inst/petabExamples/06-EK-2cond-CondSpecObservables/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)))
# -------------------------------------------------------------------------#
# Arguments ----
# -------------------------------------------------------------------------#
filename <- "petab"

# filename <- "/home/daniel/Promotion/Promotion/Software/PEtab/Benchmark-Models-PEtab/Benchmark-Models/Bachmann_MSB2011/"

NFLAGcompile = 0
.compiledFolder = "Compiled"
SFLAGbrowser = "0"

testCases = FALSE
path2TestCases = "PEtabTests/"

# -------------------------------------------------------------------------#
# OLD ----
# -------------------------------------------------------------------------#
pd <- importPEtabSBML_indiv("petab", NFLAGcompile = 0, .compiledFolder = "Compiled", SFLAGbrowser = "0")

# 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 ----