getSpeciesIC Initial values of the species in a model

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

input_model

input should be an SBML Model

Value

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

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.

Examples

sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
model <- getModel(sbml_file)
#> 
#>   filename: /home/runner/work/_temp/Library/r2sbml/examples/sbmlsimple.xml
#>   error(s): 0
#> 
#> 
#> File: /home/runner/work/_temp/Library/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
getSpeciesIC(model)
#>     E     S     P    ES 
#> 5e-21 1e-20 0e+00 0e+00