nmxml
Metrum Research Group
library(mrgsolve)
library(rbenchmark)
library(dplyr)
library(magrittr)There is a NONMEM run embedded in the mrgsolve package
path <- file.path(path.package("mrgsolve"),"nonmem")
list.files(path, recursive=TRUE). [1] "1005/1005.cat" "1005/1005.coi" "1005/1005.cor"
. [4] "1005/1005.cov" "1005/1005.cpu" "1005/1005.ctl"
. [7] "1005/1005.ext" "1005/1005.grd" "1005/1005.lst"
. [10] "1005/1005.phi" "1005/1005.shk" "1005/1005.shm"
. [13] "1005/1005.tab" "1005/1005.xml" "1005/1005par.tab"
. [16] "1005/INTER"
We can create a mrgsolve control stream that will import THETA,
OMEGA and SIGMA from that run using the $NMXML code block.
code <- '
$NMXML
run = 1005
project=path
olabels = c("ECL", "EVC", "EKA")
slabels = c("PROP", "ADD")
$MAIN
double CL = THETA1*exp(ECL);
double V2 = THETA2*exp(EVC);
double KA = THETA3*exp(EKA);
double Q = THETA4;
double V3 = THETA5;
$PKMODEL ncmt=2, depot=TRUE
$CMT GUT CENT PERIPH
$TABLE
double CP = (CENT/V2)*(1+PROP) + ADD/5;
$CAPTURE CP
$SET delta=4, end=96
'NOTE: in order to use this code, we need to install the xml2
package.
mod <- mcode("nmxml", code, quiet=TRUE). Loading required namespace: xml2
mod.
.
. -------- mrgsolve model object (unix) --------
. Project: /private/var/fol.../T/RtmpDCEwD2
. source: nmxml.cpp
. shared object: nmxml-so-1536e10efb261
.
. Time: start: 0 end: 96 delta: 4
. > add: <none>
. > tscale: 1
.
. Compartments: GUT CENT PERIPH [3]
. Parameters: THETA1 THETA2 THETA3 THETA4 THETA5 THETA6
. > THETA7 [7]
. Omega: 3x3
. Sigma: 2x2
.
. Solver: atol: 1e-08 rtol: 1e-08
. > maxsteps: 2000 hmin: 0 hmax: 0
param(mod).
. Model parameters (N=7):
. name value . name value
. THETA1 9.51 | THETA5 113
. THETA2 22.8 | THETA6 1.02
. THETA3 0.0714 | THETA7 1.19
. THETA4 3.47 | . .
revar(mod). $omega
. $...
. [,1] [,2] [,3]
. ECL: 0.21387884 0.12077020 -0.01162777
. EVC: 0.12077020 0.09451047 -0.03720637
. EKA: -0.01162777 -0.03720637 0.04656315
.
.
. $sigma
. $...
. [,1] [,2]
. PROP: 0.04917071 0.0000000
. ADD: 0.00000000 0.2017688
Infusion into GUT
set.seed(2922)mod %>%
ev(amt=1000, rate=1000/36, cmt="GUT") %>%
mrgsim(nid=10) %>%
plot
devtools::session_info(). ─ Session info ──────────────────────────────────────────────────────────
. setting value
. version R version 3.5.2 (2018-12-20)
. os macOS Sierra 10.12.6
. system x86_64, darwin15.6.0
. ui X11
. language (EN)
. collate en_US.UTF-8
. ctype en_US.UTF-8
. tz America/Chicago
. date 2019-01-07
.
. ─ Packages ──────────────────────────────────────────────────────────────
. package * version date lib source
. assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.0)
. backports 1.1.3 2018-12-14 [1] CRAN (R 3.5.0)
. bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.0)
. bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.0)
. callr 3.1.1 2018-12-21 [1] CRAN (R 3.5.0)
. cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.0)
. crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
. desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
. devtools 2.0.1 2018-10-26 [1] CRAN (R 3.5.2)
. digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.0)
. dplyr * 0.7.8 2018-11-10 [1] CRAN (R 3.5.0)
. evaluate 0.12 2018-10-09 [1] CRAN (R 3.5.0)
. fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.0)
. glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.0)
. highr 0.7 2018-06-09 [1] CRAN (R 3.5.0)
. htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.0)
. knitr * 1.21 2018-12-10 [1] CRAN (R 3.5.2)
. lattice 0.20-38 2018-11-04 [2] CRAN (R 3.5.2)
. magrittr * 1.5 2014-11-22 [1] CRAN (R 3.5.0)
. memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.0)
. mrgsolve * 0.8.12 2018-04-27 [1] CRAN (R 3.5.0)
. pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.0)
. pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.0)
. pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.0)
. pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.0)
. prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.0)
. processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.0)
. ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.0)
. purrr 0.2.5 2018-05-29 [1] CRAN (R 3.5.0)
. R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.0)
. rbenchmark * 1.0.0 2012-08-30 [1] CRAN (R 3.5.0)
. Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.0)
. RcppArmadillo 0.9.200.5.0 2018-11-28 [1] CRAN (R 3.5.0)
. remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.0)
. rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.5.0)
. rmarkdown 1.11 2018-12-08 [1] CRAN (R 3.5.0)
. rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
. sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.0)
. stringi 1.2.4 2018-07-20 [1] CRAN (R 3.5.0)
. stringr 1.3.1 2018-05-10 [1] CRAN (R 3.5.0)
. testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.0)
. tibble 1.4.2 2018-01-22 [1] CRAN (R 3.5.0)
. tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.0)
. usethis 1.4.0 2018-08-14 [1] CRAN (R 3.5.0)
. withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
. xfun 0.4 2018-10-23 [1] CRAN (R 3.5.0)
. xml2 1.2.0 2018-01-24 [1] CRAN (R 3.5.0)
. yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.0)
.
. [1] /Users/kyleb/Rlibs
. [2] /Library/Frameworks/R.framework/Versions/3.5/Resources/library