force on Ebola which included all top international diplomats, opposition party leaders, SLMDA doctors and key civil society members, the Health Minister Dr. Abubakar Fofanah carefully explained what had been happening under the watch of his predecessor. You just need to read the U.S. Embassy's Facebook updates posted after that Presidential Task Force meeting. (Check Sept 8th and Sept 10th U.S. Embassy updates. They speak volumes).

So, based on analytic presentation of the new Health Minister, it is now a Government policy that the death figures being announced for laboratory confirmed cases, should be reviewed - eventually. The Health Minister has already informed the CDC and the WHO on this.

As you can well imagine, after impending review, the death rates, Case Fatality Rate (CFR) and other attendant aspects will be significantly changed and a better understanding of the serious gravity of what is unfolding in Sierra Leone, will be known by the whole world. Please brace yourselves. The news is not good. However, rest assured that working together, we can overcome Ebola.

In addition, the review will also ensure proper inclusion of all SUSPECTED and PROBABLE deaths as per World Health Organisation definitions. Keen observers might have noticed that it is only recently, in last one month, that an attempt has been made to include suspected and probable deaths in the death numbers being announced.

Fellow Citizens and Friends of Sierra Leone, let us continue to keep our beautiful country's Ebola crisis in the mainstream of the world's attention. We have a very, very serious situation on our hands.

We made a lot of mistakes in the early stages because we had a steep learning curve. However, we can no longer blame a steep learning curve for any more mistakes. Let us gear up against Ebola!

# ? Oct 2, 2014 02:02

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# ? Jun 7, 2024 11:43

Paul MaudDib: May 3, 2006; TEAM NVIDIA:
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My Imaginary GF posted:

Or, its a handful in that they have their hands full tracing contacts.

This is why I don't get how people expect that the US will be doing so much better at treating ebola than Africa.

Contact tracing is a fuckton of work, and it's going to be an absolutely overwhelming workload if there's a non-trivial outbreak - even for the CDC. And the US has a rather large population that is unable to access health care. And we probably have a fair bit more travel per person per day than Africa due to widespread vehicle ownership and so on.

The US could squash Ebola if our system was set up like that. But if it works its way into the working-class population, or undocumented immigrant community, the large areas of the country that are underdeveloped (eg the south), etc then things could get really ugly really quickly.

The poor aren't going to be able to miss work just for some sniffles, nor able to afford an ER visit that could easily pass tens of thousands of dollars. The undocumented have legal risks and are probably on the poor side of things to boot. And big parts of the South aren't really much more developed than the parts of Africa that are struggling so badly with lack of beds, health care workers, and general government capability.

Paul MaudDib fucked around with this message at 02:19 on Oct 2, 2014

# ? Oct 2, 2014 02:13

Kaal: May 22, 2002; through thousands of posts in D&D over a decade, I now believe I know what I'm talking about. if I post forcefully and confidently, I can convince others that is true. no one sees through my facade.

Epitope posted:

This kinds just sounds like your opinion, and doesn't seem to have much to do with the definition/usage of "endemic" by anyone else...

An endemic, human-transmissible disease that can't be treated will be transmitted to the entire population almost by definition. If it wasn't capable of sustaining itself in the face of medical support in that area, it wouldn't be endemic.

# ? Oct 2, 2014 02:13

My Imaginary GF: Jul 17, 2005; by R. Guyovich

Paul MaudDib posted:

This is why I don't get how people expect that the US will be doing so much better at treating ebola than Africa.

Contact tracing is a fuckton of work, and it's going to be an absolutely overwhelming workload if there's a non-trivial outbreak - even for the CDC. And the US has a rather large population that is unable to access health care. And we probably have a fair bit more travel per person per day than Africa due to widespread vehicle ownership and so on.

The US could squash Ebola if our system was set up like that. But if it works its way into the working-class population, or undocumented immigrant community, the large areas of the country that are underdeveloped (eg the south), etc then things could get really ugly really quickly.

Sounds like you've been involved with contact tracing, would you care to work us through your experience?

E:

Kaal posted:

An endemic, human-transmissible disease that can't be treated will be transmitted to the entire population almost by definition. If it wasn't capable of sustaining itself in the face of medical support in that area, it wouldn't be endemic.

I agree and see no currently-used or planned-to-use, and practical, means to effectively control the outbreak in West Africa. Anything done now will be done too little, too late, unless its done massively through an over-deployment of resources. Or, mobilizing the reserve medical corps and putting in place a national program to ensure safe and effective treatment systems with an incentive structure which encourages potential patients to use in a preventative manner.

My Imaginary GF fucked around with this message at 02:21 on Oct 2, 2014

# ? Oct 2, 2014 02:17

EXTREME INSERTION: Jun 4, 2011; by LadyAmbien

Phobophilia posted:

Several pages ago.

Jesus christ, the fact that someone can say this with a straight face. Lactic acidosis occurs below pH 7.35. That's not going to touch ebola virus at all.

Wait I thought virus docking to cells was messed up at lower pH

# ? Oct 2, 2014 02:28

Paul MaudDib: May 3, 2006; TEAM NVIDIA:
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My Imaginary GF posted:

Sounds like you've been involved with contact tracing, would you care to work us through your experience?

Not from the real-world side of epidemiology - I generally work from the modeling side of things. But if it's such an easy thing to do, then why can't these African countries handle it? Is Bumfuck, Alabama going to be able to do significantly better?

I mean, let's say there's a non-trivial outbreak in a region, numbering in the thousands of infectious individuals. Typical number of interpersonal contacts per day range from 8 on the low end (Germany) to 20 on the high end (Italy). So if you're tracing every contact since infection, and there's 5000 infectious individuals, then you're talking about tracing between 40k and 100k contacts per day.

What level do you think contact tracing is fundamentally scalable to? Can we trace up to 100k contacts per day? In the worst-case figure, that's 5k infected people. Can we do a million? That's a 50k individual caseload. At some point this is just going to be too much work even for the CDC. Let alone the state-level workers in Bumfuck, Alabama that this kind of work will get handed off to in the event of an actual epidemic.

e: And note that those are just high intensity contacts - if we're tracing everyone who ever got on a bus with someone who might have had ebola, the number gets much larger.

Paul MaudDib fucked around with this message at 02:32 on Oct 2, 2014

# ? Oct 2, 2014 02:28

SkySteak: Sep 9, 2010

Paul MaudDib posted:

-US & Ebola-

So what do you expect the most likely outcome for the US outbreak to in the long term? Do you expect the US getting close to a collapse or just areas being horribly gutted?

# ? Oct 2, 2014 02:28

Salt Fish: Sep 11, 2003; Cybernetic Crumb

Paul MaudDib posted:

This is why I don't get how people expect that the US will be doing so much better at treating ebola than Africa.

Contact tracing is a fuckton of work, and it's going to be an absolutely overwhelming workload if there's a non-trivial outbreak - even for the CDC. And the US has a rather large population that is unable to access health care. And we probably have a fair bit more travel per person per day than Africa due to widespread vehicle ownership and so on.

The US could squash Ebola if our system was set up like that. But if it works its way into the working-class population, or undocumented immigrant community, the large areas of the country that are underdeveloped (eg the south), etc then things could get really ugly really quickly.

The poor aren't going to be able to miss work just for some sniffles, nor able to afford an ER visit that could easily pass tens of thousands of dollars. The undocumented have legal risks and are probably on the poor side of things to boot. And big parts of the South aren't really much more developed than the parts of Africa that are struggling so badly with lack of beds, health care workers, and general government capability.

I think there is a huge [citation needed] for the US lacking the ability to track the geographic location and contacts of an extremely large number of people. Please keep in mind that objectively we know that the US already keeps a database of all your contacts via phone tracing and that we already have a system capable of tracking geographic location of citizens without their consent via cellphones. There is no nation more capable that the US for that task and we have already spent billions of dollars developing those systems over the past 20 years. If our NSA surveillance systems aren't useful for outbreak tracking then they aren't useful for anything.

# ? Oct 2, 2014 02:35

Charlz Guybon: Nov 16, 2010

Zeroisanumber posted:

Ebola isn't a disease with a natural human reservoir, people either die from it or survive and become immune to the strain. It will, eventually, burn itself out no matter what actions we take.

Not many corpses of Ebola victims for them to eat around these parts. Without a lot of exposure, it won't jump species.

Plenty of feral pigs to eat bodies in the streets or shallow graves in W. Africa.

# ? Oct 2, 2014 02:37

PupsOfWar: Dec 6, 2013

Salt Fish posted:

I think there is a huge [citation needed] for the US lacking the ability to track the geographic location and contacts of an extremely large number of people. Please keep in mind that objectively we know that the US already keeps a database of all your contacts via phone tracing and that we already have a system capable of tracking geographic location of citizens without their consent via cellphones. There is no nation more capable that the US for that task and we have already spent billions of dollars developing those systems over the past 20 years. If our NSA surveillance systems aren't useful for outbreak tracking then they aren't useful for anything.

there is a big difference between being able to track down all of somebody's willing associates and being able to track down all of the people who might have poo poo in the same gas station bathroom within the past few days

PupsOfWar fucked around with this message at 02:45 on Oct 2, 2014

# ? Oct 2, 2014 02:42

Paul MaudDib: May 3, 2006; TEAM NVIDIA:
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SkySteak posted:

So what do you expect the most likely outcome for the US outbreak to in the long term? Do you expect the US getting close to a collapse or just areas being horribly gutted?

I think it either goes one of two ways. Hopefully we keep it out, or the CDC really stomps down on it, and it never really takes hold. If we get to the "hundreds/thousands of infectious individuals" stage of things I think it looks bad at that point, and it's really anyone's guess at how far it goes in a scenario like that. I don't have confidence that a non-trivial outbreak can be stopped once it's going for the previously mentioned reasons. If it took hold in central or south america, that would also be pretty bad. "Endemic disease" scenarios would also not be much fun.

On the other hand I modeled influenza so I'm not an expert in ebola or anything. The US does have certain things going for it that don't necessarily apply in Africa, like the general availability of running water and a basic level of education. And I do tend to be a pessimist and a worrier.

It probably won't ever come to the level of "the US collapses" - the worst case is probably something like the Spanish Flu outbreak. A significant fraction of the world's population dies (3-5% in the Spanish Flu case, maybe like 20% in the worst-case nightmare scenario), economic activity and world trade poo poo the bed and we go into a big depression, but really nothing short of nuclear war is going to bring the US government down.

Paul MaudDib fucked around with this message at 02:47 on Oct 2, 2014

# ? Oct 2, 2014 02:42

RoboChrist 9000: Dec 14, 2006; Mater Dolorosa

So... as an American, what's my best choice for country to flee to in order to avoid the imminent viral apocalypse that apparently we're now sure the country is going to have because one, maybe more than one, guy got the virus.

# ? Oct 2, 2014 02:47

Ebola Roulette: Sep 13, 2010; No matter what you ~~win~~ ~~lose~~ ragepiss.

Phobophilia posted:

Several pages ago.

Jesus christ, the fact that someone can say this with a straight face. Lactic acidosis occurs below pH 7.35. That's not going to touch ebola virus at all.

Ha, wow that was bad wording on my part. Like I said, I'm not a doctor, nurse, or pharmacist, so I was speculating. I thought maybe lactic acid could inhibit the replication of Ebola, as it has been shown that lactic acid produced by bacteria can inhibit HIV replication.

http://www.ncbi.nlm.nih.gov/pubmed/20491589

But, they're two completely different viruses, and lactic acid produced by bacteria is not the same as the kind produced by humans. And I also assumed that blood ph low enough to cause a serious medical condition might also have an effect on the ability of a virus to enter a cell and replicate. At least, that was my probably faulty thought process.

# ? Oct 2, 2014 02:47

Jackson Taus: Oct 19, 2011

Jackson Taus posted:

I agree with you that the numbers are full of crap (though it could be just not finding bodies), however your Model doesn't include the lag between case report and death. Per WP, this is 7-16 days after symptoms, clustered heavily around 8-9 days. Your projected DR models assume folks die the week they are diagnosed, and that is not the case.

Hypothetical example with 50% DR where 60% of deaths are in the period after case report, and 40% are in the week following that (because they lasted longer, or because they were diagnosed on Day 6 and died on Day 15)

Week 1: 10 cases, no deaths.
Week 2: 20 new cases, 3 deaths (3 W1 folks)
Week 3: 30 new cases, 8 deaths (2 W1, 6 W2)
Week 4: 40 new cases, 13 deaths (4 W2, 9 W3)
Week 5: 50 new cases, 18 deaths (6 W3, 12 W4)
etc...

Jackson Taus posted:

I don't have SPSS, no. But I feel like this could be done in Excel if you had the info w/ daily granularity (which you do, apparently) and knew two pieces of info: (1) CFR, (2) how "fat" the tail of that 7-16 day spread is (I got that off WP and their source doesn't have the info ether). If you're running the model with multiple CFRs to see what it looks like, then all you really need is that spread, and you could model it in Excel just fine. I actually sort of suspect nobody has the precise data on the spread, but we could likely ballpark it and end up with a better model. Send me the XLS w/ dailies and I'll take a look at tossing a formula together. Note: I am not a doctor or mathematician or anything, just a bored developer.

I just realized there's an incorrect assumption in this post - I appear to have conflated "date case was reported" and "onset of symptoms". If we instead assume that cases are getting reported closer to Day 3 of symptoms, then the lag effect I'm describing would be smaller. The longer between symptoms onset and case-reported date, the smaller the lag effect would be.

Salt Fish posted:

I think there is a huge [citation needed] for the US lacking the ability to track the geographic location and contacts of an extremely large number of people. Please keep in mind that objectively we know that the US already keeps a database of all your contacts via phone tracing and that we already have a system capable of tracking geographic location of citizens without their consent via cellphones. There is no nation more capable that the US for that task and we have already spent billions of dollars developing those systems over the past 20 years. If our NSA surveillance systems aren't useful for outbreak tracking then they aren't useful for anything.

Even if we assume all of the location data is being collected and stored, you don't have nearly the granularity to determine contacts for this purpose - sure phone GPS can tell you that Person X and Person Y were at one point within 5-10 meters of each other, but if your criteria for a contact to track is "they came within 5-10 meters" then you've got a lot more contacts than you'd get with a different threshold. Plus you need to check the contacts for symptoms, and you can't do that with phone-tracking. Plus re-purposing massive database and software like the NSA doubtless uses is not a weekend hobby project, it's a gigantic endeavor taking months.

Jackson Taus fucked around with this message at 02:52 on Oct 2, 2014

# ? Oct 2, 2014 02:48

Salt Fish: Sep 11, 2003; Cybernetic Crumb

PupsOfWar posted:

there is a big difference between being able to track down all of somebody's willing associates and being able to track down all of the people who might have poo poo in the same gas station bathroom within the past few days

There is *A* difference, but it is irrelevant to my point which is: The United States has a cutting-edge technology system designed to track citizens geographically and has the means and computing power to store and correlate movements and associations of a significant proportion of its citizens. In this regard it is more prepared than any other nation in the world to handle the complexities of contact tracing. When we combine this knowledge with the apparent success of the Nigerian contact tracing program it is ridiculous to claim that it will be the most likely issue that would end up causing a large outbreak.

edit: its also important to understand that contact tracing doesn't need to track every single person who is in contact with an infected individual to be effective. The reality is that you only have to have enough contact tracing to bring the average number of secondary infections below 1. This is done in combination with other approaches such as education and awareness, availabilty of PPE, and health care access which all combine to reduce the average number of secondary cases.

I think that its easy to underestimate the utility of even a simple query such as "How many people live in the same household as the infected?" That is trivial for the government's tools to answer. How about another question like "Did a known contact violate voluntary confinement and leave their home?" Again, we know that the existing tools can answer that immediately with no changes needed. Imagine trying to obtain that information in a 3rd world country and you can see the advantages that the US has in containing an outbreak.

Salt Fish fucked around with this message at 03:05 on Oct 2, 2014

# ? Oct 2, 2014 02:49

My Imaginary GF: Jul 17, 2005; by R. Guyovich

Paul MaudDib posted:

I think it either goes one of two ways. Hopefully we keep it out, or the CDC really stomps down on it, and it never really takes hold. If we get to the "hundreds/thousands of infectious individuals" stage of things I think it looks bad at that point, and it's really anyone's guess at how far it goes in a scenario like that. I don't have confidence that a non-trivial outbreak can be stopped once it's going for the previously mentioned reasons. If it took hold in central or south america, that would also be pretty bad. "Endemic disease" scenarios would also not be much fun.

On the other hand I modeled influenza so I'm not an expert in ebola or anything. The US does have certain things going for it that don't necessarily apply in Africa, like the general availability of running water and a basic level of education. And I do tend to be a pessimist and a worrier.

It probably won't ever come to the level of "the US collapses" - the worst case is probably something like the Spanish Flu outbreak. A significant fraction of the world's population dies (3-5% in the Spanish Flu case, maybe like 20% in the worst-case nightmare scenario), economic activity and world trade poo poo the bed and we go into a big depression, but really nothing short of nuclear war is going to bring the US government down.

What datapoints would you need for modeling EVD in America using a modification of your influenza model, if its adaptable?

In other news,
http://mobile.reuters.com/article/idUSKCN0HP2F720141002?irpc=932

Appears there may have been potential for incidental contamination and contact.

E:

RoboChrist 9000 posted:

So... as an American, what's my best choice for country to flee to in order to avoid the imminent viral apocalypse that apparently we're now sure the country is going to have because one, maybe more than one, guy got the virus.

You'd need a country with limited points of entry, effective border security, a nation-wide surveillance system in place, and public healthcare. So, Israel?

My Imaginary GF fucked around with this message at 02:52 on Oct 2, 2014

# ? Oct 2, 2014 02:50

Charlz Guybon: Nov 16, 2010

Paul MaudDib posted:

This is why I don't get how people expect that the US will be doing so much better at treating ebola than Africa.

Contact tracing is a fuckton of work, and it's going to be an absolutely overwhelming workload if there's a non-trivial outbreak - even for the CDC. And the US has a rather large population that is unable to access health care. And we probably have a fair bit more travel per person per day than Africa due to widespread vehicle ownership and so on.

The US could squash Ebola if our system was set up like that. But if it works its way into the working-class population, or undocumented immigrant community, the large areas of the country that are underdeveloped (eg the south), etc then things could get really ugly really quickly.

The poor aren't going to be able to miss work just for some sniffles, nor able to afford an ER visit that could easily pass tens of thousands of dollars. The undocumented have legal risks and are probably on the poor side of things to boot. And big parts of the South aren't really much more developed than the parts of Africa that are struggling so badly with lack of beds, health care workers, and general government capability.

I was with you until this last part which is laughably untrue. Even Mississippi is a good fifty years more developed than almost any African country you can name.

# ? Oct 2, 2014 02:53

Goatse James Bond: Mar 28, 2010; If you see me posting please remind me that I have Charlie Work in the reports forum to do instead

My Imaginary GF posted:

You wouldn't have a copy of SPSS on hand, by chance? I'm thinking that there are now enough cases that one can apply CDC's methodology and numbers to determine likely week of fatality/what we should expect to see.

Can't you just use R?

# ? Oct 2, 2014 03:02

Charlz Guybon: Nov 16, 2010

Paul MaudDib posted:

e: And note that those are just high intensity contacts - if we're tracing everyone who ever got on a bus with someone who might have had ebola, the number gets much larger.

The U.S. managed to do this with Smallpox back in the day. If we could do it with Smallpox, we can do it with Ebola.

# ? Oct 2, 2014 03:04

My Imaginary GF: Jul 17, 2005; by R. Guyovich

GreyjoyBastard posted:

Can't you just use R?

How do you calculate R? How do you calculate k?

Simple answer is, not exactly, especially since the R0 and R adjusted values for EVD appear to fluctuate wildly.

E:

Charlz Guybon posted:

The U.S. managed to do this with Smallpox back in the day. If we could do it with Smallpox, we can do it with Ebola.

There were different system dynamics at work at the time.

# ? Oct 2, 2014 03:05

Goatse James Bond: Mar 28, 2010; If you see me posting please remind me that I have Charlie Work in the reports forum to do instead

Charlz Guybon posted:

Plenty of feral pigs to eat bodies in the streets or shallow graves in W. Africa.

My preferred danger scenario is the feral pig population in the US getting infected and a couple Appalachian towns periodically ceasing to exist because they can't be bothered to follow protocol.

Edit: MIGF, I was referring to the program. http://www.r-project.org/

It's clunky, but I've hardly ever ACTUALLY needed MATLAB in my work, I just use MATLAB for standardization with other folks.

# ? Oct 2, 2014 03:06

Xandu: Feb 19, 2006; It's hard to be humble when you're as great as I am.

My Imaginary GF posted:

How do you calculate R? How do you calculate k?

Simple answer is, not exactly, especially since the R0 and R adjusted values for EVD appear to fluctuate wildly.

E:

There were different system dynamics at work at the time.

http://www.r-project.org/

# ? Oct 2, 2014 03:06

ma i married a tuna: Apr 24, 2005; Numbers add up to nothing; Pillbug

Paul MaudDib posted:

The poor aren't going to be able to miss work just for some sniffles, nor able to afford an ER visit that could easily pass tens of thousands of dollars. The undocumented have legal risks and are probably on the poor side of things to boot. And big parts of the South aren't really much more developed than the parts of Africa that are struggling so badly with lack of beds, health care workers, and general government capability.

Let's not get carried away here. Yes, it appears that the first American ebola case was not handled ideally; but if people have become infected, that number is likely very low. R0 is not a very precise metric, and the numbers from West Africa have not been reliable - but in Liberia, where conditions were about as adverse as they can be, that number was 1.8 or so. It seems very unlikely that as many as 10 people will become infected from this incident.

And comparing Liberia and Sierra Leone to the South? Come on. Yes, parts of the South are underdeveloped, but they're a far cry from the poorest countries on earth with a history of recent civil war.

# ? Oct 2, 2014 03:07

Lote: Aug 5, 2001; Place your bets

Ebola Roulette posted:

Ha, wow that was bad wording on my part. Like I said, I'm not a doctor, nurse, or pharmacist, so I was speculating. I thought maybe lactic acid could inhibit the replication of Ebola, as it has been shown that lactic acid produced by bacteria can inhibit HIV replication.

http://www.ncbi.nlm.nih.gov/pubmed/20491589

But, they're two completely different viruses, and lactic acid produced by bacteria is not the same as the kind produced by humans. And I also assumed that blood ph low enough to cause a serious medical condition might also have an effect on the ability of a virus to enter a cell and replicate. At least, that was my probably faulty thought process.

The only problem is that a lactate level of >10-15 mmol/L is an "Oh poo poo!" value that probably has a similar mortality to Ebola if you measured that in the hospital. You probably get a better antiviral effect from the low pH and protein denaturization but few people can live below pH 7.

# ? Oct 2, 2014 03:07

Paul MaudDib: May 3, 2006; TEAM NVIDIA:
FORUM POLICE

zen death robot posted:

I think the real point is that the CDC can adequately track a case like what is occurring in Dallas, TX right now because it's involving a fairly small number of people. If the U.S. were to have a more widespread outbreak, then it could easily overwhelm our ability to trace contacts because of the population and how easily we travel when compared to West Africa.

Exactly. And not just tracing capacity - things like diagnostic lab capacity, hospital beds, and staff will eventually be overwhelmed too. The US has more of these things than rural Africa, but it's not unlimited, it's likely a single-digit multiple.

Charlz Guybon posted:

I was with you until this last part which is laughably untrue. Even Mississippi is a good fifty years more developed than almost any African country you can name.

That's 50 years, not 50 times. In practical terms, take something like hospital beds. Liberia has 0.8 beds per 100k population, the US has on average 2.9 beds. So we work out to 3.6x more capacity per-capita in that metric. We're some better, but not orders of magnitude better. And access to that capacity is probably very unevenly distributed, because of lack of universal care and uninsured and undocumented individuals and so on. Again probably like a poor African country.

# ? Oct 2, 2014 03:12

Ebola Roulette: Sep 13, 2010; No matter what you ~~win~~ ~~lose~~ ragepiss.

Charlz Guybon posted:

The U.S. managed to do this with Smallpox back in the day. If we could do it with Smallpox, we can do it with Ebola.

True. Although smallpox causes a specific rash, while Ebola doesn't have specific symptoms.

http://www.bt.cdc.gov/agent/smallpox/overview/disease-facts.asp

# ? Oct 2, 2014 03:15

My Imaginary GF: Jul 17, 2005; by R. Guyovich

GreyjoyBastard posted:

My preferred nightmare scenario is the feral pig population in the US getting infected and a couple Appalachian towns periodically ceasing to exist because they can't be bothered to follow protocol.

From a few pages back, I quoted a report from the man in charge of constructing 17 treatment centers in Monrovia. One of the issues that has popped up repeatedly is that the high costal water table has often allowed feral pig populations to dig up and consume ebola corpses. So, there could be a feral pig reservoir out there.

A video of Perry giving a press conference on the Dallas case:

http://www.youtube.com/watch?v=vuzguJw5AT8

Oh, and reports on Anderson Cooper tonight that the hospital didn't contact CDC, it was the index case's friend:

http://www.cnn.com/2014/10/01/health/ebola-us/index.html

"The close associate, who does not want to be identified because of the sensitivity of the case, contacted the CDC with concerns that the hospital wasn't moving quickly enough after Duncan's second hospital visit."

Explains the lag in decontaminating the ambulance. It appears we're looking at a series of serious fuckups and not just an isolated fuckup.

E:

Xandu posted:

http://www.r-project.org/

Er, how would you recommend I correct that statement for improved accuracy?

E2: Specific question, when does onset of inability to eat begin in cases of EVD?

My Imaginary GF fucked around with this message at 03:24 on Oct 2, 2014

# ? Oct 2, 2014 03:17

ma i married a tuna: Apr 24, 2005; Numbers add up to nothing; Pillbug

Paul MaudDib posted:

That's 50 years, not 50 times. In practical terms, take something like hospital beds. Liberia has 0.8 beds per 100k population, the US has on average 2.9 beds. So we work out to 3.6x more capacity per-capita in that metric. We're some better, but not orders of magnitude better. And access to that capacity is probably very unevenly distributed, because of lack of universal care and uninsured and undocumented individuals and so on. Again probably like a poor African country.

We're orders of magnitude better in terms of trained healthcare workers, though, as we are in terms of available supplies, logistics, etc. If the US Army had to set up a 1000 bed field hospital in rural Louisiana by Tuesday, they could. If 50 doctors caught EHF, it wouldn't mean half of the country's MDs were gone. The comparison makes no sense.

# ? Oct 2, 2014 03:19

Paul MaudDib: May 3, 2006; TEAM NVIDIA:
FORUM POLICE

My Imaginary GF posted:

What datapoints would you need for modeling EVD in America using a modification of your influenza model, if its adaptable?

Average viral shedding loads for each day of the infection for various scenarios of disease progression (patient recovers, patient dies etc), relative likelihood of each scenario (ideally based on factors like age, treatments, etc), basic reproduction number, specific intervention strategies including things like failure/non-compliance rates, available quantities of vaccines/drugs/beds, etc.

You could adapt the general approach, but the specifics probably look pretty different. Most influenza simulations don't include families having to dispose of infectious bodies themselves as a factor in disease spread. The compliance rates for intervention probably look a lot better when it's "stay home until you recover from the flu" instead of "go to an ebola ward and die". And so on.

Paul MaudDib fucked around with this message at 03:29 on Oct 2, 2014

# ? Oct 2, 2014 03:20

Lote: Aug 5, 2001; Place your bets

Paul MaudDib posted:

Exactly. And not just tracing capacity - things like diagnostic lab capacity, hospital beds, and staff will eventually be overwhelmed too. The US has more of these things than rural Africa, but it's not unlimited, it's likely a single-digit multiple.

That's 50 years, not 50 times. In practical terms, take something like hospital beds. Liberia has 0.8 beds per 100k population, the US has on average 2.9 beds. So we work out to 3.6x more capacity per-capita in that metric. We're some better, but not orders of magnitude better. And access to that capacity is probably very unevenly distributed, because of lack of universal care and uninsured and undocumented individuals and so on. Again probably like a poor African country.

I don't think that number is right for the USA. You're saying that a city of 5 million like the Dallas Fort Worth area has 150 beds. Presbyterian Hospital alone has over 800 beds. And Presbyterian is the 4th or 5th largest hospital in Dallas not including the city of Ft. Worth.

# ? Oct 2, 2014 03:21

ReidRansom: Oct 25, 2004

My Imaginary GF posted:

From a few pages back, I quoted a report from the man in charge of constructing 17 treatment centers in Monrovia. One of the issues that has popped up repeatedly is that the high costal water table has often allowed feral pig populations to dig up and consume ebola corpses. So, there could be a feral pig reservoir out there.

A video of Perry giving a press conference on the Dallas case:

http://www.youtube.com/watch?v=vuzguJw5AT8

Oh, and reports on Anderson Cooper tonight that the hospital didn't contact CDC, it was the index case's friend:

http://www.cnn.com/2014/10/01/health/ebola-us/index.html

"The close associate, who does not want to be identified because of the sensitivity of the case, contacted the CDC with concerns that the hospital wasn't moving quickly enough after Duncan's second hospital visit."

Explains the lag in decontaminating the ambulance. It appears we're looking at a series of serious fuckups and not just an isolated fuckup.

If I might try to put a positive spin on all that, at least all the fallout from this series of fuckups will help ensure that it doesn't happen again elsewhere. I'd hate to be the hospital that repeats these same mistakes and fails to take a patient so so many red flags as seriously as they should. Of course that doesn't mean it hasn't already happened somewhere else, but I suppose we'll know that within the next week or so.

# ? Oct 2, 2014 03:26

Charlz Guybon: Nov 16, 2010

Charlz Guybon posted:

I assumed it was something like this but it's depressing to get it confirmed. There's at least another thousand dead out there.

Also, "May their souls rest in perfect peace" seems like the traditional phrase of choice in Liberia when talking of the dead.
http://news.sl/drwebsite/publish/article_200526287.shtml

No response to this. I guess everyone just factored this into their calculations already?

# ? Oct 2, 2014 03:30

Jackson Taus: Oct 19, 2011

Lote posted:

I don't think that number is right for the USA. You're saying that a city of 5 million like the Dallas Fort Worth area has 150 beds. Presbyterian Hospital alone has over 800 beds. And Presbyterian is the 4th or 5th largest hospital in Dallas not including the city of Ft. Worth.

Yeah, but that's in a large city. A lot of folks live in suburbs or rural areas, which might have a different ratio.

Charlz Guybon posted:

No response to this. I guess everyone just factored this into their calculations already?

Yeah, immediately above your post were all talking about how the SL numbers were way-the-gently caress-understated and I think I mentioned it was probably "haven't found the bodies" as the cause for that. So it's not really a shock.

# ? Oct 2, 2014 03:31

Salt Fish: Sep 11, 2003; Cybernetic Crumb

Paul MaudDib posted:

Exactly. And not just tracing capacity - things like diagnostic lab capacity, hospital beds, and staff will eventually be overwhelmed too. The US has more of these things than rural Africa, but it's not unlimited, it's likely a single-digit multiple.

That's 50 years, not 50 times. In practical terms, take something like hospital beds. Liberia has 0.8 beds per 100k population, the US has on average 2.9 beds. So we work out to 3.6x more capacity per-capita in that metric. We're some better, but not orders of magnitude better. And access to that capacity is probably very unevenly distributed, because of lack of universal care and uninsured and undocumented individuals and so on. Again probably like a poor African country.

This strikes me as exceptionally bad logic. Yes, if you assume that an outbreak has an arbitrary size then any amount of resources is inadequate. There is not an arbitrary size of outbreak. There is a single primary case.

# ? Oct 2, 2014 03:33

Jackson Taus: Oct 19, 2011

Salt Fish posted:

This strikes me as exceptionally bad logic. Yes, if you assume that an outbreak has an arbitrary size then any amount of resources is inadequate. There is not an arbitrary size of outbreak. There is a single primary case.

It's sort of a tautology - if the disease becomes endemic we'll be unable to handle it, but then again, the disease only becomes endemic if we fail to handle it.

There's a vicious spiral in these outbreaks - as more folks get infected, hospitals become more dangerous, so people become less willing to go to hospitals, which just increases the infection rate. The difference between the US and Africa is that we're at the top of this spiral and our hospital capacity means the disease will have to get a lot more out of hand before folks start to be afraid of going to the hospital. Right now, if you're in the USA, you're symptomatic and there's a chance you have Ebola, the smart move is getting to the hospital as fast as you can, because that probably doubles your odds of survival. Right now in Sierra Leone, going to the hospital doesn't really improve your chances of survival much, and you're pretty likely to be exposed to Ebola if you go, so fleeing the hospital until you're literally puking blood is more or less the smart move.

Jackson Taus fucked around with this message at 03:58 on Oct 2, 2014

# ? Oct 2, 2014 03:35

Phobophilia: Apr 26, 2008; by Hand Knit

Ebola Roulette posted:

Ha, wow that was bad wording on my part. Like I said, I'm not a doctor, nurse, or pharmacist, so I was speculating. I thought maybe lactic acid could inhibit the replication of Ebola, as it has been shown that lactic acid produced by bacteria can inhibit HIV replication.

http://www.ncbi.nlm.nih.gov/pubmed/20491589

But, they're two completely different viruses, and lactic acid produced by bacteria is not the same as the kind produced by humans. And I also assumed that blood ph low enough to cause a serious medical condition might also have an effect on the ability of a virus to enter a cell and replicate. At least, that was my probably faulty thought process.

Lactic acid is lactic acid. Most life forms don't live very well in acidic environments. The point of that study is to study what inhibits mother-to-child transmission of HIV. One hypothesis would be that lactic acid inside the lumen of milk-secreting tissue is inhibits HIV. Even then, that paper doesn't show that the lactic acid produced by bacteria is what inhibits the virus.

It's like trying to cure yourself of an infection by injecting bleach into your veins. You'd be long dead before most of the pathogen is.

# ? Oct 2, 2014 03:37

My Imaginary GF: Jul 17, 2005; by R. Guyovich

Salt Fish posted:

This strikes me as exceptionally bad logic. Yes, if you assume that an outbreak has an arbitrary size then any amount of resources is inadequate. There is not an arbitrary size of outbreak. There is a single primary case.

That we know of, for now. There will be more cases. There may be more cases at a wide geographic dispersion who present concurrently or with a co-infection of another tropical disease. There may have been cases already who fell through the cracks. As Texas Presbytarian demonstrates, it happens. Not only did it happen at one hospital once, it happened to them twice.

# ? Oct 2, 2014 03:39

Ebola Roulette: Sep 13, 2010; No matter what you ~~win~~ ~~lose~~ ragepiss.

Phobophilia posted:

Lactic acid is lactic acid. Most life forms don't live very well in acidic environments. The point of that study is to study what inhibits mother-to-child transmission of HIV. One hypothesis would be that lactic acid inside the lumen of milk-secreting tissue is inhibits HIV. Even then, that paper doesn't show that the lactic acid produced by bacteria is what inhibits the virus.

It's like trying to cure yourself of an infection by injecting bleach into your veins. You'd be long dead before most of the pathogen is.

For sure. Lactic acid should not be looked at as a treatment. That was more of a vague possibility as to why HIV drugs helped patients with Ebola.

# ? Oct 2, 2014 03:41

Colin Mockery: Jun 24, 2007; Rawr

Jackson Taus posted:

Yeah, but that's in a large city. A lot of folks live in suburbs or rural areas, which might have a different ratio.

Actually, the US measures in hospital beds per thousand people.

0.8 per 100k versus 2.6 per 1000 means the original comparison was off by literally two orders of magnitude.

http://kff.org/other/state-indicator/beds/

# ? Oct 2, 2014 03:42

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# ? Jun 7, 2024 11:43

got any sevens: Feb 9, 2013; by Cyrano4747

RoboChrist 9000 posted:

So... as an American, what's my best choice for country to flee to in order to avoid the imminent viral apocalypse that apparently we're now sure the country is going to have because one, maybe more than one, guy got the virus.

Nowhere, everywhere's connected now. And if the virus is widespread enough it'll loop around a few times probably. Just act normally, you'll either live or die to it.

# ? Oct 2, 2014 03:44

The Something Awful Forums > Discussion > Debate & Discussion > Ebolavirus 2014: the r0 from shitposting is 6.9

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