Access model output file data from an xpdb object.
Usage
get_file(
xpdb,
file = NULL,
ext = NULL,
.problem = NULL,
.subprob = NULL,
.method = NULL,
quiet
)Arguments
- xpdb
An
xpose_dataobject from which the model output file data will be extracted.- file
Full name of the file to be extracted from the xpdb e.g. 'run001.phi'. Alternative to the 'ext' argument.
- ext
Extension of the file to be extracted from the xpdb e.g. 'phi'. Alternative to the 'file' argument.
- .problem
The problem to be used, by default returns the last one for each file.
- .subprob
The subproblem to be used, by default returns the last one for each file.
- .method
The estimation method to be used (e.g. 'foce', 'imp', 'saem'), by default returns the last one for each file.
- quiet
Logical, if
FALSEmessages are printed to the console.
Examples
# Single file (returns a tibble)
ext_file <- get_file(xpdb_ex_pk, file = 'run001.ext')
#> Returning data from run001.ext, $prob no.1, subprob no.1, method foce
ext_file
#> # A tibble: 28 × 16
#> ITERATION THETA1 THETA2 THETA3 THETA4 THETA5 THETA6 THETA7 `SIGMA(1,1)`
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0 25.4 1.47 7.45 0.214 0.200 0.00983 0.00601 1
#> 2 1 26.3 1.26 7.35 0.219 0.217 0.00989 0.00602 1
#> 3 2 25.6 1.47 7.29 0.216 0.212 0.00987 0.00603 1
#> 4 3 26.8 1.49 5.76 0.213 0.213 0.00979 0.00628 1
#> 5 4 26.7 1.49 5.69 0.213 0.212 0.00979 0.00629 1
#> 6 5 26.7 1.49 5.66 0.213 0.212 0.00979 0.00630 1
#> 7 6 26.6 1.49 5.03 0.210 0.217 0.0100 0.00652 1
#> 8 7 26.6 1.49 4.93 0.205 0.217 0.0100 0.00658 1
#> 9 8 26.6 1.48 4.62 0.211 0.217 0.00951 0.00735 1
#> 10 9 26.6 1.46 4.41 0.209 0.217 0.00903 0.00874 1
#> # ℹ 18 more rows
#> # ℹ 7 more variables: `OMEGA(1,1)` <dbl>, `OMEGA(2,1)` <dbl>,
#> # `OMEGA(2,2)` <dbl>, `OMEGA(3,1)` <dbl>, `OMEGA(3,2)` <dbl>,
#> # `OMEGA(3,3)` <dbl>, OBJ <dbl>
# Multiple files (returns a list)
files <- get_file(xpdb_ex_pk, file = c('run001.ext', 'run001.phi'))
#> Returning data from run001.ext, run001.phi
files
#> $run001.ext_prob_1_subprob_1_foce
#> # A tibble: 28 × 16
#> ITERATION THETA1 THETA2 THETA3 THETA4 THETA5 THETA6 THETA7 `SIGMA(1,1)`
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0 25.4 1.47 7.45 0.214 0.200 0.00983 0.00601 1
#> 2 1 26.3 1.26 7.35 0.219 0.217 0.00989 0.00602 1
#> 3 2 25.6 1.47 7.29 0.216 0.212 0.00987 0.00603 1
#> 4 3 26.8 1.49 5.76 0.213 0.213 0.00979 0.00628 1
#> 5 4 26.7 1.49 5.69 0.213 0.212 0.00979 0.00629 1
#> 6 5 26.7 1.49 5.66 0.213 0.212 0.00979 0.00630 1
#> 7 6 26.6 1.49 5.03 0.210 0.217 0.0100 0.00652 1
#> 8 7 26.6 1.49 4.93 0.205 0.217 0.0100 0.00658 1
#> 9 8 26.6 1.48 4.62 0.211 0.217 0.00951 0.00735 1
#> 10 9 26.6 1.46 4.41 0.209 0.217 0.00903 0.00874 1
#> # ℹ 18 more rows
#> # ℹ 7 more variables: `OMEGA(1,1)` <dbl>, `OMEGA(2,1)` <dbl>,
#> # `OMEGA(2,2)` <dbl>, `OMEGA(3,1)` <dbl>, `OMEGA(3,2)` <dbl>,
#> # `OMEGA(3,3)` <dbl>, OBJ <dbl>
#>
#> $run001.phi_prob_1_subprob_1_foce
#> # A tibble: 74 × 12
#> SUBJECT_NO ID `ETA(1)` `ETA(2)` `ETA(3)` `ETC(1,1)` `ETC(2,1)` `ETC(2,2)`
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 110 -0.0370 -0.00596 -2.14 0.0258 -0.00961 0.0339
#> 2 2 112 -0.0495 0.122 -0.0235 0.0140 -0.00219 0.0138
#> 3 3 113 0.332 0.0259 -1.15 0.00995 0.000300 0.0257
#> 4 4 121 0.304 0.249 1.89 0.00741 0.00362 0.0137
#> 5 5 123 0.0271 -0.0801 1.09 0.00794 0.00267 0.0135
#> 6 6 124 0.332 0.111 -1.54 0.0110 -0.00219 0.0307
#> 7 7 126 0.190 -0.0315 2.20 0.00785 0.00300 0.0136
#> 8 8 127 0.190 -0.0750 0.415 0.0112 0.00469 0.0153
#> 9 9 128 -0.0138 -0.00130 -1.27 0.0120 0.0000333 0.0287
#> 10 10 210 -0.307 -0.108 -0.0168 0.00988 0.00112 0.0163
#> # ℹ 64 more rows
#> # ℹ 4 more variables: `ETC(3,1)` <dbl>, `ETC(3,2)` <dbl>, `ETC(3,3)` <dbl>,
#> # OBJ <dbl>
#>
# Tip to list available files 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