RunNM {PKtools}R Documentation

RunNM

Description

RunNM runs the function pk to create pharmacokinetics datasets for R and NONMEM, runs the system commend to run NONMEM, and reads the NONMEM datasets.

Usage

 RunNM(inputStructure, data, nameData) 

Arguments

inputStructure the standard NONMEM control file
data list of data files including pk data and covariate data with length of the full dataset
nameData list of names, including, covnames, yvarlab, xvarlab, params

Details

nameData is a list of the labels including the names of the covariates in the order there are given in the covariate dataset, y and x variable, the random parameters (reparams -should match the list random effects defined in the control file), fixed parameters (params -should match the list for fixed effects in the control file), label for transformed parameters ( in the Theo example the model parameters are on a log scale tparam=c("log(Ka)","log(V)","log(Cl)") and the names of the variance parameters should list the parameters for the upper triangle of variance covariance table.

Value

The output from NMoutput are data tables of the results, including the objective function (ob), population parameters (params), random effects (re), individual parameters (ip), covariates (cov), predicted values (pred). If the objects of class NONMEM is called NM, then the objective function can be accessed by typing NM$ob, similarly the population parameters can be accessed by typing NM$param.

Author(s)

M.S. Blanchard <sblanchard@coh.org>

References

Boeckmann, A.J. and Sheiner, L.B. and Beal, S.L. (1994). "NONMEM Users Guide- Part V, Introductory Guide". NONMEM Project Group:UCSF.

See Also

pk, coVar.id, RunNLME,RunWB

Examples

 
#NONMEM example
if (.Platform$OS.type =="windows"){
curwd=getwd()
if (file.exists("C:/nmv/run")) {
  setwd("C:/nmv/run")
  library(PKtools)
  data(Theoph)
  Theoph<-Theoph[Theoph$Time!=0,]
  id<-as.numeric(as.character(Theoph$Subject))
  dose<-Theoph$Dose
  time<-Theoph$Time
  concblq<-round(sqrt(Theoph$conc),4)
  conc<-concblq
  Theo<-data.frame(cbind(id,dose,time,conc))
  names(Theo)<-c("id","dose","time","conc")
  wt.v<-Theoph$Wt

  data<-list(pkvar=Theo, cov=wt.v)

  nameData<-list(covnames=c("wt"), 
               yvarlab="Sqrt(Theop. Conc.) Sqrt(mg/L)",
               xvarlab="Time since dose (hrs)",
               reparams=c("Ka", "V", "Cl"),
               params=c("Ka", "V", "Cl"),
               tparams=c("log(Ka)", "log(V)", "log(Cl)"),
               varnames=c("D[1,1]","D[1,2]","D[2,2]","D[1,3]","D[2,3]","D[3,3]")
               )

  NM<-RunNM(inputStructure="control.model5", data=data, nameData=nameData) 
  print(NM)
  setwd(curwd)
  }
else{
    "You do not have NONMEM."
  }
  } 
  

[Package PKtools version 1.4-0 Index]