# What is happening in the delay distribution samiverse? **URL:** \ **Category:** Uncategorized\ **Created:** [10 March 2026 19:11 UTC](https://community.epinowcast.org/t/what-is-happening-in-the-delay-distribution-samiverse/393 "2026-03-10T19:11:19Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![samabbott](https://dub1.discourse-cdn.com/flex005/user_avatar/community.epinowcast.org/samabbott/32/5_2.png) [@samabbott](https://community.epinowcast.org/u/samabbott)\ **Post date:** [10 March 2026 19:11 UTC](https://community.epinowcast.org/t/what-is-happening-in-the-delay-distribution-samiverse/393/1 "2026-03-10T19:11:19Z")
I got asked to write up a little something on what I have been doing (with others) on delay estimation and what the future holds. I thought others might like to see the semi-incoherent babble. For anyone involved in this stuff, sorry if I mislabelled, got things wrong, etc please flag and correct as you like. I just threw this together so apologies for clarity. I may also have missed things or not properly connected things so please flag. > samiverse This is a joke around being asked for what I have done - obviously, all of the below work is very team-oriented, and in several instances, all I did was cheerlead. The TLDR is I am not keen on keeping implementing shards of the same model to support y feature, which is what is part of the motivation for my push to composable Julia (amongst other motivations). - A slide deck from a few years ago: [https://samabbott.co.uk/presentations/2024/why-am-i-so-late.pdf](https://samabbott.co.uk/presentations/2024/why-am-i-so-late.pdf) - Estimating epidemiological delay distributions [https://www.medrxiv.org/content/10.1101/2024.01.12.24301247v1](https://www.medrxiv.org/content/10.1101/2024.01.12.24301247v1) - Best practices for estimating epi delay distributions [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012520](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012520) - Primarycensored: [https://primarycensored.epinowcast.org/](https://primarycensored.epinowcast.org/) - epidist: [https://epidist.epinowcast.org/](https://epidist.epinowcast.org/) - Epinowcast: [https://package.epinowcast.org/](https://package.epinowcast.org/) - [CensoredDistributions.jl](http://censoreddistributions.jl): [https://censoreddistributions.epiaware.org/dev/](https://censoreddistributions.epiaware.org/dev/) - EpiNow2: [Estimate and Forecast Real-Time Infection Dynamics • EpiNow2](https://epiforecasts.io/EpiNow2/) - Baselinenowcast: [https://baselinenowcast.epinowcast.org/](https://baselinenowcast.epinowcast.org/) ## Work in progress - Mixture and non-parametric support for primarycensored and epidist (see issues). Mostly stuck due to time constraints. - Implementing primarycensored model to replace the delay estimation model in EpiNow2 with support for the EpiNow2 delay interface/priors, etc. - Support for non-joint delay estimating, negative count updates, and improved forecast tooling in epinowcast (see issues - also lots of stuff could be done here, but time/money). Somewhat stuck due to time constraints. - Work with Barbora Němcová and Johannes Bracher to find better observation models for marginal nowcasting approaches that better capture observation level variance vs process variance (in the delays, etc., etc.) as flagged by Stoner et al. 2020 - Paper with Johannes Bracher, Jacco Wallinga and the nowcasting methods crew to summarise the current state of ID epi nowcasting methods. In draft. - Paper as part of the Insight net collaboration to guide Public health practitioners in the US on how to deal with reporting challenges in surveillance data. Aiming to facilitate discussion between practitioners, i.e., we have X challenges and modellers we have Y solutions, and to find what the Z gaps are. Contributions welcome, see [https://www.epinowcast.org/GuideToSTLTReportingDelays/](https://www.epinowcast.org/GuideToSTLTReportingDelays/) - Work with Kylie Ainslee, Sang Woo Park and others on establishing an MVP generation time estimation framework for future modular expansion and to serve as a baseline. See [https://community.epinowcast.org/t/minimum-viable-model-for-generation-time-estimation/387/9](https://community.epinowcast.org/t/minimum-viable-model-for-generation-time-estimation/387/9) - Proposed (rejected) grant to extend generation time estimation methods to include time-to-event approaches. Along the way, the suggestion was to extend the primarycensoring approach to be nested (for generation time estimation) to leverage efficiency and to hit mixture and convolved primary and truncated dists. Big focus on modular infection processes to link to wider composability work. See grant app here: [https://community.epinowcast.org/t/addressing-critical-gaps-in-generation-time-estimation-during-outbreaks-grant-application/317/5](https://community.epinowcast.org/t/addressing-critical-gaps-in-generation-time-estimation-during-outbreaks-grant-application/317/5) still thinking about pathways forward. Joint estimation stands out here as a big gap in my opinion across lots of delays, where the relationship between them and observation is complex, i.e. paired convolved/mixtures of distributions with observation level biases and the potential role of infection processes (the most critical being where the infection process has a role) - Work with Nyall Jamieson, Lauren Meyers, Chris Overton and others on solving more analytical primarycensored distributions. - Work with Nyall Jamieson, Lauren Meyers, Ian Hall and others relating epi delay estimating with non-infectious diseases and biohazard release modelling. TLDR primary censoring and release modelling are kind of the same. Trendy. Might unlock insights in epi delays. Definitely allows for the use of existing delay tools in release modelling. See [https://pubmed.ncbi.nlm.nih.gov/21242803/](https://pubmed.ncbi.nlm.nih.gov/21242803/) and draw a diagram to get the link. - Work with Nyall Jamieson et al to derive a generation time and other epi delay distributions along the same lines as for the incubation period. Early stage. Lots of scope for exploration here. - Not really delays, but involved in developing brms in Julia. The connection is I am helping by iterating using [CensoredDistributions.jl](http://censoreddistributions.jl) to recreate what we can do in epidist, but without a multi-year dev effort (i.e. using native Julia composability). This should be a good approach for the future for those looking at flexible and multi-strata, etc., etc. models without all the eng effort of rolling your own at home. Very exciting. - Related to this is to do everything again, but this time in a modular Julia ecosystem, so not have to keep reimplementing for all the various shades of model expression and inference approaches. Also, to implement lessons learnt, etc., etc., on which methods we need and what they should look like for most real-world use. Big focus on creating modular joint models as well as robust staged approaches. ## Gaps For me, aside from the somewhat in-progress work (lots of which I think are pretty important and there are multiple viable pathways towards + the vast majority also need more boots on the ground), other forms of paired delay and all the many different edge cases and complexities. I.e what happens when estimating IFR and you need delays for both dead and not dead, what happens in households, what kinds of paired data are common, and what biases and delays do these have? At some point, we start to connect with tree based who infected who methods. What is the theory overlap (i.e similar to nowcasting and delay estimation)? How do we implement modular models for these that are efficient and get the basics right? Of the in-progress stuff, if the derived epi dists don’t work out, what dist and when is a key question. There is also near infinite stuff in observation errors to think about and model. I think that is really only something that can be done in a modular ecosystem because it becomes high-dimensional fast. ---
**Author:** ![samabbott](https://dub1.discourse-cdn.com/flex005/user_avatar/community.epinowcast.org/samabbott/32/5_2.png) [@samabbott](https://community.epinowcast.org/u/samabbott)\ **Post date:** [10 March 2026 19:21 UTC](https://community.epinowcast.org/t/what-is-happening-in-the-delay-distribution-samiverse/393/2 "2026-03-10T19:21:21Z")
Not sure why I have future work in here to be honest these days I mostly just configure my dotfiles…. [GitHub - seabbs/dotfiles: Personal dotfile and configuration · GitHub](https://github.com/seabbs/dotfiles)