inst/examples/S002-petab-fit.R

In dlill/conveniencefunctions: Convenience Functions

# library(conveniencefunctions)
devtools::load_all("~/Promotion/Promotion/Software/dMod")
devtools::load_all("~/Promotion/Promotion/Projects/conveniencefunctions")
try(setwd(dirname(rstudioapi::getSourceEditorContext()$path)))

setwd("/home/daniel/Promotion/Promotion/Projects/conveniencefunctions/inst/examples")
warning("absolute file path")
# -------------------------------------------------------------------------#
# Create enzyme kinetics model and data ----
# -------------------------------------------------------------------------#
pe <- readPetab("petab/enzymeKinetics.petab")
pd <- importPEtabSBML_indiv("petab/enzymeKinetics.petab", NFLAGcompile = 0)

pred <- pd$prd(seq(0,100), pd$pars)
pd$obj_data(pd$pars)

myfit <- trust(pd$obj_data, pd$pars,1,10,iterlim = 1000)
plotCombined(pd$prd(seq(0,100), pd$pars), pd$data)
plotCombined(pd$prd(seq(0,100), myfit$argument), pd$data)



# cfoutput_MdTable(getSpeciesInfo(el), NFLAGtribble = 2)
# sbml_exportEquationList(el, filename, parInfo = parInfo)

# Exit ----