Add infection struct input to replace manual parameter values

CHANGELOG.md

@@ -5,7 +5,45 @@ 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).
 
-## [Unreleased]
+## [0.0.6] - 2026-03-16
+
+### Changed (Breaking)
+- **`daedalus()` function signature refactored**: second positional argument now takes infection parameters (`infection`) instead of scalar/vector `r0`. Users must pass parameters via `InfectionData` object rather than individual keyword arguments
+  - **Old interface**: `daedalus(country, r0::Float64; sigma=..., epsilon=..., eta=..., ...)`
+  - **New interface**: `daedalus(country, infection; npi=..., log_rt=..., time_end=..., increment=..., n_threads=...)`
+- Removed all infection-parameter keyword arguments: `sigma`, `p_sigma`, `epsilon`, `rho`, `eta`, `omega`, `gamma_Ia`, `gamma_Is`, `gamma_H`, `nu`
+  - All epidemiological parameters now encapsulated in `InfectionData` object
+  - Users customize parameters by fetching `InfectionData` and modifying fields before calling `daedalus()`
+
+### Added
+- New dispatch methods for `daedalus()`:
+  1. String pathogen name: `daedalus(country, "sars-cov-2 delta"; ...)`
+  2. Single `InfectionData`: `daedalus(country, infection_obj; ...)`
+  3. Vector `InfectionData`: `daedalus(country, [inf1, inf2, ...]; ...)`
+- `extract_infection_params()` helper function to extract and expand epidemiological parameters from `InfectionData`
+- `InfectionData` is mutable, allowing users to customize parameters post-fetch: `inf = get_pathogen("sars-cov-2 delta"); inf.r0 = 2.5`
+- **Infection names are normalized to lowercase**: all pathogen names are stored and looked up as lowercase strings (e.g., `"sars-cov-2 delta"`, `"influenza 2009"`)
+
+### Migration Guide
+```julia
+# Old (no longer works):
+result = daedalus("Australia", 2.5, sigma=0.217, epsilon=0.58, time_end=200.0)
+
+# New (string pathogen, lowercase names):
+result = daedalus("Australia", "sars-cov-2 delta", time_end=200.0)
+
+# New (custom infection):
+infection = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection.r0 = 2.5
+result = daedalus("Australia", infection, time_end=200.0)
+
+# New (vector of infections):
+infections = [
+    Daedalus.DataLoader.get_pathogen("sars-cov-2 delta"),
+    Daedalus.DataLoader.get_pathogen("influenza 2009")
+]
+results = daedalus("Australia", infections, time_end=200.0)
+```
 
 ## [0.0.5] - 2026-03-09
 

Project.toml

@@ -1,7 +1,7 @@
 name = "Daedalus"
 uuid = "05fc9732-d2bf-478b-9a56-f88318f7a02f"
 authors = ["Pratik Gupte <pratikgupte16@gmail.com> and contributors"]
-version = "0.0.5"
+version = "0.0.6"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

README.md

@@ -26,7 +26,7 @@ Pkg.add(url="git@github.com:pratikunterwegs/Daedalus.jl.git")
 ```julia
 using Daedalus
 
-daedalus("Australia", 5.0, time_end=600.0)
+result = daedalus("Australia", "sars-cov-2 delta", time_end=600.0)
 ```
 
 ## Related projects

docs/src/benchmarking.md

@@ -13,15 +13,19 @@ This section shows various benchmarks.
 using Daedalus
 using BenchmarkTools
 
-@benchmark daedalus("Australia", 2.5, time_end=600.0)
+infection_01 = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_01.r0 = 2.5
+@benchmark daedalus("Australia", infection_01, time_end=600.0)
 ```
 
 ```@example benchmarking_02
 # benchmark for an RTM-exercise run of 100 days
 using Daedalus
 using BenchmarkTools
 
-@benchmark daedalus("Australia", 2.5, time_end=100.0)
+infection_02 = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_02.r0 = 2.5
+@benchmark daedalus("Australia", infection_02, time_end=100.0)
 ```
 
 ## Effect of logging $R_t$
@@ -33,7 +37,9 @@ using Daedalus
 using BenchmarkTools
 
 # turn off Rt logging and compare with benchmark above
-@benchmark daedalus("Australia", 2.5, log_rt=false, time_end=600.0)
+infection_rt = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_rt.r0 = 2.5
+@benchmark daedalus("Australia", infection_rt, log_rt=false, time_end=600.0)
 ```
 
 ## Reactive events
@@ -47,12 +53,16 @@ using BenchmarkTools
 
 npi = Daedalus.DaedalusStructs.Npi(20000.0, (coef=0.7,));
 
-@benchmark daedalus("Australia", 5.0, npi=npi, time_end=600.0)
+infection_re = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_re.r0 = 5.0
+@benchmark daedalus("Australia", infection_re, npi=npi, time_end=600.0)
 ```
 
 ```@example benchmarking_reactive_event
 # shorter duration
-@benchmark daedalus("Australia", 5.0, npi=npi, time_end=100.0)
+infection_re2 = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_re2.r0 = 5.0
+@benchmark daedalus("Australia", infection_re2, npi=npi, time_end=100.0)
 ```
 
 ## Timed events
@@ -69,11 +79,15 @@ timed_npi = Daedalus.DaedalusStructs.TimedNpi(
     "three_phase_lockdown"
 )
 
-@benchmark daedalus("Australia", 3.0, npi=timed_npi, time_end=600.0)
+infection_te = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_te.r0 = 3.0
+@benchmark daedalus("Australia", infection_te, npi=timed_npi, time_end=600.0)
 ```
 
 Timed events do not need $R_t$ logging and can be benchmarked without it.
 
 ```@example benchmarking_timed_event
-@benchmark daedalus("Australia", 3.0, npi=timed_npi, time_end=600.0, log_rt=false)
+infection_te2 = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_te2.r0 = 3.0
+@benchmark daedalus("Australia", infection_te2, npi=timed_npi, time_end=600.0, log_rt=false)
 ```

docs/src/country_data.md

@@ -59,28 +59,30 @@ uk.contact_matrix
 ```@example pathogen_struct
 using Daedalus
 
-delta = Daedalus.DataLoader.get_pathogen("SARS-CoV-2 delta")
+delta = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
 
 delta
 ```
 
 ## Preparing country inputs for the model
 
-Pass a country name string directly to [`daedalus`](@ref) to run the model with country-specific demography, contacts, and workforce data:
+Pass a country name string and a pathogen name to [`daedalus`](@ref) to run the model with country-specific demography, contacts, and workforce data:
 
 ```@example country_inputs
 using Daedalus
 
-result = daedalus("United Kingdom", 2.5, time_end=600.0)
+result = daedalus("United Kingdom", "sars-cov-2 delta", time_end=600.0)
 ```
 
-You can also pass a [`DataLoader.CountryData`](@ref) struct directly.
-This is useful when you want to pre-fetch or modify country data before running the model:
+You can also pass a [`DataLoader.CountryData`](@ref) struct directly and customize infection parameters.
+This is useful when you want to pre-fetch or modify country or infection data before running the model:
 
 ```@example country_inputs
 # Pre-fetch country data and pass the struct directly
 uk = Daedalus.DataLoader.get_country("United Kingdom")
-result2 = daedalus(uk, 2.5, time_end=600.0)
+infection = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection.r0 = 2.5
+result2 = daedalus(uk, infection, time_end=600.0)
 ```
 
 The `Data` sub-module also exposes lower-level functions for inspecting or manipulating the country arrays directly.

docs/src/ensemble.md

@@ -11,15 +11,22 @@ Better functionality for working with ensemble outputs, using the inbuilt DE.jl
 
 ## Basic ensemble run
 
-Pass a `Vector{Float64}` as the `r0` argument instead of a scalar value:
+Pass a `Vector{InfectionData}` with different R0 values:
 
 ```@example ensemble_basic
 using Daedalus
 using Plots
 
 # Run model with three different R0 values
-r0_values = [1.5, 2.5, 3.5]
-results = daedalus("Australia", r0_values, time_end=600.0);
+infections = [
+    Daedalus.DataLoader.get_pathogen("sars-cov-2 delta"),
+    Daedalus.DataLoader.get_pathogen("sars-cov-2 delta"),
+    Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+]
+infections[1].r0 = 1.5
+infections[2].r0 = 2.5
+infections[3].r0 = 3.5
+results = daedalus("Australia", infections, time_end=600.0);
 
 # Each result contains: sol, saves, npi, r0
 println("Number of results: ", length(results))
@@ -97,7 +104,11 @@ npi = Daedalus.DaedalusStructs.Npi(10000.0, (coef=0.5,))
 
 # Run ensemble with same NPI applied to all R0 values
 r0_range = [1.5, 2.0, 2.5, 3.0, 3.5]
-results_with_npi = daedalus("Australia", r0_range, npi=npi, time_end=600.0)
+infections_npi = [Daedalus.DataLoader.get_pathogen("sars-cov-2 delta") for _ in r0_range]
+for (i, r0) in enumerate(r0_range)
+    infections_npi[i].r0 = r0
+end
+results_with_npi = daedalus("Australia", infections_npi, npi=npi, time_end=600.0)
 ```
 
 ## Large-scale parameter sweeps
@@ -107,7 +118,11 @@ For broader sensitivity analyses, you can define finer-grained R0 ranges:
 ```@example ensemble_basic
 # Fine-grained sweep from 1.0 to 5.0 in 0.5 increments
 r0_sweep = collect(1.0:0.5:5.0)
-results_sweep = daedalus("Australia", r0_sweep, time_end=300.0);
+infections_sweep = [Daedalus.DataLoader.get_pathogen("sars-cov-2 delta") for _ in r0_sweep]
+for (i, r0) in enumerate(r0_sweep)
+    infections_sweep[i].r0 = r0
+end
+results_sweep = daedalus("Australia", infections_sweep, time_end=300.0);
 
 # NOTE: add plot of infectious or exposed
 ```

docs/src/index.md

@@ -34,7 +34,9 @@ using Daedalus
 using Plots
 
 # pump up r0 to get peak within 50 days
-data = daedalus("Canada", 5.0, time_end=600.0);
+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)
@@ -66,7 +68,9 @@ using Daedalus
 using Plots
 
 # Run the model using UK demography and contact patterns
-data_uk = daedalus("United Kingdom", 2.5, time_end=600.0)
+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)

docs/src/npis.md

@@ -16,8 +16,14 @@ using Plots
 hosp_threshold=20000.0
 a = Daedalus.DaedalusStructs.Npi(hosp_threshold, (coef=0.7,));
 
-data = daedalus("Australia", 3.0, npi=a, time_end=600.0);
-data_default = daedalus("Australia", 3.0, time_end=600.0);
+# Create infection data for both runs
+infection = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection.r0 = 3.0
+infection_default = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_default.r0 = 3.0
+
+data = daedalus("Australia", infection, npi=a, time_end=600.0);
+data_default = daedalus("Australia", infection_default, time_end=600.0);
 
 # plot new hosp over time
 iHosp = Daedalus.Constants.get_indices("H")
@@ -61,7 +67,11 @@ timed_npi = Daedalus.DaedalusStructs.TimedNpi(
     "three_phase_lockdown"
 )
 
-data = daedalus("Australia", 3.0, npi=timed_npi, time_end=600.0);
+# Create infection data
+infection_timed = Daedalus.DataLoader.get_pathogen("sars-cov-2 delta")
+infection_timed.r0 = 3.0
+
+data = daedalus("Australia", infection_timed, npi=timed_npi, time_end=600.0);
 
 # get exposed
 iExpo = Daedalus.Constants.get_indices("E")