Matthew Hall

@fgonzalef It helps somewhat, but it doesn't prevent the problem.

@mdhall272 What's the effect of increasing the number of categories?

Something we noticed when analysing HIV sequences with the classic Gamma rate heterogeneity model biorxiv.org/content/10.110…

@lixingguang It's in the preprint. FreeRate is not subject to this problem but maybe is best seen as a stopgap.

@mdhall272 do you have any better choice?

New research article Demographics of sources of #HIV-1 transmission in #Zambia: a molecular epidemiology analysis in the HPTN 071 #PopART study thelancet.com/journals/lanmi… #InfectiousDiseases

👏Congratulations to @mdhall272 and team on their publication in the Lancet. The study showed that men 25-40 years account for a disproportionate fraction of #HIV transmission. thelancet.com/journals/lanmi… @ChristoPhraser @tanyagolubchik @drlimbada @DrSimwinga @helen_ayles

Super happy about our new paper in @PNASNexus! It is a collaborative approach that combines phylogeny, network theory and epidemic modelling to estimate the pandemic potential of emergent variants from limited/noisy data doi.org/10.1093/pnasne… a 🧵

When can phylogenetic methods alone predict the direction of transmission? We (@Chjulian, @katrina_lythgoe, @mdhall272, @BaxtrJames et al.) help to quantify this in our new @PNASNews study out today! doi.org/10.1073/pnas.2…

Hey #rstats, delighted to bring you another issue of R Weekly (@rweekly_org) 🔗: rweekly.org/2022-W30.html Highlights 🌟: 1⃣ {nplyr}: Nested data manipulation - @markjrieke 2⃣ {rtweet}: ✅ consistent output - @Lluis_Revilla 3⃣ {ggarchery}: Flexible ↕️ geoms for #ggplot2 - M. Hall

My little package ggarchery github.com/mdhall272/ggar… makes R Weekly #rstats

Summer internship, aimed at 2nd/3rd year undergrads or Masters students, at @bdi_oxford with @katrina_lythgoe and myself on SARS-CoV-2 coinfections bdi.ox.ac.uk/study/bdi-summ…

The main enhancements being a) to allow arrowheads mid-segment, and b) to shave the starts and ends of segments to make it so that arrows don’t hit the things they point at or from.

I shoved the things I always seem to end up doing with arrows in ggplot2 into a package github.com/mdhall272/ggar… cran.r-project.org/web/packages/g…

New work by @valentindruelle on mutations that make the HIV-1 genome closer to the global HIV consensus: - These mutations are positively selected within host. - At the population level, these mutations result in spuriously low rate estimates. 1/ biorxiv.org/content/10.110…

We discovered a highly virulent variant of HIV in the Netherlands, now published in Science. Levels of virus 3.5-5.5x higher, immune cell decline 2x faster, increased transmissibility. Striking eg of evolution. W @ChristoPhraser @HIVMonitoringNL & partners science.org/doi/10.1126/sc…

Work with @ISARIC1 on the change in hospital journey for COVID-19 over the first year of the pandemic now published at @eLife elifesciences.org/articles/70970

Me taking a COVID test in 2020: sanitising entire room, triple washing hands, following instructions page by page. Me taking one now: In one smooth movement wipe crumbs off nearest surface, open the shot of buffer solution with my teeth and start violating my nostril.

New paper with @ISARIC1 (non-genomic) on variations in the hospital journey of COVID-19 patients during last year. Main cautionary point - using e.g. death or ICU admission as an outcome variable is inadvisable during a rapidly-changing situation. elifesciences.org/articles/70970