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XihongLin's profile
Xihong Lin
Xihong Lin
Xihong Lin
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@XihongLin

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Xihong LinVerified account

@XihongLin

Professor of @HarvardBiostats & @harvard statistics, Data Science, Genomics, Epidemiology, Health, Education, COVID19 analysis, intervention, Views are all mine

Boston, MA
hsph.harvard.edu/xihong-lin/
Joined August 2017

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    Xihong Lin‏Verified account @XihongLin 12 Jun 2020

    I am very pleased to announce our new site http://metrics.covid19-analysis.org , an interactive visualization for daily effective reproduction number(Rt) at multiple resolutions: countries, US states & counties. Check the Maps & Rt tables for current vulnerable regions with rising spread (1/)pic.twitter.com/QZ1UcZ6dju

    1:43 PM - 12 Jun 2020
    • 101 Retweets
    • 220 Likes
    • Alfonso Navarro Carvallo #ESDfor2030 #EliteSDGs Eunhee Kim Lisa Dean Takeout is Homemade Celery Aron Roberts ascendance (bnuy) Ray An Taylor Priest
    13 replies 101 retweets 220 likes
      1. New conversation
      2. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        The user can display the Rt map by date at the country level, the state/province level for the US, Australia, Canada, and China; and county level for the US. Clicking on a country, or a state or a county will bring up the Rt curve over time (2/)pic.twitter.com/I5HOSzNu6N

        2 replies 3 retweets 14 likes
        Show this thread
      3. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        The states in US that currently have the highest spreads are located in the South, Southwest, and the West coast (3/)pic.twitter.com/lgMr2D0bbV

        2 replies 1 retweet 14 likes
        Show this thread
      4. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        Estimated Rt values are also provided in a table below the map that can be sorted in ascending or descending order. Here are the top 20 states currently w/ the highest estimated spread rates(highest Rt’s using data up to 6/9), including VT, OR, SC, FL, AZ, NV, UT, AR, NC, WA(4/)pic.twitter.com/VLamZOuHMZ

        1 reply 1 retweet 10 likes
        Show this thread
      5. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        Oregon's high Rt value is driven by an outlier, the number of cases reported on June 8. The reason of this outlier needs to be investigated, e.g. whether the # of reported cases on June 8 includes positive antibody tests. The number of cases in Vt is small: a few recent spikespic.twitter.com/CaFsHS1MXt

        1 reply 1 retweet 8 likes
        Show this thread
      6. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        The 20 states in US that currently have the lowest spread rates (lowest estimated Rt values): MI, DE, WV, CT, NJ, IL, NH, MA, NY, NE. Their estimated current Rt values are between 0.5-0.75 (5/)pic.twitter.com/ygDgtwYmGa

        1 reply 2 retweets 7 likes
        Show this thread
      7. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        One can use "Compare Rt" to compare estimated Rt curves of multiple states. Here is a comparison of Rt curves and # of case trajectories of a few states whose numbers of cases have been rising in recent weeks after reopening:OR, SC, FL, AR & NV (Fig1) & UT, AK, NC, CA (Fig2)(6/)pic.twitter.com/iEfCPVOtSd

        1 reply 1 retweet 3 likes
        Show this thread
      8. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        Attention is needed for these vulnerable states to ensure plans for implementing 6 pillars after reopening are in place: mask wearing, testing, tracing, isolation&quarantine, social distancing, treatment. The reopening playbooks consist of multiple phases. Adherence is important.

        1 reply 1 retweet 6 likes
        Show this thread
      9. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        Here are Rt curves & # of case trajectories of a few states with low Rt's (0.5-0.75) and bended curves: CT, MA, MI, NY, NJ. These states have used the test-trace-isolate measure & have gradually re-opened at multi-phases. NY, NJ & MA were hit hardest at the early stage(7/)pic.twitter.com/AV5vJh1GWw

        2 replies 1 retweet 6 likes
        Show this thread
      10. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        On the Rt-map page, hitting the arrow button below the slider allows one to see the US States Rt animation on how Rt has changed over time (8/)pic.twitter.com/PvkJ98zSfr

        1 reply 2 retweets 5 likes
        Show this thread
      11. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        On the Rt-map page, choosing resolution=world, hitting the arrow button below the slider allows one to see the country Rt animation on how Rt's have changed over time in different countries (8/) pic.twitter.com/PvkJ98zSfrpic.twitter.com/Qs1O1z3MnO

        1 reply 2 retweets 4 likes
        Show this thread
      12. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        Here are the countries that currently have the highest Rt values. When the #s of daily new cases are small, estimated Rt values might not be stable. Note high Rt values of some countries are driven by outliers. One needs to look at both estimated Rt curves and # of case curves.pic.twitter.com/LAKuHASmI6

        1 reply 1 retweet 4 likes
        Show this thread
      13. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        On the Rt-map page, choosing resolution=US counties shows estimated Rt map for about 1200 counties that have sufficient data. When #s of daily new cases are small or there are single day spikes, estimated Rt's might not be stable. Caution is needed. Check both Rt & case curvespic.twitter.com/Y4Uiqs1IGV

        1 reply 2 retweets 2 likes
        Show this thread
      14. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        Visit the Explore State tab to compare the Rt trajectories between different counties within the same state. Here is the comparison between the counties in the state of MA. The ranked counties by Rt-values are given in the table below the mappic.twitter.com/yr8cDhng5n

        2 replies 1 retweet 3 likes
        Show this thread
      15. Xihong Lin‏Verified account @XihongLin 12 Jun 2020

        Here is a tutorial that shows how to use the site.pic.twitter.com/ksir3WJmLb

        2 replies 2 retweets 8 likes
        Show this thread
      16. Xihong Lin‏Verified account @XihongLin 4 Jul 2020

        We've added a new Rt forest plot in http://metrics.covid19-analysis.org  that compares the Rt values of all the US states & all the countries by sorting their Rt values from the highest to the lowest on any given date.pic.twitter.com/g5vpPBplUE

        1 reply 0 retweets 2 likes
        Show this thread
      17. Xihong Lin‏Verified account @XihongLin 5 Jul 2020

        Use multiple metrics. As a transmission rate est, Rt is a metrics on the multiplicative scale (not stable for small n). It does not tell the magnitude of spread on the absolute scale, eg., DL has Rt=1.6 & # of new cases=192, while FL has Rt=1.3 & # of new cases=9488. Check both.

        1 reply 1 retweet 0 likes
        Show this thread
      18. Xihong Lin‏Verified account @XihongLin 5 Jul 2020

        Rt estimates how rapid a spread is, but not the number of people infected. Although DL has a higher Rt than FL, the number of daily new infected cases is much smaller than FL, since it has a larger case base. So epidemic is more severe in FL than DL.

        1 reply 1 retweet 3 likes
        Show this thread
      19. Xihong Lin‏Verified account @XihongLin 5 Jul 2020

        The website http://metrics.covid19-analysis.org  hence provides multiple metrics. You can see both the Rt curve and the case curve, as well as the # of new cases, # of total cases, case rate, # of new deaths, # of total deaths, and death rate.

        1 reply 0 retweets 1 like
        Show this thread
      20. End of conversation

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