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So @NickHudsonCT seems to think @Kevin_McKernan “DEMOLISHED” my recent thread on @ClareCraigPath ‘s pretty awful PANDA document https://twitter.com/dr_barrett/status/1378878486027309057?s=21
Let’s">https://twitter.com/dr_barret... examine that proposition - I ask you to please share&retweet as this will be fun ..
#COVID19 #Medtwitter #scicoms
Let’s">https://twitter.com/dr_barret... examine that proposition - I ask you to please share&retweet as this will be fun ..
#COVID19 #Medtwitter #scicoms
This is Kevin seen in video by “vaccines can make you time travel” @naomirwolf (senior fellow at AEIR based at #GreatBarrington) - he is showing her a fungus on agar plate because that has something to do with sars-CoV2 diagnostic PCRs ... 
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🤷🏻♂️" title="Achselzuckender Mann (heller Hautton)" aria-label="Emoji: Achselzuckender Mann (heller Hautton)">
" title="This is Kevin seen in video by “vaccines can make you time travel” @naomirwolf (senior fellow at AEIR based at #GreatBarrington) - he is showing her a fungus on agar plate because that has something to do with sars-CoV2 diagnostic PCRs ... https://abs.twimg.com/emoji/v2/... draggable="false" alt="🤷🏻♂️" title="Achselzuckender Mann (heller Hautton)" aria-label="Emoji: Achselzuckender Mann (heller Hautton)">">
" title="This is Kevin seen in video by “vaccines can make you time travel” @naomirwolf (senior fellow at AEIR based at #GreatBarrington) - he is showing her a fungus on agar plate because that has something to do with sars-CoV2 diagnostic PCRs ... https://abs.twimg.com/emoji/v2/... draggable="false" alt="🤷🏻♂️" title="Achselzuckender Mann (heller Hautton)" aria-label="Emoji: Achselzuckender Mann (heller Hautton)">">
" title="This is Kevin seen in video by “vaccines can make you time travel” @naomirwolf (senior fellow at AEIR based at #GreatBarrington) - he is showing her a fungus on agar plate because that has something to do with sars-CoV2 diagnostic PCRs ... https://abs.twimg.com/emoji/v2/... draggable="false" alt="🤷🏻♂️" title="Achselzuckender Mann (heller Hautton)" aria-label="Emoji: Achselzuckender Mann (heller Hautton)">">
Kevin dropped a number of “clangers” trying to rebut my thread some worthy of LONG threads... (those that follow me know I do LONG https://abs.twimg.com/emoji/v2/... draggable="false" alt="🧵" title="Thread" aria-label="Emoji: Thread">s)- for now let’s look at this one - I might end up doing a series on Kevin’s @BadCOVID19Takes for now let’s look at this criticism https://abs.twimg.com/emoji/v2/... draggable="false" alt="👇🏻" title="Rückhand Zeigefinger nach unten (heller Hautton)" aria-label="Emoji: Rückhand Zeigefinger nach unten (heller Hautton)">
s)- for now let’s look at this one - I might end up doing a series on Kevin’s @BadCOVID19Takes for now let’s look at this criticism https://abs.twimg.com/emoji/v2/... draggable="false" alt="👇🏻" title="Rückhand Zeigefinger nach unten (heller Hautton)" aria-label="Emoji: Rückhand Zeigefinger nach unten (heller Hautton)">" title="Kevin dropped a number of “clangers” trying to rebut my thread some worthy of LONG threads... (those that follow me know I do LONG https://abs.twimg.com/emoji/v2/... draggable="false" alt="🧵" title="Thread" aria-label="Emoji: Thread">s)- for now let’s look at this one - I might end up doing a series on Kevin’s @BadCOVID19Takes for now let’s look at this criticism https://abs.twimg.com/emoji/v2/... draggable="false" alt="👇🏻" title="Rückhand Zeigefinger nach unten (heller Hautton)" aria-label="Emoji: Rückhand Zeigefinger nach unten (heller Hautton)">" class="img-responsive" style="max-width:100%;"/>
It relates to this tweet in my https://abs.twimg.com/emoji/v2/... draggable="false" alt="🧵" title="Thread" aria-label="Emoji: Thread">- based on this Nat Comms paper https://www.nature.com/articles/s41467-020-20235-8">https://www.nature.com/articles/... Kevin takes issue with my DENOMINATOR in Postive Predictive Value calculation ... https://twitter.com/dr_barrett/status/1378878562418184193">https://twitter.com/dr_barret...
Refresher for benefit of @Kevin_McKernan - Positive Predictive Value is probability that a positive test result is a TRUE positive. The BASIC formula for PPV is this https://abs.twimg.com/emoji/v2/... draggable="false" alt="👇🏻" title="Rückhand Zeigefinger nach unten (heller Hautton)" aria-label="Emoji: Rückhand Zeigefinger nach unten (heller Hautton)">
" title="Refresher for benefit of @Kevin_McKernan - Positive Predictive Value is probability that a positive test result is a TRUE positive. The BASIC formula for PPV is this https://abs.twimg.com/emoji/v2/... draggable="false" alt="👇🏻" title="Rückhand Zeigefinger nach unten (heller Hautton)" aria-label="Emoji: Rückhand Zeigefinger nach unten (heller Hautton)">" class="img-responsive" style="max-width:100%;"/>
So let’s look at Kevin’s criticism again ... one thing Kevin wants is me to include the probable cases (false negatives) in my PPV calculation but False negatives means TESTED NEGATIVE - therefore they have NO PLACE in a PPV calculation #Kevinfail ... so there is that ... https://abs.twimg.com/emoji/v2/... draggable="false" alt="🤦♂️" title="Mann schlägt sich die Hand vors Gesicht" aria-label="Emoji: Mann schlägt sich die Hand vors Gesicht">
" title="So let’s look at Kevin’s criticism again ... one thing Kevin wants is me to include the probable cases (false negatives) in my PPV calculation but False negatives means TESTED NEGATIVE - therefore they have NO PLACE in a PPV calculation #Kevinfail ... so there is that ... https://abs.twimg.com/emoji/v2/... draggable="false" alt="🤦♂️" title="Mann schlägt sich die Hand vors Gesicht" aria-label="Emoji: Mann schlägt sich die Hand vors Gesicht">" class="img-responsive" style="max-width:100%;"/>
Now let’s get this the next claim “only 773 had enough DNA to be sent for sequencing” - is that a true claim ... well no ... only 773 samples were sent by District Health Boards - as retention and sending was not mandatory at time TY for confirming that @Jemma_Geoghegan
Importantly we can see a further follow up of the August Auckland outbreak which had a total of 179 cases ... the same team also carried out sequencing of these samples ... I saw the pre-print but now these results are published .. https://twitter.com/jemma_geoghegan/status/1378047894767378432?s=12">https://twitter.com/jemma_geo...
This time they received 172/179 samples or 96% of samples from the outbreak - resulting in 145 genomes recovered ; this suggests a PPV of at Least 84% (145/172) or EVEN assuming samples not sent would be unsuccessful in sequencing 81% (145/179)
This is in the context of LOWER prevalence* in test population during the August outbreak https://abs.twimg.com/emoji/v2/... draggable="false" alt="👇🏻" title="Rückhand Zeigefinger nach unten (heller Hautton)" aria-label="Emoji: Rückhand Zeigefinger nach unten (heller Hautton)"> now what did we learn about disease prevalence & PPV ; we expect PPV lower (FDR higher) ... but MINIMUM PPV is relatively preserved despite FAR LOWER prevalence
https://twitter.com/dr_barrett/status/1378878555044601858?s=21">https://twitter.com/dr_barret...
https://twitter.com/dr_barrett/status/1378878555044601858?s=21">https://twitter.com/dr_barret...
now what did we learn about disease prevalence & PPV ; we expect PPV lower (FDR higher) ... but MINIMUM PPV is relatively preserved despite FAR LOWER prevalence https://twitter.com/dr_barret..." title="This is in the context of LOWER prevalence* in test population during the August outbreak https://abs.twimg.com/emoji/v2/... draggable="false" alt="👇🏻" title="Rückhand Zeigefinger nach unten (heller Hautton)" aria-label="Emoji: Rückhand Zeigefinger nach unten (heller Hautton)"> now what did we learn about disease prevalence & PPV ; we expect PPV lower (FDR higher) ... but MINIMUM PPV is relatively preserved despite FAR LOWER prevalence https://twitter.com/dr_barret..." class="img-responsive" style="max-width:100%;"/>
In short the PPV based on % of samples in which genomes could be recovered is broadly similar to the prior study -it argues very much against any premise that Kevin is making that the samples never sent were or poorer quality / lower Ct / lower viral loads/ lower PPV etc etc
I have already pointed out that only 4% of NZ cases don’t have a infection source identified - so the PPV is likely much higher than the already high % (given low prevalence) suggested by the viral genomic studies ... https://twitter.com/dr_barrett/status/1378878555044601858">https://twitter.com/dr_barret...
Even taking this bottom estimate of PPV - a middle of road sensitivity 75% (this genomic study suggests) suggests a specificity of the PCR of greater than 99.99% or less than 1 in 10,000 false positive rate ... In short the FPR is very very small ...
I do know this a very approximate calculation as sensitivity is a estimate (which means true prevalence is an estimate) - this is meant to just illustrate the point only @igdstrachan could probably do a better job at explaining the likely specificity from these numbers ...
So in short I don’t think @Kevin_McKernan “DESTROYED” my debunk of @ClareCraigPath’s PANDA document but rather exposed his own lack of understanding of the literature and how to evaluate characteristics of diagnostic tests ...
So I hope this retort did not disappoint .. @andrew_croxford ... for the record Kevin I didn’t need @MackayIM’s help on this - I am no high level expert but I can read a paper and understand basic concepts . https://twitter.com/andrew_croxford/status/1380264527602802694">https://twitter.com/andrew_cr...
Retweet and share if you enjoyed. ... @PanData19 a terrible organisation and needs to be challenged in their claims. @SiouxsieW @jneill @BadCOVID19Takes @DrDomPimenta @killeen_gerry @s8mb @cjsnowdon @Kevin_Fong @TakethatCt
