
Rt: Effective Reproduction Number of Covid-19 - radkapital
https://rt.live
======
lettergram
IMO 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-analysi...](https://raw.githubusercontent.com/lettergram/covid19-analysis/master/graphs/us-
test-ratios.png)

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-analysi...](https://raw.githubusercontent.com/lettergram/covid19-analysis/master/graphs/us-
tests-by-state.png)

Deaths:
[https://raw.githubusercontent.com/lettergram/covid19-analysi...](https://raw.githubusercontent.com/lettergram/covid19-analysis/master/graphs/us-
deaths-by-state.png)

Overall repo:
[https://github.com/lettergram/covid19-analysis](https://github.com/lettergram/covid19-analysis)

~~~
zaroth
The 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.

~~~
nitrogen
_I 'm not sure I understand the extreme focus on testing._

3blue1brown on YouTube created a simple model that suggests that testing and
quarantine of positive cases is the most effective way to slow the spread
(within the simplified model). Testing should allow us to isolate just the
infected, and ease off the restrictions on others.

~~~
ethbro
With statistically valid random testing, even detecting clusters / communities
(as opposed to individuals) and clearing same would be conducive to reopening
the economy.

Unfortunately, the path to doing so "I'm going to force you to get tested,
despite you having no symptoms" is political anathema.

~~~
zaroth
No, no, there’s never going to be enough testing to test asymptomatic cases —
Thats _everybody_.

And a test doesn’t tell you you aren’t going to be positive tomorrow. It just
tells you you weren’t positive 48 hours ago!

Fauci explained all this live at the press conference. I wish people would
listen. With AIDS it’s different. You can get tested, be negative, take no at-
risk behaviors, and a year later that negative test is still relevant. With
COVID by the time you have a negative test result back it’s no longer even
_relevant_. Only positive tests are relevant.

The fact is that there’s no point in testing people to demonstrate that they
are negative. And there will never be enough testing to test every
asymptomatic person, and a significant proportion of spread is from
asymptomatic carriers. Those three incontrovertible facts lead to some very
basic and sobering conclusions.

So this fear of people being forced to show a negative test assumes we’ve
somehow found our way into an anti-science twilight zone kabuki theater to
begin with. Which frankly wouldn’t be far off from where we are already, but
can we please at least acknowledge it’s based on fear and hysteria and not any
kind of science?

~~~
jlj
> With COVID by the time you have a negative test result back it’s no longer
> even relevant.

A family friend died on Friday. His heart went out on him. Big guy on his
60's. He got tested for COVID-19 before he died at the hospital. He and his
now widow had some sinus congestion. She couldn't enter to he hospital to be
with him when he died. A few days later, his widow got the negative result for
her husband. She is alone, scared, dealing with this loss. can't see her kids
or grandkids. She can sleep a little better at night knowing that death is not
knocking at her doorstep.

Relevant? From a human perspective it is most definitely relevant. Maybe not
as much from a epidemiology or number cruncher's perspective but like all
expert opinions they are open to interpretation and second opinions.
Statistics are easy to cherry pick for whatever agenda is being pushed behind
the scenes.

Just like masks were not relevent at first. They were scarce. Suddenly they
are relevant for the public to use. I believe this testing scarcity and
related lack of any cohesive national mobilization is the biggest failure of
our US government. From a public health perspective this dismissal of negative
testing is just a way to manage the demand side for testing.

Public health and epidemiology experts have very different motivations than
individuals dealing with loss and fear during this crazy time.

------
_delirium
Here'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
I'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.

------
dsukhin
Great 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
Ah, 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.

~~~
Lukas1994
Where did you find static/js/StackViz.js?

~~~
zaroth
It's in the bundle. Using dev tools in your browser you can get an expanded
view of the file/folder structure.

------
phkahler
This 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
It'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
The flu is seasonal, the first wave died down during the summer and the second
wave started in the fall.

~~~
SpicyLemonZest
"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.

------
cactus2093
It'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.

~~~
mrfusion
At the same time other countries like Belarus have done nothing and haven’t
done worse than CA. Or consider Sweden has ~81% of the rate of COVID per
capita as the UK and has ~65% of the death per capita as the UK but no
lockdown.

Edit. I don’t mean to go against the prevailing opinions but it seems like
something that merits more research. There’s a lot we don’t know about this
virus.

~~~
9nGQluzmnq3M
Here's an interesting interview with a senior epidemiologist partly
responsible for Sweden's unconventional strategy:

[https://youtu.be/bfN2JWifLCY](https://youtu.be/bfN2JWifLCY)

TL;DW: Preventing transmission in the long term is impossible and the actual
fatality rate is likely on the order of 0.1%, so general lockdowns are
pointless and being driven mostly by political considerations (something must
be done and this is something). Just protect the elderly and weak.

~~~
joshuahedlund
> actual fatality rate is likely on the order of 0.1%

This is ludicrously optimistic. The virus has already killed over 0.1% of the
_entire population_ of New York City, and it's barely starting to wind down
(i.e. will probably hit 0.2%). It's also approaching 0.1% of the entire
populations of several of the hardest hit areas across the US (Bergen County,
NJ; Chelsea, MA; Orleans Parish, NJ), with the most optimistic antibody and
random sampling studies suggesting no more than one-third of the total
populations infected at this point.

Some of the most reasonably optimistic numbers that are being bandied about
nowadays are three to four times higher than that (0.3-0.4%), though I think
the majority of the evidence points to a range more like 0.5-1.0%.

~~~
fernly
> The virus has already killed over 0.1% of the entire population of New York
> City

Wait, what? That would be one person in every 1000? Population of 8,398,748[1]
that would be... huh. Confirmed deaths, 8,448[2].

Nice, as they say on another site.

[1]
[https://en.wikipedia.org/wiki/New_York_City](https://en.wikipedia.org/wiki/New_York_City)

[2]
[https://www1.nyc.gov/site/doh/covid/covid-19-data.page](https://www1.nyc.gov/site/doh/covid/covid-19-data.page)

------
jpxw
Anyone else think this was Russia Today from the URL on first glance?

~~~
projektfu
I was pretty worried it was.

------
theaeolist
These are pretty, but given the inconsistent testing regimes, difficult to
interpret.

~~~
jachee
I believe that inconsistency is factored into, and indicated by the error bars
and the width of the range indicators for each graph.

~~~
SpicyLemonZest
I'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.

------
usaar333
Great 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/10.1101/2020.04.12.20062943v...](https://www.medrxiv.org/content/10.1101/2020.04.12.20062943v1.full.pdf)).

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btilly
They 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.

------
guscost
The 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.

------
ltbarcly3
Does 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.

------
sci_prog
Great 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
Most of those increases are artifacts of testing parameters changing or
reporting delays, not actual infection rates. WA data here is quite
misleading.

------
vardump
This 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.

------
chasers
This 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
This monitors Rt (r-effective) not R0(r-naught)

------
oliwarner
These are just toys while testing remains as sparse as it is.

Don't look at these and think it's over.

------
orasis
Beautiful! What gets measured gets managed.

------
Vivtek
Another COVID tracker that leaves Puerto Rico out of the United States. I
don't even know why I'm still surprised.

~~~
zamadatix
Looks 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....](https://github.com/k-sys/covid-19/blob/master/Realtime%20R0.ipynb)
as the data source has territories and the capital but they filtered out
anything that's not a state.

~~~
Vivtek
The District of Columbia is not a state, and yet is included.

