Report diagnostics

Quick look summary for model: 106

• Number of subjects: 160
• Number of observations: 3142
• Number of records: 4292
• Objective function value (final est. method): 30900
• Condition number: 48.5
• Dataset: ../data/derived/pk.csv
• Figures saved to: deliv/figure/106
• No Heuristic Problems Detected

parameter_names	estimate	stderr	shrinkage
THETA1	0.443	0.0643	NA
THETA2	4.12	0.0275	NA
THETA3	1.17	0.0280	NA
THETA4	4.21	0.0190	NA
THETA5	1.28	0.0348	NA
THETA6	0.485	0.0395	NA
THETA7	-0.0377	0.0635	NA
THETA8	0.419	0.0863	NA
OMEGA(1,1)	0.219	0.0526	14.4
OMEGA(2,1)	0.0668	0.0194	NA
OMEGA(2,2)	0.0824	0.00981	5.50
OMEGA(3,1)	0.121	0.0224	NA
OMEGA(3,2)	0.0703	0.00918	NA
OMEGA(3,3)	0.114	0.0128	1.25
SIGMA(1,1)	0.0399	0.00123	5.01

General diagnostic plots

DV vs PRED and IPRED

## [1] "DV vs PRED and IPRED"

## [1] "DV vs PRED and IPRED by renal function"

## [1] "DV vs PRED and by hepatic function"

NPDE plots

Combined plot with NPDE vs PRED, time and time after dose and NPDE QQ-plot and density histogram

NPDE vs continuous covariates

NPDE vs categorical covariates.

NPDE vs all covariates.

CWRES plots

Combined CWRES plots

EBEs-based diagnostics

ETA pairs plot

Continuous covariate plots

ETA vs continous covariates

## $ETA1

## 
## $ETA2

## 
## $ETA3

Categorical covariate plots

ETA vs categorical covariates

## $STUDY

## 
## $RF

## 
## $CP

## 
## $DOSE

Output summaries from bbr

── NONMEM Model Status ───────────────────────────

• Finished Running

── Absolute Model Path ───────────────────────────

• /data/home/kyleb/ghe/example-projects/foce/model/pk/106

── YAML & Model Files ───────────────────────────

• /data/home/kyleb/ghe/example-projects/foce/model/pk/106.yaml

• /data/home/kyleb/ghe/example-projects/foce/model/pk/106.ctl

── Description ───────────────────────────────

• Final Model

── Tags ──────────────────────────────────

• two-compartment + absorption

• ETA-CL

• ETA-KA

• ETA-V2

• CLWT-allo

• V2WT-allo

• QWT-allo

• V3WT-allo

• CLEGFR

• CLAGE

• CLALB

• proportional RUV

── Notes ──────────────────────────────────

• 1: Client was interested in adding Albumin to CL Dataset: ../../../data/derived/pk.csv

Records: 4292 Observations: 3142 Subjects: 160

Objective Function Value (final est. method): 30904.409

Estimation Method(s):

– First Order Conditional Estimation with Interaction

Simulation: No

No Heuristic Problems Detected

parameter_names	estimate	stderr	shrinkage
THETA1	0.443	0.0643
THETA2	4.12	0.0275
THETA3	1.17	0.0280
THETA4	4.21	0.0190
THETA5	1.28	0.0348
THETA6	0.485	0.0395
THETA7	-0.0377	0.0635
THETA8	0.419	0.0863
OMEGA(1,1)	0.219	0.0526	14.4
OMEGA(2,2)	0.0824	0.00981	5.50
OMEGA(3,3)	0.114	0.0128	1.25
SIGMA(1,1)	0.0399	0.00123	5.01

Session details

## [1] ""

## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.3.3 (2024-02-29)
##  os       Ubuntu 20.04.6 LTS
##  system   x86_64, linux-gnu
##  ui       RStudio
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       America/New_York
##  date     2025-03-14
##  rstudio  2024.12.0+467.pro1 Kousa Dogwood (server)
##  pandoc   3.3 @ /usr/bin/ (via rmarkdown)
##  quarto   1.5.55 @ /data/home/kyleb/bin/quarto
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  package      * version date (UTC) lib source
##  assertthat     0.2.1   2019-03-21 [1] CRAN (R 4.3.1)
##  backports      1.5.0   2024-05-23 [1] CRAN (R 4.3.1)
##  bbr          * 1.13.0  2025-03-03 [1] MPNDEV (R 4.3.1)
##  bit            4.5.0.1 2024-12-03 [1] CRAN (R 4.3.1)
##  bit64          4.6.0-1 2025-01-16 [1] CRAN (R 4.3.1)
##  bslib          0.9.0   2025-01-30 [1] CRAN (R 4.3.1)
##  cachem         1.1.0   2024-05-16 [1] CRAN (R 4.3.1)
##  callr          3.7.6   2024-03-25 [1] CRAN (R 4.3.1)
##  checkmate      2.3.2   2024-07-29 [1] CRAN (R 4.3.1)
##  cli            3.6.4   2025-02-13 [1] CRAN (R 4.3.1)
##  colorspace     2.1-1   2024-07-26 [1] CRAN (R 4.3.1)
##  crayon         1.5.3   2024-06-20 [1] CRAN (R 4.3.1)
##  data.table     1.17.0  2025-02-22 [1] CRAN (R 4.3.1)
##  diffobj        0.3.5   2021-10-05 [1] CRAN (R 4.3.1)
##  digest         0.6.37  2024-08-19 [1] CRAN (R 4.3.1)
##  dplyr        * 1.1.4   2023-11-17 [1] CRAN (R 4.3.1)
##  evaluate       0.24.0  2024-06-10 [1] CRAN (R 4.3.1)
##  farver         2.1.2   2024-05-13 [1] CRAN (R 4.3.1)
##  fastmap        1.2.0   2024-05-15 [1] CRAN (R 4.3.1)
##  forcats      * 1.0.0   2023-01-29 [1] CRAN (R 4.3.1)
##  fs             1.6.5   2024-10-30 [1] CRAN (R 4.3.1)
##  generics       0.1.3   2022-07-05 [1] CRAN (R 4.3.1)
##  GGally         2.2.1   2024-02-14 [1] CRAN (R 4.3.1)
##  ggplot2      * 3.5.1   2024-04-23 [1] CRAN (R 4.3.1)
##  ggstats        0.8.0   2025-01-07 [1] CRAN (R 4.3.1)
##  glue         * 1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
##  gridExtra      2.3     2017-09-09 [1] CRAN (R 4.3.1)
##  gridGraphics   0.5-1   2020-12-13 [1] CRAN (R 4.3.1)
##  gtable         0.3.6   2024-10-25 [1] CRAN (R 4.3.1)
##  here         * 1.0.1   2020-12-13 [1] CRAN (R 4.3.1)
##  hms            1.1.3   2023-03-21 [1] CRAN (R 4.3.1)
##  htmltools      0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
##  jquerylib      0.1.4   2021-04-26 [1] CRAN (R 4.3.1)
##  jsonlite       1.9.0   2025-02-19 [1] CRAN (R 4.3.1)
##  kableExtra   * 1.4.0   2024-01-24 [1] CRAN (R 4.3.1)
##  knitr          1.49    2024-11-08 [1] CRAN (R 4.3.1)
##  labeling       0.4.3   2023-08-29 [1] CRAN (R 4.3.1)
##  lattice        0.22-6  2024-03-20 [1] CRAN (R 4.3.1)
##  lifecycle      1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
##  lubridate    * 1.9.4   2024-12-08 [1] CRAN (R 4.3.1)
##  magrittr     * 2.0.3   2022-03-30 [1] CRAN (R 4.3.1)
##  Matrix         1.6-5   2024-01-11 [1] CRAN (R 4.3.1)
##  mgcv           1.9-1   2023-12-21 [1] CRAN (R 4.3.1)
##  mrggsave     * 0.4.6   2025-03-03 [1] MPNDEV (R 4.3.1)
##  mrgmisc      * 0.2.2   2025-03-03 [1] MPNDEV (R 4.3.1)
##  munsell        0.5.1   2024-04-01 [1] CRAN (R 4.3.1)
##  nlme           3.1-167 2025-01-27 [1] CRAN (R 4.3.1)
##  nmrec          0.4.0   2024-08-02 [1] MPNDEV (R 4.3.1)
##  patchwork    * 1.3.0   2024-09-16 [1] CRAN (R 4.3.1)
##  pillar         1.10.1  2025-01-07 [1] CRAN (R 4.3.1)
##  pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.3.1)
##  plyr           1.8.9   2023-10-02 [1] CRAN (R 4.3.1)
##  pmplots      * 0.5.1   2025-03-03 [1] MPNDEV (R 4.3.1)
##  pmtables     * 0.8.1   2025-03-03 [1] MPNDEV (R 4.3.1)
##  processx       3.8.6   2025-02-21 [1] CRAN (R 4.3.1)
##  ps             1.9.0   2025-02-18 [1] CRAN (R 4.3.1)
##  purrr        * 1.0.4   2025-02-05 [1] CRAN (R 4.3.1)
##  R6             2.6.1   2025-02-15 [1] CRAN (R 4.3.1)
##  RColorBrewer   1.1-3   2022-04-03 [1] CRAN (R 4.3.1)
##  Rcpp           1.0.14  2025-01-12 [1] CRAN (R 4.3.1)
##  RcppParallel   5.1.10  2025-01-24 [1] CRAN (R 4.3.1)
##  readr        * 2.1.5   2024-01-10 [1] CRAN (R 4.3.1)
##  renv           1.0.3   2023-09-19 [1] RSPM (R 4.3.0)
##  rlang          1.1.5   2025-01-17 [1] CRAN (R 4.3.1)
##  rmarkdown      2.29    2024-11-04 [1] CRAN (R 4.3.1)
##  rprojroot      2.0.4   2023-11-05 [1] CRAN (R 4.3.1)
##  rstudioapi     0.17.1  2024-10-22 [1] CRAN (R 4.3.1)
##  sass           0.4.9   2024-03-15 [1] CRAN (R 4.3.1)
##  scales         1.3.0   2023-11-28 [1] CRAN (R 4.3.1)
##  sessioninfo    1.2.3   2025-02-05 [1] CRAN (R 4.3.1)
##  stringfish     0.16.0  2023-11-28 [1] CRAN (R 4.3.1)
##  stringi        1.8.4   2024-05-06 [1] CRAN (R 4.3.1)
##  stringr      * 1.5.1   2023-11-14 [1] CRAN (R 4.3.1)
##  svglite        2.1.3   2023-12-08 [1] CRAN (R 4.3.1)
##  systemfonts    1.2.1   2025-01-20 [1] CRAN (R 4.3.1)
##  tibble       * 3.2.1   2023-03-20 [1] CRAN (R 4.3.1)
##  tidyr        * 1.3.1   2024-01-24 [1] CRAN (R 4.3.1)
##  tidyselect     1.2.1   2024-03-11 [1] CRAN (R 4.3.1)
##  tidyverse    * 2.0.0   2023-02-22 [1] CRAN (R 4.3.1)
##  timechange     0.3.0   2024-01-18 [1] CRAN (R 4.3.1)
##  tzdb           0.4.0   2023-05-12 [1] CRAN (R 4.3.1)
##  vctrs          0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
##  viridisLite    0.4.2   2023-05-02 [1] CRAN (R 4.3.1)
##  vroom          1.6.5   2023-12-05 [1] CRAN (R 4.3.1)
##  withr          3.0.2   2024-10-28 [1] CRAN (R 4.3.1)
##  xfun           0.51    2025-02-19 [1] CRAN (R 4.3.1)
##  xml2           1.3.6   2023-12-04 [1] CRAN (R 4.3.1)
##  xtable         1.8-4   2019-04-21 [1] CRAN (R 4.3.1)
##  yaml         * 2.3.10  2024-07-26 [1] CRAN (R 4.3.1)
##  yspec        * 0.7.0   2025-03-03 [1] MPNDEV (R 4.3.1)
## 
##  [1] /data/home/kyleb/ghe/example-projects/foce/renv/library/R-4.3/x86_64-pc-linux-gnu
##  [2] /data/home/kyleb/.cache/R/renv/sandbox/R-4.3/x86_64-pc-linux-gnu/40018dbe
##  * ── Packages attached to the search path.
## 
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────

## [1] "3.3.0"