Add a bit more documentation for config

Author: sirno

src/config/mod.rs

@@ -1,4 +1,81 @@
-//! Configuration data structures for simulation setups.
+//! # Settings for the simulation binary
+//!
+//! Settings are used to configure the simulation when it is run as a program.
+//! These settings are read from a YAML file and are used to initialize and run
+//! the simulation. The settings are divided into two parts: parameters and
+//! schedule. The parameters define the simulation parameters, such as the
+//! mutation rate and the maximum virus population size. The schedule defines
+//! events that occur throughout the simulation, such as transmission between
+//! compartments, sampling of individuals, or environmental changes.
+//!
+//! ## Parameters
+//!
+//! The parameters define the simulation parameters and are given as a list of
+//! [`Parameters`]. Some of the parameters require single values, while others
+//! may require more complex structures. For example, the fitness model can
+//! either be a single host model or a multi-host model. The corresponding MFED
+//! may be a neutral model, a lognormal model, or a model based on a file.
+//!
+//! ```yaml
+//! parameters:
+//!  - mutation_rate: 1e-6
+//!    recombination_rate: 0
+//!    host_population_size: 10000
+//!    infection_fraction: 1.0
+//!    basic_reproductive_number: 100.0
+//!    max_population: 10000
+//!    dilution: 0.02
+//!    substitution_matrix:
+//!      - [0.0, 1.0, 1.0, 1.0]
+//!      - [1.0, 0.0, 1.0, 1.0]
+//!      - [1.0, 1.0, 0.0, 1.0]
+//!      - [1.0, 1.0, 1.0, 0.0]
+//!    fitness_model: !SingleHost
+//!      distribution: !Exponential
+//!        weights:
+//!          beneficial: 0.29
+//!          deleterious: 0.51
+//!          lethal: 0.2
+//!          neutral: 0.0
+//!        lambda_beneficial: 0.03
+//!        lambda_deleterious: 0.21
+//!      utility: !Algebraic
+//!        upper: 1.5
+//! ```
+//!
+//! All available options can be found by looking at the type definition of the
+//! field. For example, one can find the available options for the
+//! `fitness_model` field by following the type definition to the corresponding
+//! enum: [`FitnessModelField`]. The available options can then be defined in
+//! YAML by using the corresponding tag, e.g., `!SingleHost` for a single host
+//! model.
+//!
+//! ```yaml
+//! fitness_model: !SingleHost
+//!   distribution: !Neutral
+//!   utility: !Linear
+//! ```
+//!
+//! ## Schedule
+//!
+//! The schedule is defined as a list of events that occur throughout the
+//! simulation. The events are defined by a generation expression, an event
+//! name, and a value. The generation expression is either the generation where
+//! the event should be executed, or in the case of recurring events an
+//! expression that will be executed every time the expression evaluates to 0.
+//! For example, the expression `{} % 200` will execute the event every 200
+//! generations.
+//!
+//! ```yaml
+//! schedule:
+//!  - generation: "{} % 1"
+//!    event: transmission
+//!    value: "[[0.9, 0.1], [0.1, 0.9]]"
+//!  - generation: "{} % 200"
+//!    event: sample
+//!    value: 1000
+//! ```
+//!
 
 mod parameters;
 mod schedule;

src/config/settings.rs

@@ -1,3 +1,5 @@
+//! Settings module.
+
 use super::parameters::Parameters;
 use super::schedule::Schedule;