getSpeciesNames Names of the species in a model

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

input_model

input should be an SBML Model

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)
#> 
#>   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)
getSpeciesNames(model)
#> [1] "E"  "S"  "P"  "ES"