libera/##covid-19/ Monday, 2020-08-24

de-factooh that should not happen :/00:00
de-factoLjL I guess the entries depend on what the companies producing those tests fill in the form here: https://www.finddx.org/wp-content/uploads/2020/07/FIND-SARS-Form_rev.pdf00:01
de-factoso its probably a good entry point for searching, yet verification would have to be done independently00:01
de-factobut yeah as you said there are https://www.finddx.org/covid-19/sarscov2-eval-molecular/ and https://www.finddx.org/covid-19/sarscov2-eval-immuno/00:02
de-factoso thats quite useful info there 00:03
LjLde-facto, that looks to be just for the long list, but check https://www.finddx.org/covid-19/sarscov2-eval-molecular/molecular-eval-results/ these are supposed to be from an independent evaluation. the immunoassays have a link that looks similar but in reality, for now, only covers about 5 of them00:03
LjLtoo bad because i'm more interested in the immunoassays, but well so that's a page to keep a keen eye on00:03
DocScrutinizer05Telegram                                                     │113599K│Aug 23 16:32  kills X11 by busy loop rendering 2 different wersions of GUI,  I _just_ rolled back to   *Telegram                                                     │113046K│Aug 15 14:41  hoping that will work00:03
DocScrutinizer05lucky me got btrfs on /home ;-)00:04
LjLde-facto, ↑00:08
BrainstormNew from https://covid19.specops.network *: ljl-covid: Add FindDx pages with a list of tests (all types), and preliminary ev… → https://is.gd/Kkfpmh00:10
de-factoLjL neat :)00:11
de-factoi really hope some cheap and quicktests become widely available, even if they are not so sensitive they could be a game changer if everyone could test anonymously at home on regular basis00:12
de-factoI mean right now people might be hesitant to get tests because of the "official" impact of the results (forced quarantine, possibly fines for illegal parties etc), but if tests would be commercially available to everyone and could be done anonymously people will probably do them much more often if cheap enough00:15
de-factoand i doubt there would be so many people who would not self isolate when they got a positive result00:16
de-factoi once did a test, had to wait or 31 hours in self isolation for the result, so if those could be reduced to 31 minutes it would be much more useful00:18
de-factojust imagine people could get a test prior to meetings in groups or events, if the tests are cheap enough and results quick enough they probably could exclude heavy viral shedding in a time window close to the moment the sample was taken00:20
de-factook thats speculation for now, but i think it would help a lot00:20
LjLde-facto, oh my, i've made 255 commits on the links page, next one will overflow00:23
de-factooverflow 8b? 00:25
LjLwell github is owned by microsoft now00:25
LjLthey'll assume 8 bit will be enough for everyone00:25
de-factoLOOOL00:28
BrainstormNew from r/Coronavirus: Coronavirus: One dead, 52 others test positive for coronavirus after Maine wedding → https://is.gd/PqQco000:49
LjL"around 50 people", seems like a recurring number of superspreading events01:05
LjLit was around 50 yesterday with the korea starbucks things where workers didn't get infected but most everyone else did01:05
LjLde-facto, it's only 4 so well, but when i look at https://www.finddx.org/covid-19/sarscov2-eval-immuno/immuno-eval-results/ my conclusion is that i can get either good sensitivity, or good specificity, but not really both01:07
LjLwhat happens, probabilistically speaking, if you take two tests, one with great sensitivity but crap specificity, and vice versa?01:08
BrainstormNew from r/Coronavirus: Coronavirus: New COVID-19 clusters reported at NC State fraternity and sorority → https://is.gd/2Snufq01:08
LjLi can answer to myself "a quagmire" but that's not very precise01:08
LjLalso i have a headache now because something in my DVB-T decoder blew up and the smell is still inside my head, ugh :(01:09
ryoumawhy not run 2 tests like that?  presumably because sensitivity without specificity is useles and vice-versa.  you know you are positive for something but not what.  or you got a result for what you are looking for but you don't know if it is trustworthy.  i think the keyword is receiver operating characteristics curve.  or similar.  to maximize both.01:15
ryoumanote: i speak from a position of great ignorance, so you should trust me01:16
ryoumai suppose there is some tiny value in each knowledge and perhaps that is what you are asking01:17
BrainstormNew from BMJ Open: Clinician and patient beliefs about diagnostic imaging for low back pain: a systematic qualitative evidence synthesis: Objective Overuse of diagnostic imaging for patients with low back pain remains common. The underlying beliefs about diagnostic imaging that could drive overuse remain unclear. We synthesised qualitative research [... want %more?] → https://is.gd/WOIspb01:18
de-factoLjL, i am not sure, i mean if specificity is crap the whole prediction is unuseable at some point, if sensitivity is not so good it might actually not be that tragic because if such tests rather would be used to predict infectiousness than status of being infected it would already help a lot mitigating the spread if done on regular basis providing quick results01:18
ryoumahmm01:19
de-factoi mean if a sens- spec+ test would be positive you know you REALLY are positive for that specific pathogen01:20
de-factobut if a sens+ spec- test would be positive you know you got something... not so helpful01:21
de-factowell maybe helpful to do a more sophisticated test01:22
de-factoif a sens- spec+ test would be negative it does not tell much about the status of being infected, but it probably would have been positive if there was high viral load (hence high infectiousness), hence might indicate current low viral shedding01:24
ryoumayeah it could guide further testing.  for example one could be fast or cheap.01:24
de-factoif a sens+ spec- test would be negative probably the same01:25
de-factofast + cheap could be a good indicator for current (time local) status of viral shedding (infectiousness) hence a good guide for behavior in a time window close to the sample being taken01:26
de-factoif its positive additional tests/isolation/treatment must be initiated anyhow01:27
de-factoit could catch asymptomatic cases though if a quicktest is cheap enough to do it on regular basis01:27
BrainstormNew from CNBC Health: Trump administration grants emergency authorization for coronavirus plasma treatment: President Donald Trump on Sunday will announce the emergency authorization of convalescent plasma for Covid-19, according to the Washington Post and other reports. → https://is.gd/Cqymxe01:27
BrainstormNew from Ars Technica: Policy: FDA gives blood plasma emergency use authorization for COVID-19 treatment → https://is.gd/usDFdq01:37
DocScrutinizer05anybody using linux telegram client who seen an update during last 48h?02:02
de-factoDocScrutinizer05, do you know why the number of rows in the csv from arcgis.com are less than the current cases for Germany on worldometers?02:20
de-facto187606 rows yet worldometers shows 234399 cases02:21
de-facto%cases Germany02:21
BrainstormUpdates for World: +101508 cases (now 23.7 million), +1924 deaths (now 813258) since 7 hours ago — India: +24702 cases (now 3.1 million), +429 deaths (now 57692) since 7 hours ago — US: +20270 cases (now 5.9 million), +229 deaths (now 180604) since 7 hours ago — Brazil: +16314 cases (now 3.6 million), +303 deaths (now 114772) since 7 hours ago02:21
Brainstormde-facto: In Germany, there have been 234489 confirmed cases (0.3% of the population) and 9332 deaths (4.0% of cases) as of 2 minutes ago. 10.2 million tests were performed (2.3% positive). Fatality can be broadly expected to lie between 0.5% (assuming prevalence as in tests) and less than 4.3% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Germany for time series data.02:21
de-factoyeah02:21
de-factohmm the sum of cases is 232859 so i guess that explains it02:28
de-factoone day behind or such then02:28
LjLde-facto, you have a point (well, several), it depends on what you're using them for, and there's probably one case that's more useful that the others02:31
de-factoi think cheap, quick, anonymous and widely available tests could make a big difference, every country should have a program to implement them into their strategies02:34
de-factounfortunately the lab pcr tests got a lobby already, they make a shitload of money with them02:34
LjL:\02:34
de-factoso the "experts" may be against those cheap quicktests not out of purely scientific reasons02:34
LjLde-facto, "cheap quick" got used a lot a while ago... at an inappropriate time, in inappropriate ways02:34
LjLyou can bet that now that it's the right time and they could be used in useful ways, they won't02:35
de-factowell obviously many countries need to change their containment strategy, so instead of lockdown it would be much better for them to try such tests imho02:35
LjLlockdown worked pretty well though... while it worked. of course you stop the lockdown, it stops working02:36
LjLi understand the economy is a small issue02:36
LjLbut the strategy clearly has functional merit02:37
de-factoyes but would not be much better if it could be taken under control with such tests rather than with the hammer of a full blown lockdown?02:38
de-factoimho it really would be worth a try (and probably also much less costy in terms of economic losses etc)02:39
LjLde-facto, yes, but one strategy has shown it works, the other has yet to. i think the problem here is... we stayed under lockdown to get it under control, then the story was, now we'll do immediate tests as soon as there is an issue etc02:39
LjLbut instead they didn't, we're going on like before, it's all slow and sucky02:39
LjLa lockdown should have been exactly the time to develop "quick tests" and other smart strategies *and* assess how good they worked02:40
LjLbut instead now i'd honestly rather have another lockdown than try things left and right while cases are ramping up02:40
LjLi may be speaking from a vantage point in that honestly unless the sky falls my economic problems will be limited. but everyone is speaking based on their biases, and i think in comparison to things i read, mine are pretty mild :P02:41
de-factoits not that easy, people go demonstrating against (non existent) containment already, businesses may not be able to stand a second lockdown and in general obviously participation in containment efforts seems to be with much less rigor already, hence i think lockdown really could be problematic a second time now02:42
de-factoyet even if someone does not take containment that seriously while healthy, if presented with a positive result most of those probably would go into isolation and stay away from other people02:43
LjLde-facto, but it seems there's a lot of people who are unwell, or have other reasons to suspece they have it, but dodge getting tested02:43
de-factoif people understand its in their very own hands (e.g. with such tests) and even anonymously possible for them to test themselves on a regular basis without having to invest too much money it really could make a difference02:44
BrainstormNew from r/WorldNews: worldnews: Rio Tinto executives stripped of bonuses over ancient rock shelters' destruction: A review of the loss of the ancient rock shelters has concluded it was the result of flaws in systems, data sharing, engagement with Indigenous people and poor decision-making. → https://is.gd/h8cJyk02:44
de-factoi mean if such a test would cost 1 euro or such, testing every day would be less costs than a month of rent for most people in europe02:44
de-factoyes exactly and those people who now dont get a test (afraid of consequences, too expensive, too complicated whatever) just would be able to anonymously buy a test in the supermarket and test at home (just as with those pregnancy tests)02:46
de-factothat probably even would catch asymptomatic cases, hence prevent probably the majority of infectious people now walking on the street without even having a clue they are infectious02:47
LjLde-facto, it's not abotu the cost of testing, testing is usually free in these cases02:47
LjLit's more bad bureaucracy02:47
LjLif you get tested, the result can take a long time to come (yes - a good reason for quick tests)02:47
LjLbut meanwhile, it means they have to self-isolate until the results come, and they don't get paid etc02:48
de-factoCDC estimated 40% of cases may be asymptomatic or such, those right now would never get a test unless asked to do so (e.g. by tracing or returning from holidays or such)02:48
LjLand if they turn out positive, i think as long as they're asymptomatic, they are not paid sick leave either02:48
LjLbut they still must stay at home02:48
de-factoso just testing on daily basis without symptoms would catch those02:48
de-factoyes, now imagine the result in minutes rather than days02:48
de-factoit would make big difference imho02:48
LjLde-facto, someone on r/covid19 was like "we have solid evidence that the asymptomatic cases don't spread easily"02:49
LjLwhich... i had the opposite impression about02:49
de-factogoing to visit your parents tomorrow? just stop by the supermarket get a cheap quicktest and have the result if you are infectious in minutes, if cheap enough even right before you meet them the next day again02:49
LjLbut just like people on r/covid19 can say these things, so can "expert" doctors02:50
LjLwho say this one day, and that the next02:50
de-factoLjL that is not true, we have solid evidence that asymptomatic cases spread with similar viral load than symptomatic02:50
LjLde-facto, if the result says that you're infectious and that means you have to stay home from work and you don't get paid, color yourself surprised, but people will often prefer to be infectious without anybody knowing02:50
LjLde-facto, that's what i thought, but that's the problem with people who make bold statements like that... it's a lot of work to go back and figure out where all the evidence i've seen about that comes from02:51
LjLi think in this channel we've formed a roughly uniform understanding of some things02:51
de-facto%title https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/276923502:51
LjLwhen someone says something that's outright idiotic we either make a collective effort to provide evidence to the contrary, or just ban them02:51
Brainstormde-facto: From jamanetwork.com: Clinical Course and Molecular Viral Shedding Among Asymptomatic and Symptomatic Patients With SARS-CoV-2 Infection in a Community Treatment Center in the Republic of Korea | Infectious Diseases | JAMA [...]02:51
de-factohttps://jamanetwork.com/journals/intemed/articlepdf/2769235/jamainternal_lee_2020_oi_200057.pdf02:51
LjLde-facto, thanks, i'll paste that over there, *if* i find the relevant post again :P02:52
LjLwhich is the reason why i didn't just link to the post02:52
LjLoh, something about italy02:53
LjLsomeone said "If the current exponent holds we could be looking at around 7k new cases per day two weeks from now. They may say now that they rule out a new lockdown but they will change their tune very quickly when those kinds of numbers come in."02:53
LjLnamely https://www.reddit.com/r/Coronavirus/comments/if57pz/italy_rules_out_new_lockdown_as_coronavirus_cases/g2lraq5/02:53
LjLany idea if that's true? my maths are bad02:53
de-factowell not getting an official test (for whatever reasons) or hiding the own test result are equally bad, yet people might be more careful and even go for a more quality test if their cheap test is positive, so already for those (asymptomatic) ones it would be a gain there then02:53
LjLtinwhiskers, maybe you could do something of the "how many cases will we have in a week" sort? although i realize it's probably similar to the doubling rate02:54
LjLde-facto, what i'm saying is that there needs to be less bureaucratic burden on people who get a test, including positive ones02:54
LjLthey need to be financially protected02:54
LjLno matter the kind of test02:54
de-factoafaik easiest calculation would be like N(t) = N(0) R^(t/tau) with a serial time tau = 5 days or such (N(0) being the reference number of cases where the clock starts to tick)02:56
LjLbut you need to know R? i think this person was basing it off the number of cases in the past few days02:58
de-factoso given current R and N(0) for Italy you could extrapolate with an exponent of R like 14d/5d = 2,8 or such?02:58
LjLi could get R from tinwhiskers's calculation but i'm not sure i understand how to do this. he was probably more like fitting an exponential curve to those past 5 or so days of growth03:00
LjLby the way03:00
LjLit doesn't help i don't understand maths, again03:00
LjLbut i feeeeel there has to be some decent way to estimate "real" cases or at least to "normalize" them so that they are comparable with the past and/or with other countries03:01
LjLby taking into account both the absolute number of new cases, and the ratio of new cases / new tests03:01
LjLbut i can't quite pin it down03:01
LjLcases/tests keeps growing in italy these days03:01
de-factooh btw i think they calculate the R with two rolling windows delayed by one serial time, and afaik they use 4 days for that03:01
LjLbut i don't think that is representative of real case growth, either03:01
de-factoso maybe 4days is more appropriate than 5days?03:01
LjLit has to be some combination of absolute case count, and relative to tests...03:02
LjLde-facto, "they" being?03:02
de-factoRKI in Germany for example03:02
LjLah03:02
de-factoas far as i know, if they did not change that03:02
LjLwell i don't know the R for italy, they don't really tell us this parameter as calculated by the government03:02
LjLi only have the R that tinwhiskers calculates03:02
LjLwhich is kinda quickly variable03:03
de-factoyes he uses the same method03:03
LjLah03:03
LjLgod look at this https://offloop.net/covid19/?default=Italy&cumulative=no&smooth=yes03:03
LjLi don't get it though03:04
BrainstormNew from r/WorldNews: worldnews: Canadians with U.S. licence plates plead for understanding during COVID-19, want other Canadians to stop vandalizing their cars → https://is.gd/MsxMkq03:04
LjLthey recently said that in the UK, the R has just gone >1 since the last wave03:04
LjLso since april or so03:04
de-factothe calculation can be smoothed by widening the two rolling windows, e.g. if you divide the sum of weekly cases delayed by one serial time of 4 days you get much smoother results03:04
LjLit was below 1 according to them03:04
LjLbut italy, with much fewer cases (until a week ago or so), often shows R>1 in tinwhiskers's site03:04
LjLlike... in june, july, already03:05
LjLit was only below 1 in part of april, and may03:05
DocScrutinizer05de-facto: the format reports multiple cases per row03:06
de-factoso lets assume R=1.38, 1.38^(14/4) = 3.0803:06
de-factoso around 3k cases in two weeks03:06
de-factowith current N(0) = 1071, R=1.38, it would be N(14) = N(0) R ^(t/tau) = 1071 * 1.38^(14/4) = 3306.4803:08
de-factoright?03:08
DocScrutinizer05sounds about right03:09
LjLi have no idea if it is right :(03:09
LjLbut anyway that would mean i should expect about +3000 per day in 14 days from now?03:10
LjLde-facto, mind if i kinda just copypaste this in response to the person on reddit?03:10
de-factoso if they assume 7k cases in two weeks it would be 1071* 1.71^(14/4) = 7002 hence their R=1.7103:11
de-factothat all only holds for serial time tau=4days though03:11
LjLde-facto, however if you look at the R on offloop, the R for today is quite a bit higher than for yesterday, and so on. there is no way there to change the "smoothness" of the R. so it's reasonable to presume 1.38 won't be the sustained R...?03:12
LjLthe R just ramps up a lot within the past 4-5 days03:13
LjLwell, 403:13
de-factoand btw that all is assuming that R will not change, yet there is a feedback loop, people are aware of their current situation and may be more careful or government implementing more measures, hence i doubt it would stay at R=1.7 for long times03:13
BrainstormNew from r/Coronavirus: Coronavirus: Iowa confirms state's first child death from COVID-19 → https://is.gd/SyarKE03:13
LjLde-facto, "4 days" makes some sense to look at because it's the amount of time when you can see the new cases just go up, clearly03:13
LjLde-facto, i don't know about being more careful, people have "carefulness fatigue" at this point (you even mentioned this), and the government it actually going "Italy Rules Out New Lockdown as Coronavirus Cases Rise" which is the title of the thread this is in ;(03:14
LjLis* actually03:14
de-factothe serial time is the duration between two consecutive cases in an average infection chain, hence it takes on average 4 days from one virus carrier to infect someone else03:15
LjLwhat the government has been doing is ordering testing of people coming back from airports03:15
LjLbut then it's the regions that must implement that, as usual03:15
LjLwhich means that Fiumicino (Rome) has had it for a few days03:15
LjLbut Malepensa, Linate, Orio (Milan, tons of traffic) have only *barely* started having it today03:15
de-factoactually i think i read somewhere something more like 5.2 days but not sure anymore03:16
LjLde-facto, yes, i remember that number03:16
de-factoits not the same as incubation time though03:16
LjLno it was the time to peak shedding03:16
LjLde-facto, but it may have changed because the mean age of the patients has changed a lot03:16
de-factoand thats also something in that region of duration03:16
LjLso the behavior of the disease may also have03:16
de-factoyes its all in constant temporal flux03:17
LjLitaly had around 60 years of age mean, in the first wave03:17
LjLbut now it's 3503:17
de-factonothing static at all about this dynamic03:17
de-factojust some things change more slowly than others03:17
LjLgod i don't want to go back to milan and find it more of a nightmare than when i left :(03:17
LjLwith still no idea where even to get "real" FFP2/equivalent masks03:18
LjLde-facto, https://www.reddit.com/r/Coronavirus/comments/if57pz/italy_rules_out_new_lockdown_as_coronavirus_cases/g2n9v54/03:18
de-factoyeah the young people are careless hence CFR goes down while cases rise03:18
de-factoi just ordered 10 FFP3 masks each for 7.7 Euro, just to have them in case03:19
LjLde-facto, but this is only while the young people spend the summer among themselves, abroad or whatever. now they're going back home, and they will meet their older parents. so...03:19
LjLde-facto, i am okay with paying that amount, at least for some of them03:19
LjLdid you buy them locally?03:20
de-factohaha heh i hope we did calculate that one right then :P03:21
de-factoI guess it should be correct though03:21
LjLwell no shame in being wrong, i'm just asking him how he did it instead03:21
de-factoyeah its good to discuss with equations rather than just wildly throwing naked numbers around03:22
LjLde-facto, bah, i found the post about asymptomatic supposedly not being very infectious, it's this one https://www.reddit.com/r/COVID19/comments/if2oci/sociopathic_traits_linked_to_noncompliance_with/g2l8d1h/ but the post has been locked because r/covid19 is excessively rigid03:25
LjLanyway he is providing a coupld of studies for his thesis now03:25
LjLhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219423/  https://www.acpjournals.org/doi/10.7326/M20-26703:25
LjLlet's see03:25
de-factohttps://en.wikipedia.org/wiki/Basic_reproduction_number#Simple_model03:25
LjLuh the first is on a study of 455 potentially infected people from *one* asymptomatic case03:26
LjLdoesn't sound very meaningful03:26
LjLbut i'm a bit confused on what they're actually saying03:27
de-factosecond is 40403:27
LjLthe second is a file not found ;(03:27
LjLgah03:27
DocScrutinizer05I think the 4d series length has been established some time into first wave by RKI (at least here in Germany) and won't change for the statistiks since that would mean the R is not comparable anymore03:32
LjLmakes sense, i guess. maybe not the "scientifically correct" R but something that can be used statistically03:33
DocScrutinizer05yep03:33
de-factogood point03:36
de-factoso i guess it would be the fast R = (N(t-0) + N(t-1) + N(t-2) + N(t-3)) / (N(t-4) + N(t-5) + N(t-6) + N(t-7))03:38
ryoumai don'03:39
ryoumat get all this math,with all the variables that are too variable and some suspect and all different rules in different countries and so on03:40
LjLso R can be estimated as basically the ratio between "new cases in this time slot" vs "new cases in the previous time slot", except it doesn't make sense to just do it for one day?03:40
ryoumadifferent reporting rates too03:40
LjLit is indeed a mess, ryouma 03:40
de-factoand also the slow/smoothed R = (N(t-0) + N(t-1) + N(t-2) + N(t-3) + N(t-4) + N(t-5) + N(t-6)) / (N(t-4) + N(t-5) + N(t-6) + N(t-7) + N(t-8) + N(t-9) + N(t-10))03:40
LjLthis all doesn't consider the fact that italy has ramped up testing03:40
LjLso part of it is there being more cases03:41
LjL(because even when you account for testing, it's more)03:41
LjLbut part of it is also more testing03:41
ryoumawhy are you dividing by previous differences instead of all03:41
LjL"all"?03:42
BrainstormNew from r/Coronavirus: Coronavirus: F.D.A. Allows Expanded Use of Plasma to Treat Coronavirus Patients → https://is.gd/lbhEOp03:42
ryoumadidn't sleep last night.  it seems you are making a sort of average03:42
de-factoryouma, dividing two rolling averages delayed by one serial time of 4 days03:43
LjLryouma, not quite an average, but anyway, the amount of days being considered is apparently related to the time it supposedly takes, on average, for someone to infect someone else03:43
LjLso since that's between 4 and 6 days, at least it has been estimated to be, those make sense03:43
de-factothe window for the rolling average determines the smootheness of the resulting reproduction number R03:43
ryoumahere i am screwing around with jnumbers.  forget it.  where i am is still chernobyl for cases and beirut for hospital overload and 1984 for triage.  last night was hell for my tooth.  and students already have started returning.  so i'd better accept today's really bad curve as it isn't going to get better.03:43
LjLryouma, i thought arizona was kind of tapering off03:44
de-factoyeah it would be averages but the division by the number of days just cancels from nominator and denominator03:44
de-factohence i skipped those03:44
ryoumaif you believe the numbers the cases are tapering off to still really high numbers yes.  but look at deaths and the crisis triage thing that az was the first in the nation to do and the load balancing and sending patients to new mexico and the refrigerated trucks for corpses and the non-er doctors being drafted to do a 72 hour straight shift in the er for their first er shift.03:46
ryoumai just can't imagine the returning students at the 3 major universities and various minor colleges and universities are going to be much help there.  then the snow birds will increase the population by a pretty big percent.03:48
ryouma(if they do come but nobody in the usa thinks there is a pandemic)03:48
ryoumausa is /really/ individualistic country03:49
de-facto%title https://academic.oup.com/aje/article/178/9/1505/89262 <-- LjL i think the calculation for R with this method originates from this paper here03:50
Brainstormde-facto: From academic.oup.com: New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics | American Journal of Epidemiology | Oxford Academic03:50
ryoumaok it is obvious now why you are dividing like that.  i think.03:51
de-factoyou can see the calculations in programming language R done by RKI on their example here: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Projekte_RKI/R-Wert-Erlaeuterung.pdf?__blob=publicationFile03:52
de-factoits German though, yet the program code should be easily readable i guess03:52
BrainstormNew from r/Coronavirus: Coronavirus: Argentina reports 137 new deaths and 5352 new cases. → https://is.gd/tqZP3Y04:02
de-factoso to quote their R code fast "R_Wert[t] <- sum(data$NeuErkr[t-0:3]) / sum(data$NeuErkr[t-4:7])" and slow "R7_Wert[t-1] <- sum(data$NeuErkr[t-0:6]) / sum(data$NeuErkr[t-4:10])"04:04
de-factopretty much the same than what i wrote above04:04
BrainstormNew from r/Coronavirus: Coronavirus: U.S. reports 32,718 new cases for August 23rd, lowest since June 23rd → https://is.gd/Gt4IgM04:21
lesmo9%cases Mexico04:38
BrainstormUpdates for World: +6054 cases (now 23.7 million), +332 deaths (now 813590) since 2 hours ago — Jamaica: +116 cases (now 1529) since 11 hours ago — Mexico: +3948 cases (now 560164), +226 deaths (now 60480) since 11 hours ago — Bolivia: +722 cases (now 109149), +67 deaths (now 4509) since 11 hours ago04:38
Brainstormlesmo9: In Mexico, there have been 560164 confirmed cases (0.4% of the population) and 60480 deaths (10.8% of cases) as of 6 minutes ago. 1.3 million tests were performed (44.5% positive). Fatality can be broadly expected to lie between 0.1% (assuming prevalence as in tests) and less than 13.6% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=Mexico for time series data.04:38
BrainstormNew from r/Coronavirus: Coronavirus: Seoul mandates face masks as South Korea battles spike in coronavirus → https://is.gd/9e4vk205:00
BrainstormNew from r/Coronavirus: Coronavirus: Coronavirus Tracker: 99 new cases, nine additional deaths reported in Bexar County Sunday → https://is.gd/fTwvVs05:09
xx64%cases usa05:17
Brainstormxx64: In US, there have been 5.9 million confirmed cases (1.8% of the population) and 180604 deaths (3.1% of cases) as of 45 minutes ago. 76.1 million tests were performed (7.7% positive). Fatality can be broadly expected to lie between 0.7% (assuming prevalence as in tests) and less than 5.4% (considering only deaths and recoveries). See https://offloop.net/covid19/?default=US for time series data.05:17
BrainstormNew from r/Coronavirus: Coronavirus: South Korea warns it’s on brink of nationwide pandemic → https://is.gd/bMnUdW05:19
LjLde-facto, gotta go to bed now but i've opened the tabs for tomorrow05:28
de-factonice gn805:28
LjLgood lord05:31
LjLopened the thing about the Maine wedding causes 50 cases, it's Newsweek05:31
LjLit tells me about the thing, that one died, that these events are dangerous, and then there's a poll that asks "Do you approve of Melania Trump's garden renovations?"05:31
LjLfucking seriously05:31
ryoumai have noticed that in uk newspapers too05:38
ryoumai don't think it used to occur05:38
ryoumai guess trying to grab different demographics in one page or something05:39
BrainstormNew from r/Coronavirus: Coronavirus: Surge in atrocities against Dalits and Adivasis under COVID-19 lockdown in India reported - International Dalit Solidarity Network → https://is.gd/QH242o05:48
BrainstormNew from r/Coronavirus: Coronavirus: COVID19 epidemic growth rates have declined since early March in U.S. regions with active hospitalized case surveillance → https://is.gd/Tog7DJ05:58
BrainstormNew from r/Coronavirus: Coronavirus: Singapore researchers discover new Covid-19 variant which causes milder infections → https://is.gd/qfVutw06:27
BrainstormNew from r/Coronavirus: Coronavirus: Parties around Washington State University’s Greek Row linked to ‘substantial increase’ in COVID-19 cases → https://is.gd/KLyN2U06:56
BrainstormNew from r/Coronavirus: Coronavirus: New Zealand - Covid-19: Auckland level 3 restrictions to continue to Sunday night - Ardern → https://is.gd/YG4jSz07:15
BrainstormNew from r/Coronavirus: Coronavirus: At least 15 Peru partygoers test positive for Covid-19 following deadly stampede → https://is.gd/5EdN2B07:25
BrainstormNew from r/Coronavirus: Coronavirus: How One Model Simulated 2.2 Million U.S. Deaths from COVID-19 → https://is.gd/60LF6a07:54
BrainstormNew from r/Coronavirus: Coronavirus: UK Issues Urgent Call For More Indian, South Asian COVID-19 Plasma Donors → https://is.gd/ymrze108:04
BrainstormNew from r/Coronavirus: Coronavirus: Coronavirus Daily Herd Immunity in India? → https://is.gd/ryYErW08:13
BrainstormNew from r/Coronavirus: Coronavirus: Tokyo reports 95 new COVID-19 cases for August 24th (as of 3PM JST). Lowest number of single day cases, since July 8th. → https://is.gd/XwxLFT08:52
BrainstormNew from The Indian Express: World: Coronavirus Global Updates, 24 August: Trump announces plasma treatment; China marks 8 days of no local transmission → https://is.gd/cOb2DS09:02
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai809:11
BrainstormNew from The Indian Express: World: In China, Where the Pandemic Began, Life Is Starting to Look … Normal → https://is.gd/yRn0lc09:40
BrainstormNew from BBC Health: (news): US allows emergency use of blood plasma treatment for coronavirus patients → https://is.gd/qYgkfS10:09
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai810:19
BrainstormNew from StatNews: Biotech: STAT Plus: In the race for a Covid-19 vaccine, Pfizer turns to a scientist with a history of defying skeptics — and getting results → https://is.gd/FR7YWO10:38
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai810:48
Jigsy%cases UK10:54
BrainstormUpdates for Odisha, India: +2993 cases (now 78530), +10 deaths (now 409) since 17 hours ago — Santander, Colombia: +1295 cases (now 13687), +57 deaths (now 563) since a day ago — Cesar, Colombia: +702 cases (now 7889), +35 deaths (now 200) since a day ago — Norte de Santander, Colombia: +663 cases (now 8988), +46 deaths (now 514) since a day ago10:54
BrainstormJigsy: In United Kingdom, there have been 325642 confirmed cases (0.5% of the population) and 41429 deaths (12.7% of cases) as of 17 hours ago. 18.3 million tests were performed (1.8% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.10:54
BrainstormNew from BBC Health: (news): US allows emergency use of blood plasma treatment for coronavirus patients → https://is.gd/qYgkfS10:57
BrainstormNew from r/Coronavirus: Coronavirus: Malaysia : Only 7 new cases today, with all 5 local cases in Sarawak, 184 active cases → https://is.gd/tvLBXP11:46
BrainstormNew from r/Coronavirus: Coronavirus: Facebook, Twitter must do more to stop anti-vaxxer COVID-19 lies: GPs → https://is.gd/pY7w2012:05
BrainstormNew from BMJ: Covid-19: Should doctors recommend treatments and vaccines when full data are not publicly available?: Yes—Raymond M JohnsonIn normal circumstances, insisting on full data transparency and limiting decision making to published data alone is rightly paramount. But a pandemic is far from normal, and to... → https://is.gd/BsDNr812:15
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai812:24
BrainstormNew from r/Coronavirus: Coronavirus: Data Analysis of Air Quality Before and After COVID-19 In Major Cities → https://is.gd/sPgqAq13:03
BrainstormNew from BMJ: Russian SARS-CoV-2 vaccine: The announcement by Russia’s president, Vladimir Putin, that the country has developed and approved the world’s first SARS-CoV-2 vaccine1 raises many questions. The global scientific community is... → https://is.gd/zDOAoz13:23
BrainstormNew from r/Coronavirus: Coronavirus: Pfizer says its virus vaccine could be ready for October review → https://is.gd/Ub6VHU13:42
BrainstormNew from CNBC Health: (news): Coronavirus live updates: WHO says 172 countries in on global vaccine plan; Chinese e-commerce giants see a boost → https://is.gd/urDzCQ13:51
CoronaBot04/r/covid19: FDA Issues Emergency Use Authorization for Convalescent Plasma as Potential Promising COVID–19 Treatment, Another Achievement in Administration's Fight Against Pandemic (80 votes) | https://www.fda.gov/news-events/press-announcements/fda-issues-emergency-use-authorization-convalescent-plasma-potential-promising-covid-19-treatment | https://redd.it/ifbqoc13:57
CoronaBot04/r/coronavirus: ‘How is this possible? What are the odds?’ | The novel coronavirus put two teenage brothers on life support, shaking a Virginia family. (10131 votes) | https://www.washingtonpost.com/nation/2020/08/23/brothers-coronavirus-virginia/?arc404=true | https://redd.it/ifd9t114:03
BrainstormNew from BBC Health: (news): US allows emergency use of blood plasma treatment for coronavirus patients → https://is.gd/qYgkfS14:11
BrainstormNew from CNBC Health: (news): Coronavirus live updates: WHO says 172 countries in on global vaccine plan; Chinese e-commerce giants see a boost → https://is.gd/urDzCQ14:30
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai814:40
BrainstormNew from BMJ Open: Open access: Correction: Transmission reduction and prevention with HPV vaccination (TRAP-HPV) study protocol: a randomised controlled trial of the efficacy of HPV vaccination in preventing transmission of HPV infection in heterosexual couples → https://is.gd/9MIduf14:59
BrainstormNew from r/Coronavirus: Coronavirus: Coronavirus research updates: Vaccines given through the nose could protect against infection → https://is.gd/rpopQ615:09
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai815:19
CoronaBot04/r/covid19: Genomic Analysis Reveals Many Animal Species May Be Vulnerable to SARS-CoV-2 Infection (83 votes) | https://www.ucdavis.edu/news/genomic-analysis-reveals-many-animal-species-may-be-vulnerable-sars-cov-2-infection | https://redd.it/ifm96n15:28
BrainstormNew from StatNews: First Covid-19 reinfection documented in Hong Kong, researchers say: Researchers in Hong Kong on Monday reported what appears to be the first confirmed case of Covid-19 reinfection. → https://is.gd/jf3cHg15:28
BrainstormNew from CNBC Health: (news): Coronavirus live updates: WHO says 172 countries in on global vaccine plan; Chinese e-commerce giants see a boost → https://is.gd/urDzCQ15:38
BrainstormNew from CNBC Health: (news): Dr. Scott Gottlieb: Coronavirus plasma treatment might help but 'doesn't look like a home run' → https://is.gd/08Mwcc15:57
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai816:17
metreoHow likely is the single case of reinfection a statistical anomaly?16:18
LjLmetreo, meaning that it will just not happen again? i'd say close to zero... but that it is isolated to only a small percentage of cases, likely16:55
metreoSure so say ~0.01% of cases will have a recurrent infection?17:04
LjLi have no idea the amount17:05
LjLconsidering immunity may well last for a limited time, it could well be a lot more17:05
BrainstormNew from The Indian Express: World: Covid-19: Hong Kong researchers report first documented case of re-infection → https://is.gd/7qnsXy17:05
LjLpersonally i think a lot of possible reinfections have been brushed off as continuing infections or false negative tests (or false positive initial test in the last case i heard), when that was all a bit of a stretch17:06
LjLso personally i think if they actually go do and like with this HK man and *sequence the strains*, they will find it's a lot more common than "almost never"17:06
LjLbut that's just my opinion17:06
LjLgo do -and like17:06
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai817:15
LjLde-facto, ah, we put a bad number in your equation yesterday because i was completely oblivious to the fact that while offloop said +1071 new cases, it was actually +1206 for yesterday, it just wan't up to date17:18
de-factooh sorry for that, I just quickly hovered over the graph to get number that was somewhat realistic for my example calculations17:20
de-factoso correct would have been +12.6% of our estimate then?17:21
de-factothats probably comparable to the noise anyhow17:21
de-factough netsplit17:23
LjLde-facto, yes, i did something different now (which may well be wht the person on reddit did): i took the past 6 days, which is the increasing streak (320 ... 1209), did n_day / n_previousday for each of them, and then averaged these multipliers together. then i used this averaged multiplier to predict what happens in 14 days (i'm dumb so i just made the spreadsheet multiply 14 times), and what i get is that 7 days from now, we'll have ~6000 a day, and 14 17:23
LjLdays from now, ~3000017:23
LjLso that's even more than the redditor got17:23
LjLit may be very naive but i suppose this is the simplest way to fit an exponential curve to the numbers we have17:23
LjLalso, today, fresh number, it's "only" 953, however as usual on mondays, the testing was very limited17:24
de-factobut wait, why ratio of current day and previous day?17:24
LjLso in effect, it's 2.08% cases/tests, while that was 1.79% yesterday, 1.38% the day before, and so on decreasing17:24
LjLde-facto, because that's the multiplier to obtain the current day's number from the previous day's number17:25
LjL3201.25312517:25
LjL4011.60099750623441417:25
LjL6421.30841121495327117:25
LjL8401.127380952380952417:25
LjL9471.130939809926082317:25
LjL10711.128851540616246517:25
LjL12091.25817:25
LjLlike this17:25
de-factoyes but thats not the generation numbers for R which describes the increase between two consecutive generations in an infection chain17:26
de-factofor the exponential you would need to take the serial interval (hence those 4 days) afaik17:26
LjLwell that's the exponential i would fit if i knew nothing about what this is, and i was simply told "these numbers are part of an exponential, predict how it continues"17:27
de-factoif you want to fit an exponential curve you would need to do linear regression on the logarithms of the numbers afaik17:27
LjLredditor doesn't appear to have replied17:27
de-factoyou can see it in offloops code for doubling times i think17:27
de-factofor the calculation of the reproduction number R you would need to look at how many new cases were caused in the new generation in the infection chain: if you currently have 100 cases which cause 120 cases 4 days later you would have R = 120 / 100 = 1.217:30
LjLi don't have the code, but i can see that it's doubling time is much higher than what i get, even considering only the past 6 or 4 days17:30
de-factoif you have the logarithm of an exponential you get the function in the exponent, hence if you assume an exponential increase this function in the exponent would be a linear one of time17:33
de-factoso then you take that assumed linear function with time (the logarithm of cases) and do a linear fit to it with Gaussian method of least squares (minimizing the differences of your data points to the desired linear function) called linear regression17:35
de-factoif you found that linear approximation for the exponent that way, you can plug it into your exponential function for predicting cases and should get a somewhat decent prediction under the assumption of continuous exponential development without changes to the parameters17:36
BrainstormNew from The Indian Express: World: German doctors say tests suggest Alexei Navalny was poisoned → https://is.gd/iW00Sc17:38
de-factoand btw for such predictions you should include as many data points as possible while still being "current" enough with time17:38
de-factohence a good balance in smoothing (averaging e.g. for noise and weekly periodicity) yet still include most recent momentum of increase is probably the best17:39
de-factothe main problem with all of that may be the assumption of static parameters, i would guess that almost all of them change with time in reality, e.g. people becoming aware of something and reacting, new strategies and discoveries, all such dynamics17:42
BrainstormNew from CNBC Health: (news): Coronavirus live updates: WHO says 172 countries in on global vaccine plan; Chinese e-commerce giants see a boost → https://is.gd/urDzCQ17:44
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai817:54
BrainstormNew from Scientific American: Health: How We Can Use the CITES Wildlife Trade Agreement to Help Prevent Pandemics → https://is.gd/WVa9tH18:04
Jigsyhttps://www.theguardian.com/commentisfree/2020/aug/24/the-best-way-to-keep-schools-open-stop-coronavirus-entering-them-in-the-first-place18:12
Jigsy%title18:12
BrainstormJigsy: From www.theguardian.com: The best way to keep schools open? Stop coronavirus entering them in the first place | Schools | The Guardian18:12
JigsyGenius! Why didn't anyone else think of that?18:12
BrainstormNew from CNBC Health: Scientists doubt convalescent plasma touted by Trump is a 'breakthrough' coronavirus treatment: There are no formally approved drugs or vaccines for the coronavirus. Convalescent plasma is one of several therapies being tested as a potential treatment. → https://is.gd/W6f5m318:13
BrainstormNew from CNBC Health: (news): Coronavirus live updates: WHO says 172 countries in on global vaccine plan; Chinese e-commerce giants see a boost → https://is.gd/urDzCQ18:23
BrainstormNew from CNBC Health: (news): Scientists doubt convalescent plasma touted by Trump is a 'breakthrough' coronavirus treatment → https://is.gd/W6f5m318:52
BrainstormNew from New Scientist: Covid-19 news: Researchers find first case of coronavirus reinfection: The latest coronavirus news updated every day including coronavirus cases, the latest news, features and interviews from New Scientist and essential information about the covid-19 pandemic → https://is.gd/m985BC19:02
BrainstormNew from CNBC Health: (news): Coronavirus live updates: First confirmed case of reinfection; WHO says 172 countries on global vaccine plan → https://is.gd/urDzCQ19:50
BrainstormNew from r/Coronavirus: Coronavirus: Man who believed virus was hoax loses wife to Covid-19 → https://is.gd/QxAAlX20:09
LjLde-facto, around?20:17
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai820:19
BrainstormNew from CNBC Health: (news): Coronavirus live updates: First confirmed case of reinfection; WHO says 172 countries on global vaccine plan → https://is.gd/urDzCQ20:29
BrainstormNew from Scientific American: Evidence for Convalescent Plasma Coronavirus Treatment Lags Behind Excitement: Nurse Lina Acevedo holds the plasma donated by a man who recovered from COVID-19 on August 14, 2020 in Bogota, Colombia. → https://is.gd/ZCDcF921:08
BrainstormNew from BBC Health: (news): Coronavirus: Boris Johnson says it is 'vitally important' children return to class → https://is.gd/7Z4ai821:18
CoronaBot04/r/coronavirus: We Still Don't Know All the Long-Term Consequences of 'Mild' COVID-19 (10125 votes) | https://vitals.lifehacker.com/we-still-dont-know-all-the-long-term-consequences-of-mi-1844560700 | https://redd.it/ifnqc021:19
LjLuff, they should stop just locking threads instead of removing misinformation21:21
LjLit's as if i set the channel +m because a few people post incorrect stuff21:21
LjLone thing is doing that sort of thing for pervasive spam that can't be controlled manually...21:22
BrainstormNew from r/Coronavirus: Coronavirus: Judge strikes down Florida’s school reopening order, says unconstitutional to require ‘brick and mortar’ classes this month → https://is.gd/zUozdv21:37
de-factoLjL yes sorry was outdoors21:38
BrainstormNew from r/Coronavirus: Coronavirus: Covid-19 deaths have dropped below 1,000 a day as summer surge tails off → https://is.gd/CvIXkb21:47
BrainstormNew from r/Coronavirus: Coronavirus: Nearly two dozen more flights land in Canada with passengers infected with COVID-19 → https://is.gd/vDtswO21:56
Jigsy%cases UK22:08
BrainstormUpdates for World: +127224 cases (now 23.8 million), +1975 deaths (now 815845) since 11 hours ago — Germany: +1619 cases (now 236113), +4 deaths (now 9336) since 11 hours ago — Turkey: +1443 cases (now 259692), +18 deaths (now 6139) since 19 hours ago — India: +54120 cases (now 3.2 million), +831 deaths (now 58546) since 11 hours ago22:08
BrainstormJigsy: In United Kingdom, there have been 326614 confirmed cases (0.5% of the population) and 41433 deaths (12.7% of cases) as of 4 minutes ago. 18.3 million tests were performed (1.8% positive). See https://offloop.net/covid19/?default=United%20Kingdom for time series data.22:08
BrainstormNew from r/Coronavirus: Coronavirus: Almost 50 North Texans Drank Bleach This Month, Poison Center Warns ‘Stop, It Won’t Cure COVID’ → https://is.gd/5QUu6222:16
Tobi[m]Reinfection: first lab proven case https://twitter.com/drericding/status/129785443822119731322:32
BrainstormNew from r/Coronavirus: Coronavirus: 95 positive for COVID-19 after visiting nudist beach resort in France → https://is.gd/M2qeYB22:35
CoronaBot04/r/covid19: Be well: A potential role for vitamin B in COVID-19 (80 votes) | https://linkinghub.elsevier.com/retrieve/pii/S0378512220303480 | https://redd.it/ifmwx123:02
BrainstormNew from r/Coronavirus: Coronavirus: The NFL Had No Positive Player Tests Out Of 23,000 Taken This Week → https://is.gd/i3q33423:04
BrainstormNew from r/Coronavirus: Coronavirus: ‘I’m hopeful we’re going to start to get readout early in autumn as to whether this thing works or not’ – Prof Sir John Bell on Oxford vaccine → https://is.gd/PKogWJ23:14
LjLde-facto, no problem, i was just wondering, since today as usual we have fewer cases than before because it's monday... if i wanted to make today's case count for italy comparable to yesterday, i think i could do cases_today * tests_yesterday/tests_today. that wouldn't give me a "truer" number per se, just more comparable to the one we had yesterday. now to extend this, couldn't i do cases_day_t * (tests_total/total_days)/tests_day_t ? basically the same 23:30
LjLthing, but compared to an average of testing over time. again it wouldn't give me "true" numbers, but more comparable with each other... and with the caveat that usually, the less testing there is, the more "targeted" that testing is, but i suspect that's impossible to just model with these data, because it depends on how exactly testing is performed23:30
BrainstormNew from r/Coronavirus: Coronavirus: Meatpacking Companies Dismissed Years of Warnings but Now Say Nobody Could Have Prepared for COVID-19 → https://is.gd/6XGxRm23:33
izthe entire world is the stick in bike spokes meme23:36
BrainstormNew from r/Coronavirus: Coronavirus: Health officials in multiple states report coronavirus cases linked to Sturgis → https://is.gd/jLFuKH23:43
CoronaBot04/r/covid19: The six strains of SARS-CoV-2 (82 votes) | https://www.unibo.it/en/notice-board/the-six-strains-of-sars-cov-2 | https://redd.it/ifo6av23:57

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