11 ms·
Rt: Effective Reproduction Number of Covid-19
- theaeolist 7y agoThese are pretty, but given the inconsistent testing regimes, difficult to interpret.
- jachee 7y agoI believe that inconsistency is factored into, and indicated by the error bars and the width of the range indicators for each graph.
- SpicyLemonZest 7y agoI'm not sure that "we might not be measuring the right thing in the first place" is the kind of error that can be sufficiently accounted for by error bars.
- Trombone12 7y agoSince it's not from subject matter experts, expect things like sampling bias and administrative reporting issues to be completely neglected. That is to say, the uncertainty estimate is simply based on observed variance.
- orasis 7y agoBeautiful! What gets measured gets managed.
- chasers 7y agoThis is awesome! Sure the data is not perfect but it's what we've for and the r naught is exactly what we need to be monitoring.
- isthispermanent 7y agoThis monitors Rt (r-effective) not R0(r-naught)
- dsukhin 7y agoGreat looking site. For those who don't know/realize - this is the work of Kevin Systrom, Mike Krieger (and team?) - co-founders of Instagram. Statistically speaking - love that it has error bars and timeseries. Makes it infinitely more informative to track relative to news, events, and mitigation strategies and have a sense of the confidence of the estimate. The provided Jupyter notebook is a great resource. Alphabetically speaking - I enjoyed the puzzle of figuring out how the states were sorted in the timeseries list (e.g. why was Alaska before Alabama, Iowa before Idaho, etc.). Turns out it's alphabetical by the two letter state abbreviation which is not shown - just a fun observation :)
- zaroth 7y agoAh, thank you for pointing out the author. Helps with the inferiority complex for my past attempts at data visualization dashboards. It does say in the footer: "Data analysis by Kevin Systrom and site built by Mike Krieger, with thanks to Ryan O’Rourke and Robby Stein." I particularly liked browsing the code for the hero chart, which you can find under static/js/StackViz.js. 630 lines of JS and you can see the level of attention to detail. I couldn't find a copyright or licensing statement, but there are a few pieces of StackOverflow code copied and pasted into the bundle, so in theory the whole code base is therefore open source.
- sci_prog 7y agoGreat job! I live in HI (top 4 states according to the website), it looks like they are gonna start loosening up restrictions in a couple of weeks. It will be interesting to see how Rt evolves after that. There's a couple of states where Rt started increasing again after some time (e.g. WA).
- usaar333 7y agoMost of those increases are artifacts of testing parameters changing or reporting delays, not actual infection rates. WA data here is quite misleading.
- Vivtek 7y agoAnother COVID tracker that leaves Puerto Rico out of the United States. I don't even know why I'm still surprised.
- ignoramous 7y agoYou should write to them: hello at rt.live
- Vivtek 7y agoI did, before I commented here.
- zamadatix 7y agoLooks like you can create a PR about on the notebook and/or run it now if you're curious: https://github.com/k-sys/covid-19/blob/master/Realtime%20R0.ipynb https://github.com/k-sys/covid-19/blob/master/Realtime%20R0.... as the data source has territories and the capital but they filtered out anything that's not a state.
- Vivtek 7y agoThe District of Columbia is not a state, and yet is included.
- guscost 7y agoThe ramp-up in testing has an effect on these observations (thinking specifically about the early spikes in many places): > Absolute testing levels should not affect this algorithm much, but a fast ramp or decline in testing will affect numbers.
- lettergram 7y agoIMO this looks to by a symptom of lack of testing. Overall the ratio of tests coming back positive is unchanged: https://raw.githubusercontent.com/lettergram/covid19-analysis/master/graphs/us-test-ratios.png https://raw.githubusercontent.com/lettergram/covid19-analysi... Even though we are doing more tests. Meaning the reduction in speed-of-spread likely has more to do with lack of testing. That being said, I’m sure spread is being reduced, we just don’t know to what extent because we don’t have enough effective testing. It’s also possible (probably likely) our tests are not exceptionally accurate. It’s the best we have, but given all of this is <6 months old the false positive/negative rate can be high. Generally, Testing isn’t an effective way to measure spread. Probably we should use “hospitalizations with flu symptoms“ as the best indicator. You can compare testing per state and deaths here: Tests: https://raw.githubusercontent.com/lettergram/covid19-analysis/master/graphs/us-tests-by-state.png https://raw.githubusercontent.com/lettergram/covid19-analysi... Deaths: https://raw.githubusercontent.com/lettergram/covid19-analysis/master/graphs/us-deaths-by-state.png https://raw.githubusercontent.com/lettergram/covid19-analysi... Overall repo: https://github.com/lettergram/covid19-analysis https://github.com/lettergram/covid19-analysis
- usaar333 7y agoCorrect. Testing is only a good measurement with massive testing, even randomized testing. Iceland's data is probably the closest to actual infections and many states probably look similar. (https://www.covid.is/data https://www.covid.is/data)
- zaroth 7y agoThe reported specificity and sensitivity of RT-PCR testing is quite good, but obviously not 100%. RT-PCR is considered the "gold standard" in viral testing. If you want to contact trace, we would need many orders of magnitude more testing. If you want to know prevalence over time, and therefore Rt, we could ascertain it very accurately with much less testing, but it would need to be done against statistically valid and unbiased random samples of the population, not at all what is going on today. Since the testing we are doing today doesn't really satisfy either condition, and there's also no front-line approved treatments for those that are definitively diagnosed (rather, we treat the symptoms, which are self-evident), frankly I'm not sure I understand the extreme focus on testing.
- usaar333 7y agoGreat visualizations - I'd love to see this done with hospitalizations though as case count overestimates r given increasing testing. (Granted hospitalizations are also breaking down recently due to recent disproportionate nursing home infections) E.g. CA is unlikely to have had an r above 2 even at beginning of March, but this is calculating close to 3. (Source: https://www.medrxiv.org/content/10.1101/2020.04.12.20062943v1.full.pdf https://www.medrxiv.org/content/10.1101/2020.04.12.20062943v...).
- btilly 7y agoThey list the following known issues: 1) Changes in testing will affect numbers. 2) The delay between infection and testing is ignored so actual Rt values are delayed by some amount. Both are huge actual issues.
- jpxw 7y agoAnyone else think this was Russia Today from the URL on first glance?
- projektfu 7y agoI was pretty worried it was.
- phkahler 7y agoThis really illustrates that the parameter in question is not just a characteristic of the virus, but also of the environment. I think a lot of people forget that if try to return to normal activity this is just going to shoot back up. I have yet to see an exit strategy other than "modulate social distancing such that the health care system is near capacity, we can gradually open up as more people are immune due to prior infection."
- SpicyLemonZest 7y agoIt's not obvious that it will shoot back up, depending on how careful we all about the return. People talk a lot about the multiple waves of the Spanish Flu, but the logical consequence of that is that transmission of a respiratory disease can be sustainably reduced; otherwise there would have only been the one wave.
- hilbertseries 7y agoThe flu is seasonal, the first wave died down during the summer and the second wave started in the fall.
- SpicyLemonZest 7y ago"Seasonal" just means that we see this pattern regularly every year. It's not that there's some specific property of the flu which stops it from spreading during the summer - there could be, but we don't know.
- branko_d 7y ago> more people are immune due to prior infection This is not a given. Other coronaviruses tend to confer only temporary immunity, and this one might be similar. This thing could become seasonal unless/until we make a very effective vaccine against it. <shudder/>
- mirimir 7y agoAlso, those Chinese bats and bat eaters are still there, so this won't be the last coronavirus to make the jump successfully. Edit: That's not a joke: Cheng et al. (2007) Severe Acute Respiratory Syndrome Coronavirus as an Agent of Emerging and Reemerging Infection [0] > Coronaviruses are well known to undergo genetic recombination, which may lead to new genotypes and outbreaks. The presence of a large reservoir of SARS-CoV-like viruses in horseshoe bats, together with the culture of eating exotic mammals in southern China, is a time bomb. The possibility of the reemergence of SARS and other novel viruses from animals or laboratories and therefore the need for preparedness should not be ignored. 0) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176051/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176051/
- _delirium 7y agoHere's an alternative set of per-US-state Rt estimates from the London School of Hygiene & Tropical Medicine, with somewhat different results: https://epiforecasts.io/covid/posts/national/united-states/ https://epiforecasts.io/covid/posts/national/united-states/ They believe there's insufficient data to estimate Rt today, though, due to lags in symptoms/diagnosis/testing/reporting. So their estimates lag about 10 days, with the x-axis for the Rt-over-time graphs currently running February 17 through April 7. They also have per-country estimates: https://epiforecasts.io/covid/posts/global/ https://epiforecasts.io/covid/posts/global/
- standardUser 7y agoI've been following their maps over the last week and I have noticed a lot of variation day-to-day. I have seen three different statuses for California so far, for example.
- cactus2093 7y agoIt's wild that California has been locked down for a full month and the reproduction number is still hovering around 1 and even went up a couple of days ago. If that's actually true, we shouldn't expect to see a quick decrease in cases and we probably aren't on track to end the lockdown any time before at least June. I can't help but wondering if the unlimited outside time under the guise of "exercise", but which people are clearly taking advantage of by going to hang out with friends in the park, has anything to do with it. Or perhaps it's the lack of masks in indoor areas like grocery stores that has prevented a bigger drop (in SF, only starting today has that finally changed). For all that California has been praised for acting quickly, it still feels like we've really been slow playing this lockdown by being so lenient, and without really having gained anything. And it doesn't really seem like there's any urgency anymore around continuing to increase testing, even though we know that's needed to open back up. Now we're going to be stuck inside for weeks or months longer than we would have needed to be if we had just copied what successful countries (Taiwan, South Korea) did from the beginning.
- trhway 7y agoOr may be the infection is already so widespread as some studies suggest that any observed changes is just a noise and all the lockdowns/etc. don't affect it much. Sweden for example isn't that different despite different approach. Without wide testing we don't really know and are just blindly drifting along the 5 stage model - denial, anger (that is lockdown), and now we're moving onto the negotiating with all that conditional reopening. It is pretty telling that anger to negotiating stages change is happening without improvement of the real situation.
- standardUser 7y agoSweden has one of the highest per capita death rates from COVID-19 in the world, and one of the lowest testing rates in Europe.
- trhway 7y agonice play. Those are the numbers https://www.statista.com/statistics/1104709/coronavirus-deaths-worldwide-per-million-inhabitants/ https://www.statista.com/statistics/1104709/coronavirus-deat... . The whole Europe and US have the highest deaths per capita in the world. Comparing to the peers - Western Europe - Sweden is midway in the list (and just above US) pretty much evidencing the point that whatever actions have been taken in all those countries it just doesn't seem to matter much.
- vardump 7y agoThis could also be an interesting data point for anyone who needs to pick a location for establishing a new business. Lesser Rt number might mean safer operating environment and healthier employees.
- oliwarner 7y agoThese are just toys while testing remains as sparse as it is. Don't look at these and think it's over.
- ltbarcly3 7y agoDoes anybody know if the testing numbers are per patient or per test? I was trying to run some bayes simulations yesterday and while debating it we couldn't figure out anything useful, because the statistics we were able to find are already rolled up and the methodology is hidden.