Access model output table data from an xpdb object.
Arguments
- xpdb
An
xpose_dataobject from which the model output file data will be extracted.- table
Name of the output table to be extracted from the xpdb e.g. 'sdtab001'. Alternative to the `.problem` argument.
- .problem
Accesses all tables from the specified problem. Alternative to the `table` argument.
- quiet
Logical, if
FALSEmessages are printed to the console.
Value
By default returns data from the last estimation problem. If only simulation problems are present then the data from last simulation will be returned instead. Object returned as tibble for single tables/problems or a named list for multiple tables/problems.
Examples
# By table name
sdtab <- get_data(xpdb_ex_pk, 'sdtab001')
sdtab
#> # A tibble: 550 × 18
#> ID DOSE AMT SS II TIME TAD IPRED CWRES CPRED IWRES EVID
#> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 110 200 100 0 0 0 0 0 0 0 0 1
#> 2 110 200 0 0 0 1 1 0.214 -2.83 0.584 2.40 0
#> 3 110 200 0 0 0 1.5 1.5 0.296 -1.62 0.737 1.03 0
#> 4 110 200 0 0 0 2 2 0.349 1.10 0.790 -1.71 0
#> 5 110 200 0 0 0 4 4 0.392 0.585 0.588 -0.861 0
#> 6 110 200 0 0 0 6 6 0.329 -0.0262 0.304 0.0457 0
#> 7 110 200 0 0 0 8 8 0.249 0.0940 0.127 0.0132 0
#> 8 112 200 100 0 0 0 0 0 0 0 0 1
#> 9 112 200 0 0 0 0.5 0.5 0.556 0.0341 0.627 -0.275 0
#> 10 112 200 0 0 0 1 1 0.712 -0.417 0.788 0.163 0
#> # ℹ 540 more rows
#> # ℹ 6 more variables: A1 <dbl>, A2 <dbl>, DV <dbl>, PRED <dbl>, RES <dbl>,
#> # WRES <dbl>
# By problem
tables <- get_data(xpdb_ex_pk, .problem = 1)
tables
#> # A tibble: 550 × 31
#> ID SEX MED1 MED2 DOSE AMT SS II TIME TAD IPRED CWRES
#> <fct> <fct> <fct> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 110 1 0 1 200 100 0 0 0 0 0 0
#> 2 110 1 0 1 200 0 0 0 1 1 0.214 -2.83
#> 3 110 1 0 1 200 0 0 0 1.5 1.5 0.296 -1.62
#> 4 110 1 0 1 200 0 0 0 2 2 0.349 1.10
#> 5 110 1 0 1 200 0 0 0 4 4 0.392 0.585
#> 6 110 1 0 1 200 0 0 0 6 6 0.329 -0.0262
#> 7 110 1 0 1 200 0 0 0 8 8 0.249 0.0940
#> 8 112 1 1 1 200 100 0 0 0 0 0 0
#> 9 112 1 1 1 200 0 0 0 0.5 0.5 0.556 0.0341
#> 10 112 1 1 1 200 0 0 0 1 1 0.712 -0.417
#> # ℹ 540 more rows
#> # ℹ 19 more variables: CPRED <dbl>, IWRES <dbl>, EVID <dbl>, A1 <dbl>,
#> # A2 <dbl>, DV <dbl>, PRED <dbl>, RES <dbl>, WRES <dbl>, CLCR <dbl>,
#> # AGE <dbl>, WT <dbl>, KA <dbl>, CL <dbl>, V <dbl>, ALAG1 <dbl>, ETA1 <dbl>,
#> # ETA2 <dbl>, ETA3 <dbl>
# Tip to list available tables in the xpdb
print(xpdb_ex_pk)
#> run001.lst overview:
#> - Software: nonmem 7.3.0
#> - Attached files (memory usage 1.5 Mb):
#> + obs tabs: $prob no.1: catab001.csv, cotab001, patab001, sdtab001
#> + sim tabs: $prob no.2: simtab001.zip
#> + output files: run001.cor, run001.cov, run001.ext, run001.grd, run001.phi, run001.shk
#> + special: <none>
#> - gg_theme: theme_readable
#> - xp_theme: theme_xp_default
#> - Options: dir = data, quiet = FALSE, manual_import = NULL