inst/petabExamples/08-EnzymeKinetics-Events/S002-petab-fit.R

In dlill/petab: PEtab support for R

# library(petab)
devtools::load_all("~/Promotion/Promotion/Projects/petab")
try(setwd(dirname(rstudioapi::getSourceEditorContext()$path)))
# -------------------------------------------------------------------------#
# Create enzyme kinetics model and data ----
# -------------------------------------------------------------------------#
pd <- importPEtabSBML_indiv("petab/petab.yaml", NFLAGcompile = 0, .compiledFolder = "Compiled", SFLAGbrowser = "0")

pd_predictAndPlot2(pd)

pd_fit(pd)
pd <- readPd(pd_files(pd$filenameParts)$rdsfile)
pd_predictAndPlot2(pd)


# # Test model
# pred <- pd$prd(seq(0,100), pd$pars)
# pd$obj_data(pd$pars)
# 
# # Test fitting
# myfit <- trust(pd$obj_data, pd$pars,1,10,iterlim = 1000)
# plotCombined(pd$prd(seq(0,100), pd$pars), pd$dModAtoms$data)
# plotCombined(pd$prd(seq(0,100), myfit$argument), pd$dModAtoms$data)

# # Mstrust
# center <- pepy_sample_parameter_startpoints(pd$pe, n_starts = 8)
# fits <- mstrust(pd$obj_data, center, "fit", fits = 5, iterlim = 20, cores = 8)
# fits <- as.parframe(fits)
# plotValues(fits)
# dMod_saveMstrust(fits, ".", FLAGoverwrite = TRUE)
# unlink("fit", T)


# Exit ----