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Interpret a model as an ODE

as_ode.Rd

This function accepts a list generated from a collection of TSV files (or a similar format) and interprets the contents as an ordinary differential equation (ODE).

Usage

as_ode(m, cla = requireNamespace("pracma"))

Arguments

m

a list of data.frames, each corresponding to a TSV file or sheet in a spreadsheet.

cla

a Boolean value indicating whether conservation law analysis should be performed.

Value

a list that contains a summary of this model interpreted as an ODE, crucially, the list contains the element vf, the right-hand-side (vector field) of the ODE, this is the main result of this function.

Details

The argument m can be obtained via model_from_tsv(). It has the components:

  • m$Constant

  • m$Parameter

  • m$Input

  • m$Expression

  • m$Compound

  • m$Reaction

  • m$Experiment

There can be additional components describing measured data for this model.

Examples

f <- uqsa_example("AKAR4")
m <- model_from_tsv(f)
o <- as_ode(m)
print(names(o))
#>  [1] "vf"                    "const"                 "par"                  
#>  [4] "var"                   "exp"                   "func"                 
#>  [7] "stoichiometric_matrix" "conservationLaws"      "tf"                   
#> [10] "name"                  "c_path"                "c.date"               
#> [13] "so_path"               "so.date"              
print(o$vf)
#>                   AKAR4p                        C 
#>            "+reaction_2" "-reaction_1+reaction_2"