jameel-institute · pratikunterwegs · Mar 19, 2026 · Mar 19, 2026 · Mar 19, 2026 · Mar 19, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.0.7] - 2026-03-19
+
+- Transfer repository to Jameel Institute @jameel-institute oragnisation
+- Added small script `docs/sync_readme.jl` to update package version in website index and Readme.md
+
 ## [0.0.6] - 2026-03-16
 
 ### Changed (Breaking)

diff --git a/Manifest.toml b/Manifest.toml
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Daedalus"
 uuid = "05fc9732-d2bf-478b-9a56-f88318f7a02f"
 authors = ["Pratik Gupte <pratikgupte16@gmail.com> and contributors"]
-version = "0.0.6"
+version = "0.0.7"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

diff --git a/README.md b/README.md
@@ -1,32 +1,58 @@
-# Daedalus
+# Daedalus.jl
 
 [![License:MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![Version](https://img.shields.io/badge/version-0.0.7-aquamarine.svg)](https://jameel-institute.github.io/Daedalus.jl/dev/)
 [![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://pratikunterwegs.github.io/Daedalus.jl/dev/)
-[![Build Status](https://github.com/pratikunterwegs/Daedalus.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/pratikunterwegs/Daedalus.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/pratikunterwegs/Daedalus.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/pratikunterwegs/Daedalus.jl)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://jameel-institute.github.io/Daedalus.jl/dev/)
+[![Build Status](https://github.com/jameel-institute/Daedalus.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/jameel-institute/Daedalus.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/jameel-institute/Daedalus.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/jameel-institute/Daedalus.jl)
 [![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
 
 _Daedalus.jl_ is a Julia package that aims to mirror the [R package {daedalus}](https://github.com/jameel-institute/daedalus).
 
-**Note** that this is a personal project, and comes with no current or future support.
-This documentation section is intended as a learning experience (for me) in writing Julia package documentation.
+_Daedalus.jl_ is developed at the [Jameel Institute](https://www.imperial.ac.uk/jameel-institute/) at Imperial College London as part of the [Jameel Institute-Kenneth C. Griffin Initiative for the Economics of Pandemic Preparedness (EPPI)](https://new.express.adobe.com/webpage/TXLBkz1sN9FI5?), in collaboration with the [RESIDE research software engineering team](https://reside-ic.github.io/about/).
+
+**Note that** functionality compared to the R package is still limited.
 
 ## Installation
 
 _Daedalus.jl_ can be installed from GitHub using the Julia package manager _Pkg.jl_.
 
 ```julia
 using Pkg
-Pkg.add(url="git@github.com:pratikunterwegs/Daedalus.jl.git")
+Pkg.add(url="git@github.com:jameel-institute/Daedalus.jl.git")
 ```
 
 ## Quick start
 
 ```julia
 using Daedalus
+using Plots
+
+# pump up r0 to get peak within 50 days
+infection = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection.r0 = 5.0
+data = daedalus("Canada", infection, time_end=600.0);
+
+# plot exposed group
+times = Daedalus.Outputs.get_times(data)
+# functioning get_values() bins into 90 days by default, set to 1 for no binning
+exposed = Daedalus.Outputs.get_values(data, "E", 1)
+hosp = Daedalus.Outputs.get_values(data, "H", 1)
 
-result = daedalus("Australia", "sars-cov-2 delta", time_end=600.0)
+# plot the output to see lag in hospitalisations
+plot(times, exposed, label="exposed")
+plot!(times, hosp, label="hosp")
+xlabel!("Time (days)")
+ylabel!("# individuals")
+```
+
+```julia
+# plot recorded Rt
+vecRt = Daedalus.Outputs.get_values(data, "Rt", 1)
+plot(times, vecRt, label="Rt")
+xlabel!("Time (days)")
+ylabel!("Rt")
 ```
 
 ## Related projects
@@ -35,4 +61,4 @@ result = daedalus("Australia", "sars-cov-2 delta", time_end=600.0)
 
 ## Help
 
-To report a bug, request a feature, or just start a discussion, [please open an issue](https://github.com/pratikunterwegs/Daedalus.jl/issues/new).
+To report a bug, request a feature, or just start a discussion, [please open an issue](https://github.com/jameel-institute/Daedalus.jl/issues/new).
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
diff --git a/docs/make.jl b/docs/make.jl
@@ -9,7 +9,7 @@ makedocs(;
     sitename = "Daedalus.jl",
     format = Documenter.HTML(;
         prettyurls = get(ENV, "CI", "false") == "true",
-        canonical = "https://pratikunterwegs.github.io/Daedalus.jl",
+        canonical = "https://jameel-institute.github.io/Daedalus.jl",
         edit_link = "main",
         assets = String[],
         size_threshold_ignore = [
@@ -33,6 +33,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo = "github.com/pratikunterwegs/Daedalus.jl",
+    repo = "github.com/jameel-institute/Daedalus.jl",
     devbranch = "main"
 )
diff --git a/docs/src/country_data.md b/docs/src/country_data.md
@@ -94,3 +94,40 @@ Each function accepts either a country name `String` or a `CountryData` struct:
 | `prepare_contacts(country)` | Scaled 49×49 contact matrix |
 | `worker_contacts(country)` | Per-capita within-sector contact rates (length-45 vector) |
 | `prepare_demog(country)` | 49-element population vector |
+
+## Running Daedalus with country and infection structs
+
+Pass a country name string directly to `daedalus` to use country-specific demography, contact patterns, and workforce data.
+
+```@example uk_daedalus
+using Daedalus
+using Plots
+
+# Run the model using UK demography and contact patterns
+infection_uk = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_uk.r0 = 2.5
+data_uk = daedalus("United Kingdom", infection_uk, time_end=600.0)
+
+times_uk = Daedalus.Outputs.get_times(data_uk)
+exposed_uk = Daedalus.Outputs.get_values(data_uk, "E", 1)
+hosp_uk = Daedalus.Outputs.get_values(data_uk, "H", 1)
+
+plot(times_uk, exposed_uk, label = "exposed")
+plot!(times_uk, hosp_uk, label = "hospitalised")
+xlabel!("Time (days)")
+ylabel!("# individuals")
+title!("United Kingdom — SEIR dynamics")
+```
+
+```@example uk_daedalus
+# Effective reproduction number over time
+rt_uk = Daedalus.Outputs.get_values(data_uk, "Rt", 1)
+plot(times_uk, rt_uk, label = "Rt", color = :red)
+hline!([1.0], linestyle = :dash, color = :black, label = "Rt = 1")
+xlabel!("Time (days)")
+ylabel!("Rt")
+title!("United Kingdom — effective reproduction number")
+```
+
+See [Country and pathogen data](@ref) for a full overview of the bundled
+data and how to use pathogen-specific parameters.