Struct SDE 

pub struct SDE { /* private fields */ }

Stochastic Differential Equation solver for pharmacometric models.

This struct represents a stochastic differential equation system and provides methods to simulate particles and estimate likelihood for PKPD modeling.

SDE models introduce stochasticity into the system dynamics, allowing for more realistic modeling of biological variability and uncertainty.

Implementations

impl SDE

pub fn new( drift: fn(&NalgebraVec<f64>, &NalgebraVec<f64>, f64, &mut NalgebraVec<f64>, &NalgebraVec<f64>, &Covariates), diffusion: fn(&NalgebraVec<f64>, &mut NalgebraVec<f64>), lag: fn(&NalgebraVec<f64>, f64, &Covariates) -> HashMap<usize, f64>, fa: fn(&NalgebraVec<f64>, f64, &Covariates) -> HashMap<usize, f64>, init: fn(&NalgebraVec<f64>, f64, &Covariates, &mut NalgebraVec<f64>), out: fn(&NalgebraVec<f64>, &NalgebraVec<f64>, f64, &Covariates, &mut NalgebraVec<f64>), nparticles: usize, ) -> SDE

Creates a new stochastic differential equation solver with default Neqs.

Use builder methods to configure dimensions:

SDE::new(drift, diffusion, lag, fa, init, out, nparticles)
    .with_nstates(2)
    .with_ndrugs(1)
    .with_nout(1)

pub fn with_nstates(self, nstates: usize) -> SDE

Set the number of state variables.

pub fn with_ndrugs(self, ndrugs: usize) -> SDE

Set the number of drug inputs (size of bolus[] and rateiv[]).

pub fn with_nout(self, nout: usize) -> SDE

Set the number of output equations.

pub fn with_metadata( self, metadata: ModelMetadata, ) -> Result<SDE, SdeMetadataError>

Attach validated handwritten-model metadata to this SDE model.

pub fn metadata(&self) -> Option<&ValidatedModelMetadata>

Access the validated metadata attached to this SDE model, if any.

pub fn parameter_index(&self, name: &str) -> Option<usize>

pub fn covariate_index(&self, name: &str) -> Option<usize>

pub fn state_index(&self, name: &str) -> Option<usize>

Trait Implementations

impl Cache for SDE

fn with_cache_capacity(self, size: usize) -> SDE

Enable caching with the given maximum number of entries.

fn enable_cache(self) -> SDE

Enable caching with the default size (100,000 entries).

fn clear_cache(&self)

Clear all entries from this equation’s cache, if caching is enabled.

fn disable_cache(self) -> SDE

Disable caching.

impl Clone for SDE

fn clone(&self) -> SDE

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for SDE

fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.

impl DiffusionOptimize for SDE

fn optimize_diffusion( &self, data: &Data, theta: &mut Theta, sigma_params: &[String], error_models: &AssayErrorModels, posterior: Option<&Posterior>, config: DiffusionConfig, ) -> Result<DiffusionResult>

Optimize SDE diffusion parameters for each support point independently.

impl Equation for SDE

fn estimate_likelihood( &self, subject: &Subject, parameters: &Parameters, error_models: &AssayErrorModels, ) -> Result<f64, PharmsolError>

👎Deprecated since 0.23.0:

Use estimate_log_likelihood() instead for better numerical stability

Estimates the likelihood of observed data given a model and parameters.

Arguments

• subject - Subject data containing observations
• parameters - Parameter vector for the model
• error_model - Error model to use for likelihood calculations

Returns

The log-likelihood of the observed data given the model and parameters.

fn estimate_log_likelihood( &self, subject: &Subject, parameters: &Parameters, error_models: &AssayErrorModels, ) -> Result<f64, PharmsolError>

Estimate the log-likelihood of the subject given the parameters and error model.

fn kind() -> EqnKind

fn estimate_predictions( &self, subject: &Subject, parameters: &Parameters, ) -> Result<Self::P, PharmsolError>

Generate predictions for a subject with given parameters.

fn nouteqs(&self) -> usize

Get the number of output equations in the model.

fn nstates(&self) -> usize

Get the number of state variables in the model.

fn simulate_subject( &self, subject: &Subject, parameters: &Parameters, error_models: Option<&AssayErrorModels>, ) -> Result<(Self::P, Option<f64>), PharmsolError>

Simulate a subject with given parameters and optionally calculate likelihood.

impl EquationMetadataSource for SDE

fn equation_metadata(&self) -> Option<&ValidatedModelMetadata>

impl EquationTypes for SDE

type S = Vec<Matrix<f64, Dyn, Const<1>, VecStorage<f64, Dyn, Const<1>>>>

The state vector type

type P = ArrayBase<OwnedRepr<Prediction>, Dim<[usize; 2]>>

The predictions container type