CovidColoradoCharts
Charts from Colorado's COVID data (by jasondorjeshort)
rt-from-frequency-dynamics | CovidColoradoCharts | |
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38 | 45 | |
46 | 2 | |
- | - | |
2.5 | 0.0 | |
4 months ago | over 1 year ago | |
Mathematica | ||
- | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
rt-from-frequency-dynamics
Posts with mentions or reviews of rt-from-frequency-dynamics.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-15.
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2/16 Variant Graph Update
Although several XBB.1.5 descendants are growing marginally faster, all variants that aren't XBB+486P are on the decline nationwide. This includes CH.1.1, which has been the clear #2 VOC behind XBB.1 since ~October and which has gotten some press recently.
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California tops 12 million coronavirus cases as XBB.1.5 becomes dominant
State or national variant numbers can currently be best accessed at cov-spectrum; in this link by clicking on "show regions". Covariants provides an even easier-to-read version, but it only separates a few classes of variants and in 2-week intervals. And Bedford labs variant tracker provides a unique perspective of different variant growth, but currently does not separate by states and has irregular updating.
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What we know about Omicron subvariant XBB.1.5 spreading across the U.S.
With variant tracking the main place to follow is the pango-designation project on github (but please do not post there if you go). Cov-spectrum is great for following the epidemiology of variants, as well as bedford labs. And before that covariants, but they haven't kept up with cov-spectrum's development. All of it's very simple from a modelling perspective, but applying the gisaid data to the case data is massively enlightening.
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12/8 Variant Graph Update
Though they update even more infrequently, I really like the new Bedford labs graphs. These make it very clear just how complicated trying to model the next several months would be.
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Sequencing Update - Weekend Edition
For a national perspective you can see Trevor Bedford’s GitHub. https://github.com/blab/rt-from-frequency-dynamics/tree/master/results/pango-countries
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Japan's daily COVID-19 cases rise week-on-week for 17 straight days | NHK WORLD-JAPAN News
Bedford labs splits it up into specific case counts, and shows the same thing. Here we see that BA.5 cases just stopped declining and started rising. Unfortunately they update irregularly. I'm looking specifically at the third graph here, and what makes me not want to be certain is the dark gray dots that are rising rapidly at the right. These aren't on the legend but I believe mean "other".
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October 19 2022 4 PM CDPHE Update
Bedford labs this week has added several new graphs. This looks in detail at just the US at a lot of different lineages. This looks at many countries with fewer lineages. Note that they do not have XBB.1 (everything's grouped as XBB giving variable results) and their updates are very irregular.
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October 14 2022 4 PM CDPHE Update
4 Bedford labs variant tracker is following XBB now, but not XBB.1. This isn't very useful to see growth in many countries where XBB has been spreading for a bit and XBB.1 has just been introduced, though the r~0.19 (3.8-fold weekly growth) is probably pretty accurate for Singapore.
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The level of coronavirus in Eastern Mass. waste water just shot up
covariants, cov-spectrum, outbreak.info, blab
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The Omicron SARS-CoV-2 variant is more transmissible and less fatal than seasonal influenza
But my best source, when it's updated, is Bedford labs variant tracking project.
CovidColoradoCharts
Posts with mentions or reviews of CovidColoradoCharts.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-07-08.
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September 2 2022 4 PM CDPHE Update
By onset and reported day, the case drop has stopped. It doesn't seem certain if we are in a plateau for the last few weeks, or if cases are rising, or if it's just a back-to-school plateau followed by further drops. It is not driven by new variants though; BA.4.6 is still <10% of nationwide infections and all the next-gen variants combined are <1%.
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August 26 2022 4 PM CDPHE Update
By reported and onset date, cases may have flattened. This wasn't visible in the reported-day numbers until today, but it's been showing in the onset-day numbers for a week or so. It could be variance, but the flattening of positivity at the same time makes it more likely to be real. If true though this isn't caused by a new variant; everything is still BA.5 for now.
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August 19 2022 4 PM CDPHE Update
By reported and onset date, cases are still falling.
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August 5 2022 4 PM CDPHE Update
By reported and onset date cases keep slowly dropping. Smoothed growth rate is down to -10-15% per week. Super approximate and I should probably make an actual model here, but if there were 1500 cases/day on July 20th and -2% per day, that puts us down to 1000-1100 new cases with onset day of today, which would be the lowest since the start of May.
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July 29 2022 4PM CDPHE Update
Cases by reported and onset date.
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July 15 2022 4PM CDPHE Update
By onset and reported date, cases seem to be curving up a bit, but with no rapid rise from BA.5 so far. The normal surge pattern is that the upward curving will continue until an inflection point, then it'll curve back down to and beyond the surge peak. But whether this happens soon, or if upward acceleration goes on for a while, or even if we're already past the inflection point, is likely impossible to know.
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July 8 2022 4PM CDPHE Update
By reported or onset date, there's still no definitive case rise from BA.5.
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July 1 2022 4PM CDPHE Update
By onset and reported date, cases are doing some weird up and down thing. It's probably a plateau and the variance just random, as BA.2.12.1 drops and BA.5 continues to take over. This likely won't last long; within a few weeks BA.5 will be the large majority of cases and for it to stay flat at R(t)~1 isn't unlikely.
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June 24 2022 4PM CDPHE Update
By reported and onset date, cases have firmly dropped over the last week. This represents BA.2.12.1 peaking and subsiding.
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June 17 2022 4PM CDPHE Update
There's several indications that BA.2.12.1 may have now peaked. This is based first on state case numbers by reported and onset date, which have flattened completely by onset date and have been declining slightly by reported date. And secondly, on Bedford labs' per-variant case estimates, which although they do have high error show BA.2.12.1 declining in the most recent sample collection days available.
What are some alternatives?
When comparing rt-from-frequency-dynamics and CovidColoradoCharts you can also consider the following projects:
pango-designation - Repository for suggesting new lineages that should be added to the current scheme
2020-rki-impf-archive