Sign in

James Azam

@jamesazam.bsky.social
427 followers 601 following 48 posts

Research Fellow analysing multi-pathogen wastewater data and developing maths/stats models for polio eradication. Previously RSE at Epiverse TRACE Initiative. jamesmbaazam.github.io #rstats

PostsRepliesMedia
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 28/09/2026
A few years ago we (Kelly Charniga @sangwoopark.bsky.social et al.) did some thinking on how we should estimate and report epidemiological delay distributions (i.e incubation periods etc. etc.). journals.plos.org/ploscompbiol...
journals.plos.org
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strat...
21510
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 05/08/2026
#julia for infectious disease modelling workshop @lshtm.bsky.social in September community.epinowcast.org/t/topic/427
community.epinowcast.org
𝗥𝗲𝗴𝗶𝘀𝘁𝗲𝗿 𝗬𝗼𝘂𝗿 𝗜𝗻𝘁𝗲𝗿𝗲𝘀𝘁: 𝗠𝗼𝗱𝗲𝗹𝗹𝗶𝗻𝗴 𝗘𝗽𝗶𝗱𝗲𝗺𝗶𝗰𝘀 𝘄𝗶𝘁𝗵 𝗝𝘂𝗹𝗶𝗮 𝗪𝗼𝗿𝗸𝘀𝗵𝗼𝗽
We are hosting a free 3-day workshop on 𝟭𝟲𝘁𝗵-𝟭𝟴𝘁𝗵 𝗼𝗳 𝗦𝗲𝗽𝘁𝗲𝗺𝗯𝗲𝗿 𝟮𝟬𝟮𝟲 at 𝗟𝗦𝗛𝗧𝗠! Participants will learn how to use the Julia programming language to build deterministic models from first principles, st...
173
Reposted by James Azam
CMMID @cmmid-lshtm.bsky.social · 06/08/2026
📊 Working in #InfectiousDisease modelling? It’s your last chance to apply for our @lshtm.bsky.social short course: Model Fitting and Inference for Infectious Disease Dynamics Running from 7-10 Sept 2026 #PublicHealth Apply by 23:59 BST on 7 August 🔽 www.lshtm.ac.uk/study/course...
156
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 22/05/2026
Estimating the current size of the 2026 DRC Bundibugyo virus outbreak: a joint Bayesian re-analysis of the McCabe et al. report w/ @kathsherratt.bsky.social Sam Brand and @sbfnk.bsky.social
22915
Reposted by James Azam
Adam Kucharski @adamjkucharski.bsky.social · 06/05/2026
"Based on the dataset you shared, US and UK responses differ mainly in tone, intensity, and wording style, even though they express similar emotional states" New post on what happened when I got Copilot to do some data analysis: kucharski.substack.com/p/real-signa...
kucharski.substack.com
Real signals or artificial stereotypes?
Adventures with a cultural Copilot
15338142
James Azam @jamesazam.bsky.social · 13/01/2026
Oh really? it works for me and I don't see a paywall. Maybe try a different browser?
100
James Azam @jamesazam.bsky.social · 20/10/2025
Bring it all together with... (3/3) - Gabry, J., Simpson, D., Vehtari, A., Betancourt, M., & Gelman, A. (2019). Visualization in Bayesian Workflow. Journal of the Royal Statistical Society Series A: Statistics in Society, 182(2), 389–402. doi.org/10.1111/rssa...
doi.org
Visualization in Bayesian Workflow
Abstract. Bayesian data analysis is about more than just computing a posterior distribution, and Bayesian visualization is about more than trace plots of M
020
James Azam @jamesazam.bsky.social · 20/10/2025
Bring it all together with... (2/3) - Gelman, A., Vehtari, A., Simpson, D., Margossian, C. C., Carpenter, B., Yao, Y., Kennedy, L., Gabry, J., Bürkner, P.-C., & Modrák, M. (2020). Bayesian Workflow (No. arXiv:2011.01808). arXiv. arxiv.org/abs/2011.01808
arxiv.org
Bayesian Workflow
The Bayesian approach to data analysis provides a powerful way to handle uncertainty in all observations, model parameters, and model structure using probability theory. Probabilistic programming lang...
110
James Azam @jamesazam.bsky.social · 20/10/2025
Bring it all together with... (1/3) - Schad, D. J., Betancourt, M., & Vasishth, S. (2020). Toward a principled Bayesian workflow in cognitive science (No. arXiv:1904.12765). arXiv. arxiv.org/abs/1904.12765
arxiv.org
Toward a principled Bayesian workflow in cognitive science
Experiments in research on memory, language, and in other areas of cognitive science are increasingly being analyzed using Bayesian methods. This has been facilitated by the development of probabilist...
110
James Azam @jamesazam.bsky.social · 20/10/2025
Expand your knowledge with... (3/3) - Veenman, M., Stefan, A. M., & Haaf, J. M. (2023). Bayesian hierarchical modeling: An introduction and reassessment. Behavior Research Methods. doi.org/10.3758/s134...
doi.org
Bayesian hierarchical modeling: an introduction and reassessment - Behavior Research Methods
With the recent development of easy-to-use tools for Bayesian analysis, psychologists have started to embrace Bayesian hierarchical modeling. Bayesian hierarchical models provide an intuitive account ...
110
James Azam @jamesazam.bsky.social · 20/10/2025
Expand your knowledge with... (2/3) - Lemoine, N. P. (2019). Moving beyond noninformative priors: Why and how to choose weakly informative priors in Bayesian analyses. Oikos, 128(7), 912–928. doi.org/10.1111/oik....
doi.org
Moving beyond noninformative priors: why and how to choose weakly informative priors in Bayesian analyses
Throughout the last two decades, Bayesian statistical methods have proliferated throughout ecology and evolution. Numerous previous references established both philosophical and computational guideli...
120
James Azam @jamesazam.bsky.social · 20/10/2025
Expand your knowledge with... (1/3) - Säilynoja, T., Johnson, A. R., Martin, O. A., & Vehtari, A. (2025). Recommendations for visual predictive checks in Bayesian workflow (No. arXiv:2503.01509). arXiv. doi.org/10.48550/arX...
doi.org
Recommendations for visual predictive checks in Bayesian workflow
A key step in the Bayesian workflow for model building is the graphical assessment of model predictions, whether these are drawn from the prior or posterior predictive distribution. The goal of these ...
120
James Azam @jamesazam.bsky.social · 20/10/2025
Start with... (7/7) - Nicenboim, B., & Vasishth, S. (2016). Statistical methods for linguistic research: Foundational Ideas—Part II. Language and Linguistics Compass, 10(11), 591–613.
110
James Azam @jamesazam.bsky.social · 20/10/2025
Start with... (6/7) - Goligher, E. C., Heath, A., & Harhay, M. O. (2024). Bayesian statistics for clinical research. The Lancet, 404(10457), 1067–1076. doi.org/10.1016/S014...
doi.org
Redirecting
110
James Azam @jamesazam.bsky.social · 20/10/2025
Start with... (5/7) - van de Schoot, R., Depaoli, S., King, R., Kramer, B., Märtens, K., Tadesse, M. G., Vannucci, M., Gelman, A., Veen, D., Willemsen, J., & Yau, C. (2021). Bayesian statistics and modelling. Nature Reviews Methods Primers, 1(1), 1–26. doi.org/10.1038/s435...
doi.org
Bayesian statistics and modelling - Nature Reviews Methods Primers
This Primer on Bayesian statistics summarizes the most important aspects of determining prior distributions, likelihood functions and posterior distributions, in addition to discussing different appli...
110
James Azam @jamesazam.bsky.social · 20/10/2025
Start with... (4/7) - Vasishth, S., Nicenboim, B., Beckman, M. E., Li, F., & Kong, E. J. (2018). Bayesian data analysis in the phonetic sciences: A tutorial introduction. Journal of Phonetics, 71, 147–161. doi.org/10.1016/j.wo...
doi.org
Redirecting
110
James Azam @jamesazam.bsky.social · 20/10/2025
Start with... (3/7) - Etz, A., Gronau, Q. F., Dablander, F., Edelsbrunner, P. A., & Baribault, B. (2018). How to become a Bayesian in eight easy steps: An annotated reading list. Psychonomic Bulletin & Review, 25(1), 219–234. doi.org/10.3758/s134...
doi.org
How to become a Bayesian in eight easy steps: An annotated reading list - Psychonomic Bulletin & Review
In this guide, we present a reading list to serve as a concise introduction to Bayesian data analysis. The introduction is geared toward reviewers, editors, and interested researchers who are new to B...
110
James Azam @jamesazam.bsky.social · 20/10/2025
Start with... (2/7) - Kruschke, J. K., & Liddell, T. M. (2018). Bayesian data analysis for newcomers. Psychonomic Bulletin & Review, 25(1), 155–177. doi.org/10.3758/s134...
doi.org
Bayesian data analysis for newcomers - Psychonomic Bulletin & Review
This article explains the foundational concepts of Bayesian data analysis using virtually no mathematical notation. Bayesian ideas already match your intuitions from everyday reasoning and from tradit...
110
James Azam @jamesazam.bsky.social · 20/10/2025
Start with... (1/7) - Etz, A. (2018). Introduction to the Concept of Likelihood and Its Applications. Advances in Methods and Practices in Psychological Science, 1(1), 60–69. doi.org/10.1177/2515... doi.org/10.1111/lnc3...
doi.org
Introduction to the Concept of Likelihood and Its Applications - Alexander Etz, 2018
This Tutorial explains the statistical concept known as likelihood and discusses how it underlies common frequentist and Bayesian statistical methods. The artic...
110
James Azam @jamesazam.bsky.social · 20/10/2025
Bayesian Data Analysis Primers/Tutorials I gathered these primers for learning bayesian data analysis, mainly for myself but I hope they are helpful to you too. If you know of similar articles, do share them in the comments. #bayesiananalysis #datascience #machinelearning #rstats #python
1257
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 17/10/2025
#epinowcast 0.4.0 is out! This release has been a long time coming and contains work from many contributors. It includdes new features, better better and clearer documentation. package.epinowcast.org/news/index.h...
package.epinowcast.org
Changelog
1107
Reposted by James Azam
Thomas Lin Pedersen @thomasp85.com · 11/09/2025
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
9851281
James Azam @jamesazam.bsky.social · 13/09/2025
It covers everything from introductions to methods, results, tables/figures, discussions, journal choice, and even how to respond to reviewers. If you’re writing, teaching, or mentoring, this is gold. (3/3)
010
James Azam @jamesazam.bsky.social · 13/09/2025
Its strengths are: - Clear & simple - 1-page papers with checklists - Useful for any field - Perfect for teaching & refreshing (2/3)
100
James Azam @jamesazam.bsky.social · 13/09/2025
My go-to resource for scientific writing The Writing Tips Series by the Journal of Clinical Epidemiology is hands down one of the best guides for academic writing: www.sciencedirect.com/special-issu... (1/3) #AcademicWriting #Research #PhDLife #ScientificWriting #Masters #PhD #AcademicChatter
130
James Azam @jamesazam.bsky.social · 13/09/2025
@seabbs.bsky.social Isn't this the dream for all our users?
110
James Azam @jamesazam.bsky.social · 13/09/2025
A developer's love language.
010
James Azam @jamesazam.bsky.social · 13/09/2025
I could curate that for you.
100
James Azam @jamesazam.bsky.social · 10/09/2025
5. Nature Methods – Statistics for Biologists / Points of Significance www.nature.com/collections/... Great primers on error bars, power, regression, correlation vs causation, and visualisation.
nature.com
Statistics for Biologists
A collection of articles from the publisher of Nature that discusses statistical issues biologists should be aware of and provides practical advice to improve the statistical rigor and reproducibility...
010
James Azam @jamesazam.bsky.social · 10/09/2025
4. The Lancet’s Epidemiology Series 2005 www.thelancet.com/series-do/ep... Goes deeper into sample size, controls, likelihood ratios, and multiplicity in trials.
thelancet.com
Epidemiology 2005
Appropriate sample sizing, selection of controls in case-control studies, and clear end-points and interpretation of subgroup analyses are crucial for robust epidemiological research.
210
James Azam @jamesazam.bsky.social · 10/09/2025
3. The Lancet’s Epidemiology Series 2002 www.thelancet.com/series-do/ep... Introduces study designs, bias, cohort & case-control studies, randomisation, blinding, and screening.
thelancet.com
Epidemiology 2002
Increasing demands on the time of clinicians today reduce their opportunities to stay abreast of medical literature, and many report that they cannot read the literature critically. Information on res...
110
James Azam @jamesazam.bsky.social · 10/09/2025
2. Statistics Notes – BMJOpen www.bmj.com/specialties/... Short explainers on P values from confidence intervals, bootstrap methods, odds ratios, sampling error, and more.
bmj.com
Statistics notes
120
James Azam @jamesazam.bsky.social · 10/09/2025
1. Statistics at Square One – BMJOpen www.bmj.com/about-bmj/re... Covers the basics: data display, confidence intervals, t-tests, chi-squared tests, regression, survival analysis, and study design.
bmj.com
Statistics at Square One | The BMJ
Ninth Edition T D V Swinscow Revised by M J Campbell, University of Southampton Copyright BMJ Publishing Group 1997 NB: Readers occasionally point out errors in this book and remind us that there ...
110
James Azam @jamesazam.bsky.social · 10/09/2025
These are great for teaching, refreshing your memory, or sharing with colleagues new to statistical and epidemiological methods. Do you know of other similar resources worth adding to this list?
110
James Azam @jamesazam.bsky.social · 10/09/2025
I’ve found these really useful resources for clear, accessible explanations of core statistics and epidemiology methods and concepts. These are great for teaching, refreshing your memory, or sharing with colleagues new to statistical and epidemiological methods.
110
James Azam @jamesazam.bsky.social · 10/09/2025
Statistics & Epidemiology Made Simple Without Jargon - My Go-To Resources #statistics #epidemiology #biostatistics #dataanalytics #datascience
media.tenor.com
a black and white drawing of a boy covering his face with his hands and the word statistics .
ALT: a black and white drawing of a boy covering his face with his hands and the word statistics .
441
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 09/06/2025
The other major addition in this release is lovely new stan docs thanks to @jamesazam.bsky.social primarycensored.epinowcast.org/stan/group__...
primarycensored.epinowcast.org
primarycensored: Primary Censored Distributions Functions (Vectorized)
021
Reposted by James Azam
Jiaxin ZHOU @jiaxinz.bsky.social · 11/07/2025
Back from Kenya, where I had the privilege of co-leading an Outbreak Data Science workshop with @jamesazam.bsky.social at KEMRI-Wellcome Trust. I'm proud to see open, reproducible tools like #EpiverseTRACE @epiverse-trace.bsky.social making a difference.
075
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 15/05/2025
Just been looking at deepwiki as a way of summarising packages/presenting more interactive documentation via chatting to an LLM. On the face of it seems really useful (though as normal small errors here an there) Thanks @jamesazam.bsky.social for the headsup!
deepwiki.com
epinowcast/epidist | DeepWiki
This document provides a comprehensive introduction to the `epidist` package, a specialized R package for estimating epidemiological delay distributions using Bayesian methods. The package addresses k
131
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 07/05/2025
Do you like situational awareness of infectious diseases (who doesn't). Do you like thinking about modelling with this aim in mind? Do you feel like its a bit of a niche and hard to find people to talk to about it? We have a forum: community.epinowcast.org for you.
community.epinowcast.org
Epinowcast
A community to discuss epinowcast and real-time infectious disease analysis more generally
1137
James Azam @jamesazam.bsky.social · 14/04/2025
Easier to search for stan_docs than just docs??
000
Reposted by James Azam
iddconf.bsky.social @iddconf.bsky.social · 09/04/2025
2025 here we come! iddconf.org IDDconf will be September 2-4 2025 in Ambleside. Ticket info coming soon.
iddconf.org
IDDconf 2025
A Conference on Infectious Disease Dynamics. IDDconf is the second instalment of a new meeting series focussing on innovative research in infectious disease dynamics.
0149
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 08/04/2025
Just got asked about my review processes. I don't do that much as I am not that into the whole racket especially not whilst on a short-term contract but this is my kind of approach...
111
Reposted by James Azam
Epiverse TRACE @epiverse-trace.bsky.social · 08/04/2025
📦 R Package of the Week: {linelist} Turn data frames into #linelist objects by: ✅ Tagging key epidemiological variables (so you're not tied to column names) ✅ Validation to ensure tagged variables are of the correct type ✅ Safeguard against accidental loss of tagged variables during wrangling 1/3
132
James Azam @jamesazam.bsky.social · 08/04/2025
I also recommend the following articles: - How to Be a Statistical Detective: lnkd.in/eaZGfmHZ - Ten Simple Rules for Reviewers: lnkd.in/e6Y86YM7 Feel free to share any resources you’ve found useful.
100
James Azam @jamesazam.bsky.social · 08/04/2025
- Elsevier Reviewer Hub: lnkd.in/eYYmv_cn - PLOS Reviewer Resources: lnkd.in/emhvkP4Y - Springer Nature Peer Review Guide: lnkd.in/etJbDvRP - Nature Masterclass – Being an Effective Peer Reviewer: lnkd.in/e3ibSWbx
100
James Azam @jamesazam.bsky.social · 08/04/2025
Interested in peer reviewing or looking to improve your skills? Peer review is an important part of the research process, but many people don’t receive much guidance on how to do it well. Fortunately, there are several helpful resources available: #research #peerreview #academicwriting #phdchat
media.tenor.com
a woman is looking at a piece of paper with a be + logo in the background
ALT: a woman is looking at a piece of paper with a be + logo in the background
120
Reposted by James Azam
Sam Abbott @seabbs.bsky.social · 07/04/2025
Flags that having the ability to specify functions as arguments in stan would be really quite amazing as not having this (or a class system) makes the code a lot more convoluted than the R equiv See here for the R: github.com/epinowcast/p...
github.com
primarycensored/R/pprimarycensored.R at f051ac82b1c6ea9bfbc280a6d7c15c91aab05b71 · epinowcast/primarycensored
Primary event censored distributions. Contribute to epinowcast/primarycensored development by creating an account on GitHub.
011
James Azam @jamesazam.bsky.social · 07/04/2025
I really enjoyed doing this (with feedback from @seabbs.bsky.social and the amazing stan forum). I'm now porting over learned wisdom to EpiNow2, epinowcast, EpiSewer, and other stan-heavy R packages. Here's a short clip showing the before and after #mcstan #stan #rpackage
121
Reposted by James Azam
UK Health Security Agency @ukhsa.bsky.social · 01/04/2025
Last week we published our first annual report on infectious disease trends. 📊 The report brings together all the key data from 2023 to early 2025 and outlines the steps our organisation is taking to tackle these threats. Read the full report 🔗🔽 www.gov.uk/government/p...
1118