All functions

CoRC-package

CoRC: COPASI R Connector.

addExperiments()

Add a parameter estimation experiment

addOptimizationParameter()

Add an optimization parameter

addParameterEstimationParameter()

Add a parameter estimation parameter

applyInitialState()

Apply the model's initial state

autoplot(<copasi_ts>)

Autoplot method for COPASI timeseries objects.

biomodels_url()

Generate a URL to a BioModels model.

clearCustomKineticFunctions()

Clear custom functions

clearExperiments()

Clear all parameter estimation experiments

clearOptimizationParameters()

Clear all optimization parameters

clearParameterEstimationParameters()

Clear all parameter estimation parameters

clearValidations()

Clear all parameter estimation validation data.

compileModel()

Compile the model

convertToIrreversible()

Convert the model to irreversible reactions

defineExperiments()

Define a parameter estimation experiment

defineOptimizationParameter()

Define an optimization parameter

defineParameterEstimationParameter()

Define a parameter estimation parameter

deleteCompartment()

Delete compartments

deleteEvent()

Delete events

deleteGlobalQuantity()

Delete global quantities

deleteKineticFunction()

Delete a function

deleteReaction()

Delete reactions

deleteSpecies()

Delete species

species() species_strict() quantity() quantity_strict() compartment() compartment_strict() reaction() reaction_strict() parameter() parameter_strict() event() event_strict() kinfunction() kinfunction_strict()

Entity finders

getAreaUnit()

Get the unit of area

getCompartmentReferences()

Get compartment references

getCompartments()

Get compartments

getCurrentModel()

Get the currently active model

getEvents()

Get events

getGlobalQuantities()

Get global quantities

getGlobalQuantityReferences()

Get global quantity references

getInitialTime()

Get the model's initial time

getInitialValue()

Calculate the initial value of an expression or reference

getLengthUnit()

Get the unit of length

getLinearNoiseApproximationSettings() getLNA()

Get linear noise approximation settings

getLinkMatrix()

Get link matrix

getLoadedModels()

Get a list of loaded models

getMetabolicControlAnalysisSettings() getMCA()

Get metabolic control analysis settings

getModelName()

Get the model's name

getOptimizationSettings() getOpt()

Set optimization settings

getParameterEstimationSettings() getPE()

Set parameter estimation settings

getParameterReferences()

Get reaction parameter references

getParameters()

Get reaction parameters

getQuantityUnit()

Get the unit of quantity

getReactionMappings()

Get reaction parameter mappings

getReactionReferences()

Get reaction references

getReactions()

Get reactions

getReducedStoichiometryMatrix()

Get reduced stoichiometry matrix

getSpecies()

Get species

getSpeciesReferences()

Get species references

getSteadyStateSettings() getSS()

Get steady state settings

getStoichiometryMatrix()

Get stoichiometry matrix

getTimeCourseSettings() getTC()

Get time course settings

getTimeUnit()

Get the unit of time

getValidReactionFunctions()

Get valid function names for reaction

getValue()

Calculate the value of an expression or reference

getVersion()

Get COPASI version numbers

getVolumeUnit()

Get the unit of volume

loadCombineArchive()

Load a combine archive

loadExamples()

Load example models

loadModel()

Load a model

loadModelFromString()

Load a model from a string

loadSBML()

Load an SBML model

loadSBMLFromString()

Load an SBML model from a string

newCompartment()

Create a new compartment

newEvent()

Create a new event

newGlobalQuantity()

Create a new global quantity

newKineticFunction()

Create a new kinetic function

newModel()

Load an empty model

newReaction()

Create a new reaction

newSpecies()

Create a new species

openCopasi()

Open the model in the COPASI GUI

runLinearNoiseApproximation() runLNA()

Run linear noise approximation

runMetabolicControlAnalysis() runMCA()

Run metabolic control analysis

runOptimization() runOpt()

Run optimization

runParameterEstimation() runPE()

Run parameter estimation

runSigmaPoint() runSP()

Run sigma point method

runSteadyState() runSS()

Run to steady state

runTimeCourse() runTC()

Run a time course

saveCombineArchive()

Save the model as a combine archive

saveModel()

Save the model as a .cps file

saveModelToString()

Save the model to string

saveSBML()

Save the model as a SBML file

saveSBMLToString()

Save the model to an SBML string

setAreaUnit()

Set the unit of area

setCompartments()

Set compartments

setCurrentModel()

Set the currently active model

setEvents()

Set events

setGlobalQuantities()

Set global quantities

setInitialTime()

Set the model's initial time

setLengthUnit()

Set the unit of length

setLinearNoiseApproximationSettings() setLNA()

Set linear noise approximation settings

setMetabolicControlAnalysisSettings() setMCA()

Set metabolic control analysis settings

setModelName()

Set a model's name

setOptimizationSettings() setOpt()

Set optimization settings

setParameterEstimationSettings() setPE()

Set parameter estimation settings

setParameters()

Set reaction parameters

setQuantityUnit()

Set the unit of quantity

setReactionFunction()

Set a reaction function

setReactionMappings()

Set reaction parameter mappings

setReactions()

Set reactions

setSpecies()

Set species

setSteadyStateSettings() setSS()

Set steady state settings

setTimeCourseSettings() setTC()

Set time course settings

setTimeUnit()

Set the unit of time

setVolumeUnit()

Set the unit of volume

unloadAllModels()

Unload all loaded models

unloadModel()

Unload a model

updateInitialState()

Update the model's initial state from the current state