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SimBiology Functions - Alphabetical List

Alphabetical List By Category
AbstractKineticLaw objectKinetic law information in library
accelerate(SimFunction)Prepare SimFunction object for accelerated simulations
addcompartmentCreate compartment object
addCompartmentAdd compartment to PKModelDesign object
addconfigsetCreate configuration set object and add to model object
addcontent (variant)Append content to variant object
adddoseAdd dose object to model
addeventAdd event object to model object
addkineticlaw (reaction)Create kinetic law object and add to reaction object
addparameterCreate parameter object and add to model or kinetic law object
addproduct (reaction)Add product species object to reaction object
addreactant (reaction)Add species object as reactant to reaction object
addreactionCreate reaction object and add to model object
addruleCreate rule object and add to model object
addspeciesCreate species object and add to compartment object within model object
addvariantAdd variant to model
boxplot(LeastSquaresResults,OptimResults,NLINResults)Create box plot showing the variation of estimated SimBiology model parameters
boxplot(NLMEResults)Create box plot showing the variation of estimated SimBiology model parameters
ci2tableReturn summary table of confidence interval results
commit (variant)Commit variant contents to model
Compartment objectOptions for compartments
CompileOptionsDimensional analysis and unit conversion options
ConfidenceIntervalObject containing confidence interval results
Configset objectSolver settings information for model simulation
constructConstruct SimBiology model from PKModelDesign object
constructDefaultFixedEffectValues (covmodel)Create initial estimate vector needed for fit
copyobj (any object)Copy SimBiology object and its children
CovariateModel objectDefine relationship between parameters and covariates
covariateModel(NLMEResults)Return a copy of the covariate model that was used for the nonlinear mixed-effects estimation using sbiofitmixed
createDosesCreate dose objects from groupedData object
createSimFunctionCreate SimFunction object
delete (any object)Delete SimBiology object
display (any object)Display summary of SimBiology object
EstimatedInfo objectObject containing information about estimated model quantities
Event objectStore event information
exportExport SimBiology models for deployment and standalone applications
findUnusedComponentsFind unused species, parameters, and compartments in a model
findUsages(AbstractKineticLaw)Find out how an AbstractKineticLaw object is used
findUsages(species,parameter,compartment)Find out how a species, parameter, or compartment is used in a model
findUsages(unit,unitprefix)Find out how a unit or unit prefix is used
fitted(LeastSquaresResults,OptimResults,NLINResults)Return simulation results of SimBiology model fitted using least-squares regression
fitted(NLMEResults) Return the simulation results of a fitted nonlinear mixed-effects model
get (any object)Get object properties
getadjacencymatrix (model)Get adjacency matrix from model object
getconfigsetGet configuration set object from model object
getCovariateData (pkdata)Create design matrix needed for fit
getdata (SimData)Get data from SimData object array
getdose (model)Return SimBiology dose object
getparameters (kineticlaw)Get specific parameters in kinetic law object
getsensmatrix (SimData)Get 3-D sensitivity matrix from SimData array
getspecies (kineticlaw)Get specific species in kinetic law object
getstoichmatrix (model)Get stoichiometry matrix from model object
getTable(ScheduleDose,RepeatDose)Return data from SimBiology dose object as table
getvariant (model)Get variant from model
groupedData Table-like collection of data and metadata
groupedData2tableConvert groupedData object to table
isaccelerated(SimFunction)Determine if SimFunction object is accelerated
KineticLaw objectKinetic law information for reaction
LeastSquaresResults objectResults object containing estimation results from least-squares regression
loadLoad variables from file into workspace
Model objectModel and component information
Model.getequationsReturn system of equations for model object
NLINResults objectEstimation results object, subclass of LeastSquaresResults
NLMEResults objectResults object containing estimation results from nonlinear mixed-effects modeling
OptimResults objectEstimation results object, subclass of LeastSquaresResults
Parameter objectParameter and scope information
ParameterConfidenceIntervalObject containing confidence interval results for estimated parameters
PKCompartment objectUsed by PKModelDesign to create SimBiology model
PKModelDesign objectHelper object to construct pharmacokinetic model
PKModelMap objectDefine SimBiology model components’ roles
plotPlot parameter confidence interval results
plotPlot confidence interval results for model predictions
plot(LeastSquaresResults,OptimResults,NLINResults)Compare simulation results to the training data, creating a time-course subplot for each group
plot(NLMEResults)Compare simulation results to the training data, creating a time-course subplot for each group
plotActualVersusPredicted(LeastSquaresResults,OptimResults,NLINResults)Compare predictions to actual data, creating a subplot for each response
plotActualVersusPredicted(NLMEResults)Compare predictions to actual data, creating a subplot for each response
plotResidualDistribution(LeastSquaresResults,OptimResults,NLINResults)Plot the distribution of the residuals
plotResidualDistribution(NLMEResults)Plot the distribution of the residuals
plotResiduals(LeastSquaresResults,OptimResults,NLINResults)Plot residuals for each response, using time, group, or prediction as x-axis
plotResiduals(NLMEResults)Plot the residuals for each response, using the time, group, or prediction as the x-axis
predict(LeastSquaresResults,OptimResults,NLINResults)Simulate and evaluate fitted SimBiology model
predict(NLMEResults)Simulate and evaluate fitted SimBiology model
PredictionConfidenceIntervalObject containing confidence interval results for model predictions
random(LeastSquaresResults,OptimResults,NLINResults)Simulate SimBiology model, adding variations by sampling error model
random(NLMEResults)Simulate a SimBiology model, adding variations by sampling the error model
Reaction objectOptions for model reactions
removeconfigset (model)Remove configuration set from model
removedose (model)Add dose object to model
removevariant (model)Remove variant from model
rename (compartment, parameter, species, reaction)Rename object and update expressions
reorder (model, compartment, kinetic law)Reorder component lists
RepeatDose objectDefine drug dosing protocol
resample (SimData)Resample SimData object array onto new time vector
reset (root)Delete all model objects from root object
rmcontent (variant)Remove contents from variant object
rmproduct (reaction)Remove species object from reaction object products
rmreactant (reaction)Remove species object from reaction object reactants
Root objectHold models, unit libraries, and abstract kinetic law libraries
Rule objectHold rule for species and parameters
RuntimeOptionsOptions for logged species
sbioabstractkineticlawCreate kinetic law definition
sbioacceleratePrepare model object for accelerated simulations
sbioaddtolibraryAdd to user-defined library
sbioconsmoietyFind conserved moieties in SimBiology model
sbioconvertunitsConvert unit and unit value to new unit
sbiocopylibraryCopy library to disk
sbiodesktopOpen SimBiology desktop for modeling and simulation
sbiodoseConstruct dose object
sbioensembleplotShow results of ensemble run using 2-D or 3-D plots
sbioensemblerunMultiple stochastic ensemble runs of SimBiology model
sbioensemblestatsGet statistics from ensemble run data
sbiofitPerform nonlinear least-squares regression
sbiofitmixedFit nonlinear mixed-effects model (requires Statistics and Machine Learning Toolbox software)
sbiofitstatusplotPlot status of nonlinear mixed-effects estimation
sbiofittoolOpen SimBiology desktop for population fitting
sbiogetmodelGet model object that generated simulation data
sbiolasterrorSimBiology last error message
sbiolastwarningSimBiology last warning message
sbioloadprojectLoad project from file
sbiomodelConstruct model object
sbioncaCompute noncompartmental analysis (NCA) parameters (requires Statistics and Machine Learning Toolbox)
sbioncaoptionsSpecify options to calculate noncompartmental analysis (NCA) parameters
sbionlinfitPerform nonlinear least-squares regression using SimBiology models (requires Statistics and Machine Learning Toolbox software)
sbionlmefitEstimate nonlinear mixed effects using SimBiology models (requires Statistics and Machine Learning Toolbox software)
sbionlmefitsaEstimate nonlinear mixed effects with stochastic EM algorithm (requires Statistics and Machine Learning Toolbox software)
sbionmfiledefNONMEM file definition object for sbionmimport
sbionmimportImport NONMEM-formatted data
sbioparamestimPerform parameter estimation
sbioparameterciCompute confidence intervals for estimated parameters (requires Statistics and Machine Learning Toolbox)
sbioplotPlot simulation results in one figure
sbiopredictionciCompute confidence intervals for model predictions (requires Statistics and Machine Learning Toolbox)
sbioremovefromlibrary Remove kinetic law, unit, or unit prefix from library
sbioresetDelete all model objects
sbiorootReturn SimBiology root object
sbiosampleerrorSample error based on error model and add noise to simulation data
sbiosampleparametersGenerate parameters by sampling covariate model (requires Statistics and Machine Learning Toolbox software)
sbiosaveprojectSave all models in root object
sbioselectSearch for objects with specified constraints
sbioshowunitprefixesShow unit prefixes in library
sbioshowunitsShow units in library
sbiosimulateSimulate SimBiology model
sbiosteadystate Find steady state of SimBiology model
sbiosubplotPlot simulation results in subplots
sbiotrellisPlot data or simulation results in trellis plot
sbiounitCreate user-defined unit
sbiounitcalculatorConvert value between units
sbiounitprefixCreate user-defined unit prefix
sbiovariantConstruct variant object
sbiowhosShow contents of project file, library file, or SimBiology root object
sbmlexportExport SimBiology model to SBML file
sbmlimportImport SBML-formatted file
ScheduleDose objectDefine drug dosing protocol
select (SimData)Select data from SimData object
selectbyname (SimData)Select data by name from SimData object array
SensitivityAnalysisOptionsSpecify sensitivity analysis options
set (any object)Set object properties
setactiveconfigset (model)Set active configuration set for model object
setparameter (kineticlaw)Specify specific parameters in kinetic law object
setspecies (kineticlaw)Specify species in kinetic law object
setTable(ScheduleDose,RepeatDose)Set dosing information from table to dose object
simbiologyOpen SimBiology desktop for modeling and simulation
SimBiology.export.DoseExported SimBiology model dose object
SimBiology.export.ExplicitTauSimulationOptionsSettings for explicit tau-leaping solver of exported SimBiology model
SimBiology.export.ImplicitTauSimulationOptionsSettings for implicit tau-leaping stochastic simulation of exported SimBiology model
SimBiology.export.ModelExported SimBiology model object
SimBiology.export.Model.acceleratePrepare exported SimBiology model for acceleration
SimBiology.export.Model.getdoseReturn exported SimBiology model dose object
SimBiology.export.Model.getIndexGet indices into ValueInfo and InitialValues properties
SimBiology.export.Model.isAcceleratedDetermine whether an exported SimBiology model is accelerated
SimBiology.export.Model.simulateSimulate exported SimBiology model
SimBiology.export.ODESimulationOptionsSettings for deterministic, ordinary differential equation simulation of exported SimBiology model
SimBiology.export.RepeatDoseRepeated doses for exported SimBiology model
SimBiology.export.ScheduleDoseSchedule dose for exported SimBiology model
SimBiology.export.SimulationOptionsSimulation settings for exported SimBiology model
SimBiology.export.StochasticSimulationOptionsSettings for stochastic simulation of exported SimBiology model
SimBiology.export.ValueInfoModifiable species, compartments, or parameters in exported SimBiology model
SimData objectSimulation data storage
SimFunction objectFunction-like interface to execute SimBiology models
SimFunctionSensitivity objectSimFunctionSensitivity object, subclass of SimFunction object
SolverOptionsSpecify model solver options
Species objectOptions for compartment species
summary(LeastSquaresResults,OptimResults,NLINResults)Plot a summary figure that contains estimated values and estimation statistics
Unit objectHold information about user-defined unit
UnitPrefix objectHold information about user-defined unit prefix
updateInitialAssignmentsUpdate initial assignment rules to remove order dependencies
Variant objectStore alternate component values
verifyValidate and verify SimBiology model
verify (covmodel)Check covariate model for errors