devel/run_models.R

In philipdelff/NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling

library(NMdata)
library(devtools)
library(NMsim)

## load_all()
load_all("~/wdirs/NMdata")
NMdataConf(as.fun="data.table")
load_all("~/wdirs/NMsim",export_all = FALSE)


NMdataConf(path.nonmem="/opt/nonmem/nm751/run/nmfe75")
NMdataConf(dir.psn="/opt/psn")
NMdataConf(path.nonmem="/opt/NONMEM/nm75/run/nmfe75")
NMdataConf(as.fun="data.table")


NMexec("../tests/testthat/testData/nonmem/xgxr004.mod",sge=FALSE)
NMexec("../tests/testthat/testData/nonmem/xgxr014.mod",sge=FALSE)
NMexec("../tests/testthat/testData/nonmem/xgxr018.mod",sge=FALSE,method.exec="nmsim")
NMexec("../tests/testthat/testData/nonmem/xgxr028.mod",sge=FALSE)
NMexec("../tests/testthat/testData/nonmem/xgxr033.mod",sge=FALSE)

NMexec(files="../inst/examples/nonmem/xgxr018.mod",sge=FALSE,method.exec="nmsim")
NMexec("../inst/examples/nonmem/xgxr031.mod",sge=FALSE)
NMexec(files="../inst/examples/nonmem/xgxr032.mod",sge=FALSE,method.exec="nmsim")
NMexec(files="../inst/examples/nonmem/xgxr132.mod",sge=FALSE,method.exec="nmsim")
## NMexec(files="../inst/examples/nonmem/xgxr133.mod",sge=FALSE)
NMexec(files="../inst/examples/nonmem/xgxr133.mod",sge=FALSE,method.exec="nmsim")
NMreadSection("../inst/examples/nonmem/xgxr133.mod",section="OMEGA")
NMreadExt("../inst/examples/nonmem/xgxr133.mod")
##/home/philip/wdirs/NMdata/inst/examples/nonmem/xgxr133.mod



### generating output tables with subproblems
library(NMsim)
dt.dos <- NMcreateDoses(TIME=0,AMT=100,CMT=1)
dt.sim <- addEVID2(dt.dos,time.sim=1:3,CMT=2,as.fun="data.table")
dt.sim[,ROW:=.I]
dt.sim[,BBW:=60]

getwd()
simres <- NMsim(file.mod="../tests/testthat/testData/nonmem/xgxr014.mod",
      data=dt.sim,
      dir.sims="../tests/testthat/testData/simulations",
      subproblems=4,
      name.sim="subprobs",
      path.nonmem="/opt/nonmem/nm751/run/nmfe75")


file.mod <- "../inst/examples/nonmem/xgxr132.mod"
NMexec(file.mod,sge=FALSE)

NMreadExt(file.mod)