Extract Measured Data and Simulation Experiment Instructions

This function accepts the model obtained via model_fromt_tsv or a similar function. It finds the data tables for this model (if any are present), and finds the simulation instructions to reproduce these data sets using the model.

Usage

experiments(m, o = NULL)

Arguments

m

the model (with data), as obtained via model_from_tsv(), or similar.

o

the ode derived from m, only necessary if the experiments need to take conservation laws into account

Value

a list of simulation instructions

Details

This function requires that the files the model is stored as contains measurements (data) that can be interpreted fairly easily. Each data file needs columns that are named like the observable quantities listed in the Output table.

If the data is very indirectly related to the model, then we don't interpret the data files themselves and the user needs to write a specialized likelihood function to relate the raw data in the files with something that the model does. In such cases, don't use this function.

The simulation experiments returned here, include model input parameters. Whenever conservation law analysis is perfomed, the conserved constants are set as input parameters, because the conserved amount can differ between experiments. For this reason the Experiment table is interpreted differently in the presence of conservation laws. Otherwise (no conservation laws), the o parameter can be omitted.

The instructions must be organised in a table called Experiment(s).

Examples

f <- uqsa_example("AKAR4")
m <- model_from_tsv(f)
o <- as_ode(m)
ex <- experiments(m,o)
print(names(ex))
#> [1] "400nM" "100nM" "25nM" 
print(ex[[1]]$input)
#> AKAR4_C_ConservedConst   AKAR4_ConservedConst 
#>                    0.4                   -0.2