This repository contains the code used for the analyses presented in the manuscript
"Protein intake and outcome of critically ill patients – analysis of a large international database using piece-wise exponential additive mixed models (PAMMs)"
To reproduce the results presented in the maunscript, run the file in rerun-analysis.R (it is not necessary to run the first script preproc-data.R, as the resulting data is already contained within this repository. The original, uprocessed SAS data bases could not be shared.)
Note that this could take some time (and computational ressources). Optionally,
you can run the individual lines of code in rerun-analysis.R sequentially and restart your R session in between.
The session info is given below:
> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.0.3 (2020-10-10)
os Ubuntu 20.04.3 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Berlin
date 2021-10-13
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
backports 1.2.1 2020-12-09 [1] CRAN (R 4.0.3)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.0.3)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.0.3)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)
cli 3.0.1 2021-07-17 [1] CRAN (R 4.0.3)
codetools 0.2-16 2018-12-24 [4] CRAN (R 4.0.0)
colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.0.3)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.3)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.3)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.3)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.0.3)
dplyr * 1.0.7 2021-06-18 [1] CRAN (R 4.0.3)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.3)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.0.3)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.3)
foreach 1.5.1 2020-10-15 [1] CRAN (R 4.0.3)
Formula 1.2-4 2020-10-16 [1] CRAN (R 4.0.3)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.3)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.3)
ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.0.3)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
iterators 1.0.13 2020-10-15 [1] CRAN (R 4.0.3)
lattice 0.20-41 2020-04-02 [4] CRAN (R 4.0.0)
lava 1.6.9 2021-03-11 [1] CRAN (R 4.0.3)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.0.3)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3)
Matrix 1.2-18 2019-11-27 [4] CRAN (R 4.0.0)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.3)
mgcv * 1.8-33 2020-08-27 [4] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
mvtnorm 1.1-2 2021-06-07 [1] CRAN (R 4.0.3)
nlme * 3.1-149 2020-08-23 [4] CRAN (R 4.0.2)
numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.2)
pammtools * 0.5.7 2021-06-21 [1] CRAN (R 4.0.3)
patchwork * 1.1.1 2020-12-17 [1] CRAN (R 4.0.3)
pec 2020.11.17 2020-11-16 [1] CRAN (R 4.0.3)
pillar 1.6.3 2021-09-26 [1] CRAN (R 4.0.3)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.0.3)
prodlim 2019.11.13 2019-11-17 [1] CRAN (R 4.0.2)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.3)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.0.3)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.0.3)
remotes 2.4.0 2021-06-02 [1] CRAN (R 4.0.3)
rlang 0.4.11 2021-04-30 [1] CRAN (R 4.0.3)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.3)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
survival 3.2-13 2021-08-24 [1] CRAN (R 4.0.3)
testthat 3.0.4 2021-07-01 [1] CRAN (R 4.0.3)
tibble 3.1.5 2021-09-30 [1] CRAN (R 4.0.3)
tidyr * 1.1.4 2021-09-27 [1] CRAN (R 4.0.3)
tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.0.3)
timereg 2.0.0 2021-05-20 [1] CRAN (R 4.0.3)
usethis 2.0.1 2021-02-10 [1] CRAN (R 4.0.3)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.0.3)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.0.3)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.3)