List of all items
Structs
- identifiability::egoprofile::EgoProfileLikelihoodBuilder
- identifiability::grid::ProfileGrid
- identifiability::grid::ProfileGridPoint
- identifiability::parameter::ProfileParameter
- identifiability::parameter::ProfileParameterBuilder
- identifiability::profile::ProfileLikelihoodBuilder
- identifiability::results::ProfileResult
- identifiability::results::ProfileResults
- macros::unit_maps::KIND_MAPPINGS
- macros::unit_maps::PREFIX_MAPPING
- mcmc::diagnostics::Diagnostics
- mcmc::diagnostics::ParameterDiagnostics
- mcmc::likelihood::LaplaceLikelihood
- mcmc::likelihood::NormalLikelihood
- mcmc::output::CSVOutput
- mcmc::output::DataFrameOutput
- mcmc::problem::BayesianProblem
- mcmc::problem::BayesianProblemRunBuilder
- mcmc::problem::ChainContext
- mcmc::problem::SampleMessage
- objective::loss::LogCosh
- objective::loss::MeanAbsoluteError
- objective::loss::MeanSquaredError
- objective::loss::NegativeLogLikelihood
- objective::loss::RootMeanSquaredError
- objective::loss::SumOfSquaredErrors
- optim::BS23
- optim::DP45
- optim::GL4
- optim::RALS3
- optim::RALS4
- optim::RK4
- optim::RK5
- optim::RKF45
- optim::TSIT45
- optim::bound::Bound
- optim::observer::CallbackObserver
- optim::observer::ProgressObserver
- optim::optimizers::bfgs::BFGS
- optim::optimizers::bfgs::BFGSBuilder
- optim::optimizers::ego::EGOBuilder
- optim::optimizers::ego::EfficientGlobalOptimization
- optim::optimizers::lbfgs::LBFGS
- optim::optimizers::lbfgs::LBFGSBuilder
- optim::optimizers::optimizer::InitialGuesses
- optim::optimizers::pso::PSOBuilder
- optim::optimizers::pso::ParticleSwarmOpt
- optim::optimizers::srtrust::SR1TrustRegion
- optim::optimizers::srtrust::SR1TrustRegionBuilder
- optim::problem::Problem
- optim::problem::ProblemBuilder
- optim::report::OptimizationReport
- plotting::EnzymeMLDocumentPlotMeasurementsBuilder
- simulation::BS23
- simulation::DP45
- simulation::GL4
- simulation::RALS3
- simulation::RALS4
- simulation::RK4
- simulation::RK5
- simulation::RKF45
- simulation::TSIT45
- simulation::output::MatrixResult
- simulation::result::PlotConfig
- simulation::result::SimulationResult
- simulation::setup::SimulationSetup
- simulation::setup::SimulationSetupBuilder
- simulation::system::ODESystem
- simulation::system::ODESystemContext
- suite::DatabaseEntry
- validation::consistency::Report
- validation::consistency::ValidationResult
- validation::schema::ValidationError
- validation::schema::ValidationReport
- versions::v2::BaseUnit
- versions::v2::BaseUnitBuilder
- versions::v2::Complex
- versions::v2::ComplexBuilder
- versions::v2::Creator
- versions::v2::CreatorBuilder
- versions::v2::EnzymeMLDocument
- versions::v2::EnzymeMLDocumentBuilder
- versions::v2::Equation
- versions::v2::EquationBuilder
- versions::v2::Measurement
- versions::v2::MeasurementBuilder
- versions::v2::MeasurementData
- versions::v2::MeasurementDataBuilder
- versions::v2::ModifierElement
- versions::v2::ModifierElementBuilder
- versions::v2::Parameter
- versions::v2::ParameterBuilder
- versions::v2::Protein
- versions::v2::ProteinBuilder
- versions::v2::Reaction
- versions::v2::ReactionBuilder
- versions::v2::ReactionElement
- versions::v2::ReactionElementBuilder
- versions::v2::SmallMolecule
- versions::v2::SmallMoleculeBuilder
- versions::v2::UnitDefinition
- versions::v2::UnitDefinitionBuilder
- versions::v2::Variable
- versions::v2::VariableBuilder
- versions::v2::Vessel
- versions::v2::VesselBuilder
Enums
- conversion::ConversionError
- equation::EnzymeMLDocState
- io::IOError
- llm::LLMError
- llm::PromptInput
- mcmc::error::MCMCError
- mcmc::likelihood::LikelihoodFunction
- mcmc::priors::Prior
- objective::error::ObjectiveError
- objective::loss::LossFunction
- optim::ImplicitSolver
- optim::error::OptimizeError
- optim::optimizers::srtrust::SubProblem
- optim::transformation::Transformation
- plotting::PlotError
- simulation::ImplicitSolver
- simulation::error::SimulationError
- simulation::setup::SimulationSetupBuilderError
- simulation::system::Mode
- suite::SuiteError
- system::ODEError
- system::SystemType
- validation::consistency::Severity
- versions::v2::BaseUnitBuilderError
- versions::v2::ComplexBuilderError
- versions::v2::CreatorBuilderError
- versions::v2::DataTypes
- versions::v2::EnzymeMLDocumentBuilderError
- versions::v2::EquationBuilderError
- versions::v2::EquationType
- versions::v2::MeasurementBuilderError
- versions::v2::MeasurementDataBuilderError
- versions::v2::ModifierElementBuilderError
- versions::v2::ModifierRole
- versions::v2::ParameterBuilderError
- versions::v2::ProteinBuilderError
- versions::v2::ReactionBuilderError
- versions::v2::ReactionElementBuilderError
- versions::v2::SmallMoleculeBuilderError
- versions::v2::UnitDefinitionBuilderError
- versions::v2::UnitType
- versions::v2::VariableBuilderError
- versions::v2::VesselBuilderError
Traits
- mcmc::likelihood::Likelihood
- mcmc::output::SampleOutput
- mcmc::priors::DiffablePrior
- objective::objfun::ObjectiveFunction
- optim::CostFunction
- optim::Gradient
- optim::optimizers::optimizer::Optimizer
- simulation::output::OutputFormat
Macros
- build_base_unit
- build_reaction
- build_unit_name
- collect_base_units
- create_stoich_eq_jit
- extract_all
- inverse_unit
- ratio_unit
- simple_unit
- unit
- unwrap_enum
- unwrap_list
Functions
- equation::create_equation
- equation::extract_symbols
- identifiability::egoprofile::ego_profile_likelihood
- identifiability::egoprofile::ego_profile_likelihood_core
- identifiability::profile::profile_likelihood
- identifiability::results::plot_pair_contour
- io::load_enzmldoc
- io::save_enzmldoc
- llm::query_llm
- optim::metrics::akaike_information_criterion
- optim::metrics::bayesian_information_criterion
- optim::metrics::mean_absolute_error
- optim::metrics::mean_squared_error
- optim::metrics::root_mean_squared_error
- optim::metrics::sum_of_squared_errors
- simulation::init_cond::extract_initial_conditions
- simulation::interpolation::interpolate
- suite::fetch_document_from_suite
- suite::list_documents_from_suite
- suite::push_document_to_suite
- system::build_species_equations
- system::derive_system
- tabular::reader::read_excel
- tabular::writer::create_workbook
- utils::measurement_not_empty
- validation::consistency::check_consistency
- validation::consistency::get_species_ids
- validation::schema::validate_json