James Azam
@jamesazam.bsky.social
Research Fellow analysing multi-pathogen wastewater data and developing maths/stats models for polio eradication. Previously RSE at Epiverse TRACE Initiative. https://jamesmbaazam.github.io/ #rstats
Pinned
James Azam
@jamesazam.bsky.social
· Apr 7
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
Here's a short clip showing the before and after #mcstan #stan #rpackage
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
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
October 20, 2025 at 11:51 AM
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
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
Reposted by James Azam
#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/news/index.h...
Changelog
package.epinowcast.org
October 17, 2025 at 3:10 PM
#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/news/index.h...
Reposted by James Azam
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
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
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 11:20 AM
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
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
September 13, 2025 at 11:23 AM
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
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
A developer's love language.
Anyone else compulsively try to read every page of docs before using a library? It's a huge waste of time but I can't stop! 😂
September 13, 2025 at 11:15 AM
A developer's love language.
Statistics & Epidemiology Made Simple Without Jargon - My Go-To Resources
#statistics #epidemiology #biostatistics #dataanalytics #datascience
#statistics #epidemiology #biostatistics #dataanalytics #datascience
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 .
media.tenor.com
September 10, 2025 at 3:47 PM
Statistics & Epidemiology Made Simple Without Jargon - My Go-To Resources
#statistics #epidemiology #biostatistics #dataanalytics #datascience
#statistics #epidemiology #biostatistics #dataanalytics #datascience
Reposted by James Azam
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/stan/group__...
primarycensored: Primary Censored Distributions Functions (Vectorized)
primarycensored.epinowcast.org
June 9, 2025 at 3:22 PM
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/stan/group__...
Reposted by James Azam
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.
July 11, 2025 at 2:01 PM
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.
Reposted by James Azam
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!
On the face of it seems really useful (though as normal small errors here an there)
Thanks @jamesazam.bsky.social for the headsup!
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
deepwiki.com
May 15, 2025 at 1:46 PM
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!
On the face of it seems really useful (though as normal small errors here an there)
Thanks @jamesazam.bsky.social for the headsup!
Reposted by James Azam
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.
We have a forum: community.epinowcast.org for you.
Epinowcast
A community to discuss epinowcast and real-time infectious disease analysis more generally
community.epinowcast.org
May 7, 2025 at 3:08 PM
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.
We have a forum: community.epinowcast.org for you.
Reposted by James Azam
2025 here we come!
iddconf.org
IDDconf will be September 2-4 2025 in Ambleside.
Ticket info coming soon.
iddconf.org
IDDconf will be September 2-4 2025 in Ambleside.
Ticket info coming soon.
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.
iddconf.org
April 9, 2025 at 2:23 PM
2025 here we come!
iddconf.org
IDDconf will be September 2-4 2025 in Ambleside.
Ticket info coming soon.
iddconf.org
IDDconf will be September 2-4 2025 in Ambleside.
Ticket info coming soon.
Reposted by James Azam
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...
April 8, 2025 at 11:18 AM
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...
Reposted by James Azam
📦 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
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
April 8, 2025 at 2:54 PM
📦 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
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
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
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
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
media.tenor.com
April 8, 2025 at 3:17 PM
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
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
Reposted by James Azam
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...
See here for the R: github.com/epinowcast/p...
primarycensored/R/pprimarycensored.R at f051ac82b1c6ea9bfbc280a6d7c15c91aab05b71 · epinowcast/primarycensored
Primary event censored distributions. Contribute to epinowcast/primarycensored development by creating an account on GitHub.
github.com
April 7, 2025 at 2:02 PM
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...
See here for the R: github.com/epinowcast/p...
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
Here's a short clip showing the before and after #mcstan #stan #rpackage
April 7, 2025 at 3:50 PM
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
Here's a short clip showing the before and after #mcstan #stan #rpackage
Reposted by James Azam
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...
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...
April 1, 2025 at 12:17 PM
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...
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...
Here's a summary of our training materials.
March 28, 2025 at 12:32 PM
Here's a summary of our training materials.
In case you were wondering how to bookmark posts on bluesky, checkout this Chrome extension.
hypefury.com/bluesky/how-...
hypefury.com/bluesky/how-...
How to Bookmark Bluesky Posts - Hypefury
Bluesky does not have an official way of bookmarking posts. In this article, you will learn how you can Bookmark Bluesky posts.
hypefury.com
March 25, 2025 at 11:45 AM
In case you were wondering how to bookmark posts on bluesky, checkout this Chrome extension.
hypefury.com/bluesky/how-...
hypefury.com/bluesky/how-...
Reposted by James Azam
When an epidemic hits, how long does it take to get going with common epidemic analysis tasks?
A couple of weeks ago, we asked representatives from over a dozen UK organisations and universities who work actively on epidemic analysis and modelling how long the below tasks would take them....
1/
A couple of weeks ago, we asked representatives from over a dozen UK organisations and universities who work actively on epidemic analysis and modelling how long the below tasks would take them....
1/
February 25, 2025 at 10:04 PM
When an epidemic hits, how long does it take to get going with common epidemic analysis tasks?
A couple of weeks ago, we asked representatives from over a dozen UK organisations and universities who work actively on epidemic analysis and modelling how long the below tasks would take them....
1/
A couple of weeks ago, we asked representatives from over a dozen UK organisations and universities who work actively on epidemic analysis and modelling how long the below tasks would take them....
1/
"An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England | PLOS Computational Biology" from a team at UKHSA
community.epinowcast.org/t/nowcasting...
community.epinowcast.org/t/nowcasting...
Nowcasting norovirus cases (shameless self plug)
My team at UKHSA’s paper on nowcasting norovirus methods has now been published here: An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England | PLOS Computatio...
community.epinowcast.org
March 25, 2025 at 10:47 AM
Reposted by James Azam
Folks, if you use substantial amounts of people's code (either as a package or just copy and paste) please cite them.
Mentioning it in your SI or URL in your code repo doesn't really help as its so hard to discover and summarise for funders etc.
This is quite spread wide spread for what I see.
Mentioning it in your SI or URL in your code repo doesn't really help as its so hard to discover and summarise for funders etc.
This is quite spread wide spread for what I see.
March 4, 2025 at 11:20 AM
Folks, if you use substantial amounts of people's code (either as a package or just copy and paste) please cite them.
Mentioning it in your SI or URL in your code repo doesn't really help as its so hard to discover and summarise for funders etc.
This is quite spread wide spread for what I see.
Mentioning it in your SI or URL in your code repo doesn't really help as its so hard to discover and summarise for funders etc.
This is quite spread wide spread for what I see.
Reposted by James Azam
@jamesazam.bsky.social and @sbfnk.bsky.social are doing a lot of EpiNow2 dev at the moment. As part of this hey have started using PRs to hash out design docs before implementation and I'm enjoying it as a process vs just using issues or having calls.
Example: github.com/epiforecasts...
Example: github.com/epiforecasts...
Initial draft of design doc for fitting to multiple data streams by sbfnk · Pull Request #1018 · epiforecasts/EpiNow2
Combining multiple observation models
The overall premise is that there is a single latent process (modelled as GP or with the renewal equation) that informs multiple observation processes. Each of...
github.com
March 10, 2025 at 2:37 PM
@jamesazam.bsky.social and @sbfnk.bsky.social are doing a lot of EpiNow2 dev at the moment. As part of this hey have started using PRs to hash out design docs before implementation and I'm enjoying it as a process vs just using issues or having calls.
Example: github.com/epiforecasts...
Example: github.com/epiforecasts...
Do check this out and let us know how we can improve it. Is there any sections you found difficult to navigate? We're iterating on this across our other packages that use stan as the backend, i.e., epinowcast, primarycensored, EpiSewer, epidist, etc. #stan
I am obsessed with this nicely rendered doxygen for the Stan code in EpiNow2 that @jamesazam.bsky.social just added.
epiforecasts.io/EpiNow2/stan/
epiforecasts.io/EpiNow2/stan/
EpiNow2 Stan Functions: EpiNow2 Stan Functions
epiforecasts.io
March 25, 2025 at 10:30 AM
Do check this out and let us know how we can improve it. Is there any sections you found difficult to navigate? We're iterating on this across our other packages that use stan as the backend, i.e., epinowcast, primarycensored, EpiSewer, epidist, etc. #stan
Reposted by James Azam
One of the reasons it was possible to generate estimates so quickly was thanks to new R tools like:
epiverse-trace.github.io/epichains/
primarycensored.epinowcast.org
epiverse-trace.github.io/epiparameter/
epiverse-trace.github.io/epichains/
primarycensored.epinowcast.org
epiverse-trace.github.io/epiparameter/
January 27, 2025 at 9:28 PM
One of the reasons it was possible to generate estimates so quickly was thanks to new R tools like:
epiverse-trace.github.io/epichains/
primarycensored.epinowcast.org
epiverse-trace.github.io/epiparameter/
epiverse-trace.github.io/epichains/
primarycensored.epinowcast.org
epiverse-trace.github.io/epiparameter/