importPEtabSBML_indiv: Import an SBML model and corresponding PEtab objects

In dlill/petab: PEtab support for R

Import an SBML model and corresponding PEtab objects

Description

This function imports an SBML model and corresponding PEtab files, e.g. from the Benchmark collection.

Usage

importPEtabSBML_indiv(
  filename = "enzymeKinetics/enzymeKinetics.yaml",
  testCases = FALSE,
  path2TestCases = "PEtabTests/",
  .compiledFolder = file.path("CompiledObjects"),
  NFLAGcompile = c(Auto = 3, Recompile = 0, RebuildGrids = 1, LoadPrevious = 2)[3],
  SFLAGbrowser = c("0None", "1Beginning", "2BuildGrids", "3Compilation",
    "4CollectList", "5Scales", "6ParameterFormulaInjection")[1]
)

Arguments

filename	"path/to/modelname.petab". Will look for files like "path/to/modelname/model_modelname.xml"
path2TestCases	path to feature test case folder
TestCases	TRUE to load feature test cases
compile	if FALSE, g, ODEmodel and err are loaded from .RData (if present) and compilation time is saved

Details

Objects such as model equations, parameters or data are automatically assigned to the following standard variables and written to your current working directory (via <<-): reactions, observables, errors, g, x, p0, err, obj, mydata, ODEmodel, condition.grid, trafoL, pouter, times. Compiled objects (g, ODEmodel and err) are saved in .RData.

Value

list of dMod model objects with entries

• symbolicEquations

• odemodel

• data

• gridlist

• e

• fns

• prd

• obj_data

• pars

Author(s)

Daniel Lill ([e-mail]) building on the original function of Marcus and Svenja

dlill/petab documentation built on Oct. 9, 2022, 3:07 p.m.