Sign in

Alexander Bartel

@ndevln.biostats.dev
25 followers 22 following 14 posts
PostsRepliesMedia
Alexander Bartel @ndevln.biostats.dev · 28/03/2026
It's just a solution for tracked changes and comments in Markdown. How do you support this currently, since you wrote your tool works like Google docs. Collaboration needs this to suggest changes and to discuss them. But you could implement it as a seperate layer, but why would you?
100
Alexander Bartel @ndevln.biostats.dev · 27/03/2026
Does it support CriticMarkup or something similar? github.com/CriticMarkup...
github.com
GitHub - CriticMarkup/CriticMarkup-toolkit: Various tools to use CriticMarkup in your daily workflow
Various tools to use CriticMarkup in your daily workflow - CriticMarkup/CriticMarkup-toolkit
100
Alexander Bartel @ndevln.biostats.dev · 27/03/2026
The good news: Prasse et al. from @ecdc.europa.eu show that even a moderate increase in vaccination coverage of 2.5–5% among sexually active people substantially reduces the risk of outbreaks. doi.org/qxd5 Vaccination against #mpox remains key. Find resources for Berlin here sidekicks.berlin/mpox/
doi.org
Modelling the outbreak risk of monkeypox virus clade Ib among MSM in the EU/EEA and the impact of targeted vaccination
Since the upsurge of monkeypox virus (MPXV) clade Ib in the Democratic Republic of the Congo and neighbouring countries in 2024, there have been multiple importations into Europe. So far, secondary tr...
011
Alexander Bartel @ndevln.biostats.dev · 27/03/2026
No evidence that clade Ib causes increased clinical severity compared to clade IIb. Furthermore, the WHO TAG-VE concludes that clade Ib should not exhibit immune escape against vaccine-induced immunity. cdn.who.int/media/docs/default-source/documents/epp/tag-ve/mpxv_clade_ib_risk_evaluation.pdf
cdn.who.int
111
Alexander Bartel @ndevln.biostats.dev · 27/03/2026
Our new rapid communication in @eurosurveillance.org: We currently observe mpox clade Ib transmission among MSM in Berlin. 35 cases mostly reported local exposure. Sequencing showed high genomic relatedness, suggesting a larger transmission network. Vaccination remains key. 🔗 doi.org/10.2807/1560...
Epidemiological curve showing the number of reported mpox cases in Berlin by reporting week, from week 45 of 2025 through week 10 of 2026. Case counts are low with up to three cases from weeks 45–49 of 2025, with primarily clade IIb and some unknown cases. The first clade Ib case is observed in week 50 with five cases overall in this week. Starting around week 1 of 2026, clade Ib cases begin appearing alongside clade IIb cases, while cases increase to up to five per week. From week 6 onward, there is an increase in reported mpox cases dominated by clade Ib, with nine cases in week 9.Phylogenetic tree of MPXV sequences. The tree is rooted with clade Ia sequences at the base, followed by a clearly labeled clade Ib branch that includes the majority of sequences shown. Within clade Ib sequences a tightly clustered group is shown. This cluster includes all Berlin and Germany MSM-associated sequences and a small number of sequences from Netherlands, Brazil and Belgium. Travel or household associated sequences from Germany interspersed throughout the clade Ib branch, which also includes sequences from the USA, DRC, Kenya, Uganda, India, Thailand, France, Pakistan, Sweden and Canada. Clade Ia sequences appear at the base of the tree as an outgroup.
233
Alexander Bartel @ndevln.biostats.dev · 11/02/2026
Change is hard, but Germany is building solutions: www.opendesk.eu
opendesk.eu
Die Office-Suite für die Öffentliche Verwaltung
openDesk bietet kollaborative Office-Anwendungen für die Öffentliche Verwaltung: Textverarbeitung, Chat, Dateifreigabe, Videokonferenzen und Projektmanagement.
020
Reposted by Alexander Bartel
Nils Gubela @nillegu.bsky.social · 08/01/2026
In our latest publication, we analyzed how transient reductions in contacts influenced the 2022 mpox outbreak. Read it here: www.nature.com/articles/s43...
nature.com
Client Challenge
111
Alexander Bartel @ndevln.biostats.dev · 29/10/2025
Hi, it think adding diagnostics would be really helpful. From the examples p_worse always seems to be quite high, even when |elpd_diff|<4. Could be confusing. Also there are also examples with |elpd_diff|<4 and diag only reports N<100. I would prefer it to report all warnings (N, elpd_diff, khat).
100
Alexander Bartel @ndevln.biostats.dev · 05/07/2025
Thanks :)
010
Alexander Bartel @ndevln.biostats.dev · 05/07/2025
I recommend Statistical Rethinking: youtube.com/playlist?lis... Please focus on statistical intuition and what constitutes evidence for a scientific hypothesis. Please avoid talking about significance and p-values all the time, these are mostly used as a way to avoid thinking about your data.
youtube.com
Statistical Rethinking 2023 - YouTube
See full course materials and topical outline here: https://github.com/rmcelreath/stat_rethinking_2024
130
Alexander Bartel @ndevln.biostats.dev · 04/07/2025
📦 My R package {ggsurveillance} now supports nested date scales. All thanks to the fantastic {legendry} package by @teunbrand.bsky.social 🔗 ggsurveillance.biostats.dev/ 🔗 teunbrand.github.io/legendry/ ggplot rules supreme #rstats #ggplot #DataViz
Nested Date scales in ggplot2:
> scale_x_datetime(date_breaks = "2 month", date_labels = "%b-%Y",
>                 guide = ggsurveillance::guide_axis_nested_date())Nested Date Scale example. Measles Cases per Month as an epicurve.
13611
Reposted by Alexander Bartel
John Green @johngreensbluesky.bsky.social · 07/02/2025
Just received this photo from a friend of a warehouse in Kinshasa. These are tuberculosis medications--ALREADY PAID FOR--that aren't being distributed due to the Trump Administration's stop work order. TB treatment is being interrupted in SO many patients around the world. What does that mean? (1/2)
Photograph of a warehouse in Kinshasa where unboxed tuberculosis medications are going undistributed due to the stop work order by the Trump Administration.
15971262971
Reposted by Alexander Bartel
CRAN Package Updates Bot @cranberriesfeed.bsky.social · 31/01/2025
New CRAN package ggsurveillance with initial version 0.1.1 #rstats cran.r-project.org/package=ggsurvei…
cran.r-project.org
CRAN: Package ggsurveillance
Create epicurves or epigantt charts in 'ggplot2'. Prepare data for visualisation or other reporting for infectious disease surveillance and outbreak investigation. Includes functions to solve date based transformations for common reporting tasks, like (A) seasonal date alignment for respiratory disease surveillance, (B) date-based case binning based on specified time intervals like isoweek, epiweek, month and more, (C) automated detection and marking of the new year based on the date/datetime axis of the 'ggplot2'. An introduction on how to use epicurves can be found on the US CDC website (2012, &lt;<a href="https://www.cdc.gov/training/quicklearns/epimode/index.html" target="_top">https://www.cdc.gov/training/quicklearns/epimode/index.html</a>&gt;).
002
Alexander Bartel @ndevln.biostats.dev · 24/01/2025
PMC is mirrored in Europe europepmc.org And Medline was updated yesterday: ftp.ncbi.nlm.nih.gov/pubmed/updat... Let's wait for the update today and see what happens.
europepmc.org
Europe PMCHome - Europe PMC
Europe PMC is an archive of life sciences journal literature.
030
Alexander Bartel @ndevln.biostats.dev · 24/01/2025
europepmc.org Komplette Kopie von PMC und die Suche sollte auch eine Medline/pubmed Kopie durchsuchen. Zukünftig muss die EU dann das updaten von Medline (Europe Edition) übernehmen.
europepmc.org
Europe PMCHome - Europe PMC
Europe PMC is an archive of life sciences journal literature.
040
Reposted by Alexander Bartel
Emanuel Wyler @ewyler.bsky.social · 18/12/2024
Looking for ways to improve detection of viral RNAs from wastewater? Check out our technical paper by Berliner Wasserbetriebe, Lageso Berlin, Amedes and @mdc-berlin.bsky.social on the use of inhibitor removal columns for better sensitivity: www.mdpi.com/2076-2607/12...
mdpi.com
Effective Inhibitor Removal from Wastewater Samples Increases Sensitivity of RT-dPCR and Sequencing Analyses and Enhances the Stability of Wastewater-Based Surveillance
Wastewater-based surveillance (WBS) is a proven tool for monitoring population-level infection events. Wastewater contains high concentrations of inhibitors, which contaminate the total nucleic acids ...
0126
Alexander Bartel @ndevln.biostats.dev · 03/08/2024
Scheint jetzt alles KP.3 zu sein. Aber KP.3 hat sich aus JN.1 entwickelt. Ganz was neues ist es also nicht. Quelle: data.lageso.de/lageso/coron...
Ergebnisse der SARS-CoV-2 Abwassersequenzierung der Berliner Klärwerke Ruhleben, Schönerlinde und Waßmannsdorf.
100
Alexander Bartel @ndevln.biostats.dev · 20/07/2024
In Düsseldorf wurde die Methode nicht geändert und da sieht es schlimmer aus: edoc.rki.de/handle/17690... Viele Städte in BW sind auch dabei schnell aufzuholen. Leider werden beim RKI für Berlin die Rohdaten ohne Korrektur für die Umstellung gezeigt.
edoc.rki.de
Abwassersurveillance zu SARS-CoV-2
020