This function creates a simulation model from an original NONMEM model where dollar blocks are replaced and/or commented based on input file and other simulation functions within package
Arguments
- omod
character string for the original model
- smod
character string for the simulation model (for writing the model to disk)
- data
character string for the input dataset for the simulation
- subprobs
numeric indicating the number of subproblems in simulation model
- table
character of length 1 with the items for the dollar table block (if null it will use items in input dataset)
- sigma_ext
character with the name of the ext file which includes the sigma value (in case residual error is coded in the dollar sigma block)
Details
The function will adapt an original model in such a way that it can be used directly for simulations the assumptions are that an input dataset is created using sample_par and simdata. This means that all THETA and ETA values are available in the simulation dataset as respectively STHETAN and SETAN (simulated THETA/ETA n). Furthermore it is assumed that the input dataset is a csv file. The function will first comment all applicable dollar blocks. Then a OMEGA is added with 0 FIX and the INPUT, DATA and TABLE blocks are appended with information based on the input dataset. Finally all THETAs and ETAs are replaced with the items in the dataset and the simulation model is written to disk.
Examples
nmmod <- system.file("example_models","PK.1CMT.ORAL.mod", package = "amp.sim")
dat <- simdata(0:24, dosetime = 0, doseheight = 10, addl = 2, ii = 24,
numid = 50, STHETA1= 1, STHETA2 = 2, STHETA3 = 1,
SETA1 = 0, SETA2 = 0)
tmp_out <- tempfile(fileext = ".csv")
mod_out <- tempfile(fileext = ".mod")
write.csv(dat,file=tmp_out, na=".", quote=FALSE, row.names = FALSE)
make_nmsimmodel(nmmod, mod_out, data=tmp_out)
#> Check residual error; in case coded as sigma use 'sigma_ext' otherwise check if the correct THETA is used icw uncertainty
readLines(mod_out) |> head(n=15) |> cat(sep="\n")
#> ;; Importance: 0
#> ;; Description: 1 CMT PK model with oral absorption
#> $PROB 1 CMT PK model with oral absorption
#> $DATA file1c971d812856.csv IGNORE=@
#> $INPUT
#> ID DOSE TIME AMT ADDL II DV STHETA1 STHETA2 STHETA3 SETA1 SETA2
#> ; $INPUT
#> ; STUDYID ID TRT CMT AMT TIME TAFD TALD DV EVID MDV CNTRY SEX AGE WEIGHT HEIGHT BMI FLAGPK STIME
#> ; $DATA NM.theoph.02B.csv IGNORE=@
#> $SUBROUTINES ADVAN6 TOL=3
#> $MODEL
#> COMP = (ABS)
#> COMP = (CENTRAL)
#>
#> $PK