nmxml
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
theta=TRUE, omega=TRUE,sigma=TRUE
olabels = s(ECL, EVC, EKA)
slabels = s(PROP, ADD)
$MAIN
pred_CL = THETA1*exp(ECL);
pred_V2 = THETA2*exp(EVC);
pred_KA = THETA3*exp(EKA);
pred_Q = THETA4;
pred_V3 = THETA5;
$ADVAN4
$CMT GUT CENT PERIPH
$TABLE
table(CP) = (CENT/pred_V2)*(1+PROP) + ADD/50;
$SET delta=4, end=96
'NOTE: in order to use this code, we need to install the XML package.
mod <- mcode("nmxml", code, warn=FALSE ,quiet=TRUE). Loading required namespace: XML
mod.
.
. -------- mrgsolve model object (unix) --------
. Project: /private/var/fol...dbsj0x4637ptj4hnd7kg900000gp/T/Rtmp3G4eW1
. source: nmxml.cpp
. shared object: 2a796d0508df (loaded)
.
. compile date: 04/15 00:08
. 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 3.2.3 (2015-12-10)
. system x86_64, darwin13.4.0
. ui X11
. language (EN)
. collate en_US.UTF-8
. tz America/Chicago
. date 2016-04-15
. Packages ------------------------------------------------------------------
. package * version date source
. assertthat 0.1 2013-11-08 local
. DBI 0.3.1 2014-09-24 CRAN (R 3.1.1)
. devtools 1.10.0 2016-01-23 CRAN (R 3.2.1)
. digest 0.6.9 2016-01-08 CRAN (R 3.2.1)
. dplyr * 0.4.3 2015-09-01 CRAN (R 3.2.1)
. evaluate 0.8.3 2016-03-05 CRAN (R 3.2.3)
. formatR 1.3 2016-03-05 CRAN (R 3.2.3)
. htmltools 0.3.5 2016-03-21 CRAN (R 3.2.3)
. knitr * 1.12.3 2016-01-22 CRAN (R 3.2.1)
. lattice 0.20-33 2015-07-14 CRAN (R 3.2.3)
. lazyeval 0.1.10 2015-01-02 CRAN (R 3.1.2)
. magrittr * 1.5 2014-11-22 CRAN (R 3.1.2)
. memoise 1.0.0 2016-01-29 CRAN (R 3.2.1)
. mrgsolve * 0.5.12.9000 2016-04-14 local
. R6 2.1.2 2016-01-26 CRAN (R 3.2.3)
. rbenchmark * 1.0.0 2012-08-30 CRAN (R 3.0.3)
. Rcpp 0.12.4 2016-03-26 CRAN (R 3.2.3)
. rmarkdown 0.9.5 2016-02-22 CRAN (R 3.2.3)
. stringi 1.0-1 2015-10-22 CRAN (R 3.2.1)
. stringr 1.0.0 2015-04-30 CRAN (R 3.1.3)
. XML 3.98-1.4 2016-03-01 CRAN (R 3.2.3)
. yaml 2.1.13 2014-06-12 CRAN (R 3.0.2)