The xpose package was designed as a standardized interface between model outputs and R. Hence model output files can easily be imported in R and used to summarize data or create plots.
The files attached to an xpdb object can be displayed to the console simply by writing the xpdb name to the console or by using the print() function. Any of these files can be accessed from the xpdb using one of the functions listed below.
xpdb # or print(xpdb)run001.lst overview:
- Software: nonmem 7.3.0
- Attached files (memory usage 1.3 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 = analysis/models/pk/, quiet = FALSE, manual_import = NULLThe get_code() function can be used to access the parsed model code from the xpdb. This code was used to create the summary and find table names. The parsed code can be used to get additional information about the run. If the argument .problem is specified a subset of the code can be returned based on $PROBLEM.
Note that general code warnings and PsN outputs appended are listed as problem 0.
code <- get_code(xpdb)
code# A tibble: 764 x 5
problem level subroutine code comment
* <int> <int> <chr> <chr> <chr>
1 0 0 oth Mon Oct 16 13:34:28 CEST 2017 ""
2 0 0 oth "" ; 1. Based on: …
3 0 0 oth "" "; 2. Descripti…
4 0 0 oth "" ; NONMEM PK exa…
5 1 1 pro Parameter estimation ""
6 1 2 inp ID DOSE DV SCR AGE SEX CLASS WT ACE MED1 MED2 TAD TIME ""
7 1 2 inp " CLCR AMT SS II EVID" ""
8 1 3 dat ../../mx19_2.csv IGNORE=@ ""
9 1 4 abb DERIV2=NO ""
10 1 5 sub ADVAN2 TRANS1 ""
# ... with 754 more rowsThe get_data() function can be used to access the imported table files. Tables can be accessed by table name or by .problem. In the latter a single dataset containing all aggregated tables is returned. If more than one table name or .problem number is provided a named list is returned.
Note when providing a table name it is not guaranteed that the table will be identical to its file (i.e. the order of the columns may have been changed and tables with FIRSTONLY will no longer be deduplicated).
data <- get_data(xpdb, table = 'cotab001')
data# A tibble: 550 x 4
ID CLCR AGE WT
<fct> <dbl> <dbl> <dbl>
1 110 66.0 68.0 105
2 110 66.0 68.0 105
3 110 66.0 68.0 105
4 110 66.0 68.0 105
5 110 66.0 68.0 105
6 110 66.0 68.0 105
7 110 66.0 68.0 105
8 112 47.0 73.0 80.0
9 112 47.0 73.0 80.0
10 112 47.0 73.0 80.0
# ... with 540 more rowsThe get_file() function can be used to access the imported output files. Files can be accessed by file name, by .problem, .subprob and/or .method. If more than one file name, .problem, .subprob, or .method is provided a named list is returned.
file <- get_file(xpdb, file = 'run001.ext')
file# A tibble: 28 x 16
ITERATION THETA1 THETA2 THETA3 THETA4 THETA5 THETA6 THETA7 `SIGMA(1,1)` `OMEGA(1,1)`
<dbl> <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 1.00 0.0740
2 1.00 26.3 1.26 7.35 0.219 0.217 0.00989 0.00602 1.00 0.0744
3 2.00 25.6 1.47 7.29 0.216 0.212 0.00987 0.00603 1.00 0.0741
4 3.00 26.8 1.49 5.76 0.213 0.213 0.00979 0.00628 1.00 0.0730
5 4.00 26.7 1.49 5.69 0.213 0.212 0.00979 0.00629 1.00 0.0730
6 5.00 26.7 1.49 5.66 0.213 0.212 0.00979 0.00630 1.00 0.0730
7 6.00 26.6 1.49 5.03 0.210 0.217 0.0100 0.00652 1.00 0.0724
8 7.00 26.6 1.49 4.93 0.205 0.217 0.0100 0.00658 1.00 0.0717
9 8.00 26.6 1.48 4.62 0.211 0.217 0.00951 0.00735 1.00 0.0633
10 9.00 26.6 1.46 4.41 0.209 0.217 0.00903 0.00874 1.00 0.0766
# ... with 18 more rows, and 6 more variables: `OMEGA(2,1)` <dbl>, `OMEGA(2,2)` <dbl>,
# `OMEGA(3,1)` <dbl>, `OMEGA(3,2)` <dbl>, `OMEGA(3,3)` <dbl>, OBJ <dbl>The get_prm() function can be used to access the parameter estimates. To get a nice parameter table printed to the console use the function prm_table() instead. The arguments .problem, .subprob and .method can be used to select the parameter estimates to output.
# Raw output for editing
prm <- get_prm(xpdb, digits = 4)
prm# A tibble: 11 x 10
type name label value se rse fixed diagonal m n
* <chr> <chr> <chr> <dbl> <dbl> <dbl> <lgl> <lgl> <dbl> <dbl>
1 the THETA1 TVCL 26.3 0.892 0.0339 F NA 1.00 NA
2 the THETA2 TVV 1.35 0.0438 0.0325 F NA 2.00 NA
3 the THETA3 TVKA 4.20 0.809 0.192 F NA 3.00 NA
4 the THETA4 LAG 0.208 0.0157 0.0755 F NA 4.00 NA
5 the THETA5 Prop. Err 0.205 0.0224 0.110 F NA 5.00 NA
6 the THETA6 Add. Err 0.0106 0.00366 0.347 F NA 6.00 NA
7 the THETA7 CRCL on CL 0.00717 0.00170 0.237 F NA 7.00 NA
8 ome OMEGA(1,1) IIV CL 0.270 0.0233 0.0862 F T 1.00 1.00
9 ome OMEGA(2,2) IIV V 0.195 0.0320 0.164 F T 2.00 2.00
10 ome OMEGA(3,3) IIV KA 1.38 0.202 0.146 F T 3.00 3.00
11 sig SIGMA(1,1) "" 1.00 NA NA T T 1.00 1.00# Nicely formated table
prm_table(xpdb, digits = 4)
Reporting transformed parameters:
For the OMEGA and SIGMA matrices, values are reported as standard deviations for the diagonal elements and as correlations for the off-diagonal elements. The relative standard errors (RSE) for OMEGA and SIGMA are reported on the approximate standard deviation scale (SE/variance estimate)/2. Use `transform = FALSE` to report untransformed parameters.
Estimates for $prob no.1, subprob no.0, method foce
Parameter Label Value RSE
THETA1 TVCL 26.29 0.03391
THETA2 TVV 1.348 0.0325
THETA3 TVKA 4.204 0.1925
THETA4 LAG 0.208 0.07554
THETA5 Prop. Err 0.2046 0.1097
THETA6 Add. Err 0.01055 0.3466
THETA7 CRCL on CL 0.007172 0.2366
OMEGA(1,1) IIV CL 0.2701 0.08616
OMEGA(2,2) IIV V 0.195 0.1643
OMEGA(3,3) IIV KA 1.381 0.1463
SIGMA(1,1) 1 fix - The get_summary() function can be used to access the generated run summary from which the template_titles. If the argument .problem is specified a subset of the summary can be returned based on $PROBLEM.
Note that general summary information are listed as problem 0.
run_sum <- get_summary(xpdb, .problem = 0)
run_sum# A tibble: 12 x 5
problem subprob descr label value
<dbl> <dbl> <chr> <chr> <chr>
1 0 0 Run description descr NONMEM PK example for xpose
2 0 0 Run directory dir analysis/models/pk/
3 0 0 Run errors errors na
4 0 0 ESAMPLE seed number esampleseed na
5 0 0 Run file file run001.lst
6 0 0 Number of ESAMPLE nesample na
7 0 0 Reference model ref 000
8 0 0 Run number run run001
9 0 0 Software software nonmem
10 0 0 Run start time timestart Mon Oct 16 13:34:28 CEST 2017
11 0 0 Run stop time timestop Mon Oct 16 13:34:35 CEST 2017
12 0 0 Software version version 7.3.0