Package {r2sbml}

Convert an SBML model to simulation code

Description

Writes the model's mass balances, rules and parameters as code for the chosen simulation tool, ready to simulate.

Usage

convertReactions(infile, outfile, format = "R")

Arguments

Value

NULL invisibly

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
out_file <- tempfile(fileext = ".R")
convertReactions(sbml_file, out_file, format = "R")
out_file_mrg <- tempfile(fileext = ".cpp")
convertReactions(sbml_file, out_file_mrg, format = "mrgsolve")
out_file_rx <- tempfile(fileext = ".R")
convertReactions(sbml_file, out_file_rx, format = "nlmixr2")
out_file_m <- tempfile(fileext = ".m")
convertReactions(sbml_file, out_file_m, format = "MATLAB")
out_file_jl <- tempfile(fileext = ".jl")
convertReactions(sbml_file, out_file_jl, format = "Julia")
out_file_ub <- tempfile(fileext = ".txt")
convertReactions(sbml_file, out_file_ub, format = "ubiquity")

Check an SBML file for errors

Description

Reads the file and prints the number of diagnostics libSBML reports, then the diagnostics themselves.

Usage

echoSBML(filename)

Arguments

Value

the number of diagnostics, as an integer

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
echoSBML(sbml_file)

Names of the compartments in a model

Description

Returns the name where one is set and falls back to the id otherwise, the same rule getSpeciesNames() uses. Previously this returned the id unconditionally while getSpeciesNames() returned the name, so the two disagreed about what a "name" was. For a model whose compartments set no name – which is all ten of the bundled examples – the result is unchanged.

Usage

getCmtNames(input_model)

Arguments

Value

a character vector, one entry per compartment, in model order

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getCmtNames(model)

Sizes of the compartments in a model

Description

Reports each compartment's declared size, as the file states it.

Usage

getCmtSizes(input_model)

Arguments

Value

a numeric vector, one entry per compartment, in model order

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getCmtSizes(model)

Print the events of a model

Description

Prints each event's trigger and assignments as infix math.

Usage

getEventMath(input_model)

Arguments

Value

0; called for the printed output

Examples

sbml_file <- system.file("examples", "sbmlevent.xml", package = "r2sbml")
model <- getModel(sbml_file)
getEventMath(model)

Print the function definitions of a model

Description

Prints each function definition's arguments and body as infix math.

Usage

getFunctionDefinition(input_model)

Arguments

Value

0; called for the printed output

Examples

sbml_file <- system.file("examples", "sbmlfunctiondefinition.xml", package = "r2sbml")
model <- getModel(sbml_file)
getFunctionDefinition(model)

Read an SBML model

Description

Reads an SBML file and keeps the parsed document alive for the other query functions. A file with error- or fatal-severity diagnostics is an error; lesser diagnostics are raised as warnings.

Usage

getModel(filename)

Arguments

Value

an external pointer to the model, to pass to the other functions

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)

Number of species in a model

Description

Counts the species the model declares.

Usage

getNumSpecies(input_model)

Arguments

Value

an integer, the number of species

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getNumSpecies(model)

Table of the parameters in a model

Description

Lists each global parameter with its declared value and units.

Usage

getParameterTable(input_model)

Arguments

Value

a data frame with one row per parameter and columns Number, ID, Name, Value and Units

Examples

sbml_file <- system.file("examples", "sbmlassignmentrules.xml", package = "r2sbml")
model <- getModel(sbml_file)
getParameterTable(model)

Print the rate laws of a model

Description

Prints each reaction's kinetic law as infix math.

Usage

getReactionMath(input_model)

Arguments

Value

0; called for the printed output

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getReactionMath(model)

Table of the reactions in a model

Description

Lists each reaction with its rate law written as infix math.

Usage

getReactionTable(input_model)

Arguments

Value

a data frame with one row per reaction and columns Number, ID, Name, Reversible and RateLaw

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getReactionTable(model)

Print the rules of a model

Description

Prints each rule as infix math; an algebraic rule is printed as f = 0.

Usage

getRuleMath(input_model)

Arguments

Value

0; called for the printed output

Examples

sbml_file <- system.file("examples", "sbmlassignmentrules.xml", package = "r2sbml")
model <- getModel(sbml_file)
getRuleMath(model)

Initial values of the species in a model

Description

A species carries initialAmount or initialConcentration, never both, and the unset one reads back as NaN. Asking only for the concentration therefore returned NaN for every species in an amount-based model. This returns whichever attribute the model actually sets.

Usage

getSpeciesIC(input_model)

Arguments

Details

The value is reported as the file states it, with no unit conversion, so a model that mixes amount-valued and concentration-valued species yields a vector that mixes units too – getSpeciesTable() shows which column each species used. This deliberately differs from convertReactions(), which must divide an amount by the compartment volume because the ODE it generates integrates concentrations.

A species that sets neither attribute – its value comes from an initial assignment or a rule – is reported as NA, not 0.

Value

a named numeric vector, one entry per species, named by species id

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getSpeciesIC(model)

Names of the species in a model

Description

SBML separates id, which every species must have, from name, which is an optional human-readable label. Most models in the wild set only id, so returning name alone gave a vector of empty strings. This returns the name where one is set and falls back to the id otherwise, which is how SBML tools conventionally display a species. getCmtNames() follows the same rule. Use getSpeciesTable() when you need the two columns separately.

Usage

getSpeciesNames(input_model)

Arguments

Value

a character vector, one entry per species, in model order

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getSpeciesNames(model)

Table of the species in a model

Description

Lists each species with its initial value, compartment and flags.

Usage

getSpeciesTable(input_model)

Arguments

Value

a data frame with one row per species and columns Number, Name, ID, InitialConcentration, InitialAmount, Compartment, CompartmentVol, BoundaryCondition and Constant

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
getSpeciesTable(model)

Summarise an SBML file

Description

Prints the file's SBML level and version and how many of each component its model has.

Usage

printSBML(filename)

Arguments

Value

0 on success and 1 when the file has errors or no model; called for the printed summary

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
printSBML(sbml_file)