Title: | Converts 'NONMEM' Models to 'rxode2' |
---|---|
Description: | 'NONMEM' has been a tool for running nonlinear mixed effects models since the 80s and is still used today (Bauer 2019 <doi:10.1002/psp4.12404>). This tool allows you to convert 'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax (Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2' syntax requires the residual specification to be included and it is not always translated. If available, the 'rxode2' model will read in the 'NONMEM' data and compare the simulation for the population model ('PRED') individual model ('IPRED') and residual model ('IWRES') to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'NONMEM' and can convert the objects converted from 'nonmem2rx' to a full 'nlmixr2' fit. |
Authors: | Matthew Fidler [aut, cre] , Philip Delff [ctb], Gabriel Staples [ctb] (string insensitive compare) |
Maintainer: | Matthew Fidler <[email protected]> |
License: | GPL (>= 3) |
Version: | 0.1.6 |
Built: | 2024-11-28 19:20:27 UTC |
Source: | https://github.com/nlmixr2/nonmem2rx |
Convert a model to a nonmem2rx model
as.nonmem2rx(model1, model2, compress = TRUE)
as.nonmem2rx(model1, model2, compress = TRUE)
model1 |
Input model 1 |
model2 |
Input model 2 |
compress |
boolean to compress the ui at the end |
nonmem2rx model
Matthew L. Fidler
mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), determineError=FALSE, lst=".res", save=FALSE) mod2 <-function() { ini({ lcl <- 1.37034036528946 lvc <- 4.19814911033061 lq <- 1.38003493562413 lvp <- 3.87657341967489 RSV <- c(0, 0.196446108190896, 1) eta.cl ~ 0.101251418415006 eta.v ~ 0.0993872449483344 eta.q ~ 0.101302674763154 eta.v2 ~ 0.0730497519364148 }) model({ cmt(CENTRAL) cmt(PERI) cl <- exp(lcl + eta.cl) v <- exp(lvc + eta.v) q <- exp(lq + eta.q) v2 <- exp(lvp + eta.v2) v1 <- v scale1 <- v k21 <- q/v2 k12 <- q/v d/dt(CENTRAL) <- k21 * PERI - k12 * CENTRAL - cl * CENTRAL/v1 d/dt(PERI) <- -k21 * PERI + k12 * CENTRAL f <- CENTRAL/scale1 f ~ prop(RSV) }) } new <- try(as.nonmem2rx(mod2, mod)) if (!inherits(new, "try-error")) print(new, page=1)
mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), determineError=FALSE, lst=".res", save=FALSE) mod2 <-function() { ini({ lcl <- 1.37034036528946 lvc <- 4.19814911033061 lq <- 1.38003493562413 lvp <- 3.87657341967489 RSV <- c(0, 0.196446108190896, 1) eta.cl ~ 0.101251418415006 eta.v ~ 0.0993872449483344 eta.q ~ 0.101302674763154 eta.v2 ~ 0.0730497519364148 }) model({ cmt(CENTRAL) cmt(PERI) cl <- exp(lcl + eta.cl) v <- exp(lvc + eta.v) q <- exp(lq + eta.q) v2 <- exp(lvp + eta.v2) v1 <- v scale1 <- v k21 <- q/v2 k12 <- q/v d/dt(CENTRAL) <- k21 * PERI - k12 * CENTRAL - cl * CENTRAL/v1 d/dt(PERI) <- -k21 * PERI + k12 * CENTRAL f <- CENTRAL/scale1 f ~ prop(RSV) }) } new <- try(as.nonmem2rx(mod2, mod)) if (!inherits(new, "try-error")) print(new, page=1)
Read in data file
nmcov(file, ...)
nmcov(file, ...)
file |
file name to read the results from |
... |
other parameters passed to |
A matrix with covariance step from NONMEM
Philip Delff and Matthew L. Fidler
nmcov(system.file("mods/cpt/runODE032.cov", package="nonmem2rx"))
nmcov(system.file("mods/cpt/runODE032.cov", package="nonmem2rx"))
.ext
file for final parameter informationReads the NONMEM .ext
file for final parameter information
nmext(file)
nmext(file)
file |
File where the list is located |
return a list with $theta
, $eta
and $eps
Matthew L. Fidler
nmext(system.file("run001.ext", package="nonmem2rx"))
nmext(system.file("run001.ext", package="nonmem2rx"))
Get the most accurate information you can get from NONMEM
nminfo( file, mod = ".mod", xml = ".xml", ext = ".ext", cov = ".cov", phi = ".phi", lst = ".lst", useXml = TRUE, useExt = TRUE, useCov = TRUE, usePhi = TRUE, useLst = TRUE, strictLst = FALSE, verbose = FALSE )
nminfo( file, mod = ".mod", xml = ".xml", ext = ".ext", cov = ".cov", phi = ".phi", lst = ".lst", useXml = TRUE, useExt = TRUE, useCov = TRUE, usePhi = TRUE, useLst = TRUE, strictLst = FALSE, verbose = FALSE )
file |
nonmem file, like control stream, phi. This function will remove the extension to try to get the right information. It preferentially selects the most accurate estimates from the file. |
mod |
the NONMEM output extension, defaults to |
xml |
the NONMEM xml file extension , defaults to |
ext |
the NONMEM ext file extension, defaults to |
cov |
the NONMEM covariance file extension, defaults to |
phi |
the NONMEM eta/phi file extension, defaults to |
lst |
the NONMEM output extension, defaults to |
useXml |
if present, use the NONMEM xml file to import much of the NONMEM information |
useExt |
if present, use the NONMEM ext file to extract
parameter estimates (default |
useCov |
if present, use the NONMEM cov file to import the covariance, otherwise import the covariance with list file |
usePhi |
if present, use the NONMEM phi file to extract etas
(default |
useLst |
if present, use the NONMEM lst file to extract NONMEM information |
strictLst |
The list parsing needs to be correct for a
successful load (default |
verbose |
this is a flag to be more verbose when reading information in, by default this is |
list of NONMEM information
Matthew L. Fidler
nminfo(system.file("mods/cpt/runODE032.res", package="nonmem2rx"))
nminfo(system.file("mods/cpt/runODE032.res", package="nonmem2rx"))
.lst
file for final parameter informationReads the NONMEM .lst
file for final parameter information
nmlst(file, strictLst = FALSE)
nmlst(file, strictLst = FALSE)
file |
File where the list is located |
strictLst |
The list parsing needs to be correct for a
successful load (default |
return a list with $theta
, $eta
and $eps
and other
information about the control stream
Matthew L. Fidler
nmlst(system.file("mods/DDMODEL00000322/HCQ1CMT.lst", package="nonmem2rx")) nmlst(system.file("mods/DDMODEL00000302/run1.lst", package="nonmem2rx")) nmlst(system.file("mods/DDMODEL00000301/run3.lst", package="nonmem2rx")) nmlst(system.file("mods/cpt/runODE032.res", package="nonmem2rx"))
nmlst(system.file("mods/DDMODEL00000322/HCQ1CMT.lst", package="nonmem2rx")) nmlst(system.file("mods/DDMODEL00000302/run1.lst", package="nonmem2rx")) nmlst(system.file("mods/DDMODEL00000301/run3.lst", package="nonmem2rx")) nmlst(system.file("mods/cpt/runODE032.res", package="nonmem2rx"))
Read nonmem table file
nmtab(file, ...)
nmtab(file, ...)
file |
file name to read the results from |
... |
other parameters passed to |
data frame of the read table
Philip Delff, Matthew L. Fidler
nmtab(system.file("mods/cpt/runODE032.csv", package="nonmem2rx"))
nmtab(system.file("mods/cpt/runODE032.csv", package="nonmem2rx"))
nmlst()
Read a nonmem xml and create output similar to the nmlst()
nmxml(xml)
nmxml(xml)
xml |
xml file |
list of nonmem information
Matthew L. Fidler
nmxml(system.file("mods/cpt/runODE032.xml", package="nonmem2rx"))
nmxml(system.file("mods/cpt/runODE032.xml", package="nonmem2rx"))
Convert a NONMEM source file to a rxode model (nlmixr2-syle)
nonmem2rx( file, inputData = NULL, nonmemOutputDir = NULL, rename = NULL, tolowerLhs = TRUE, thetaNames = TRUE, etaNames = TRUE, cmtNames = TRUE, updateFinal = TRUE, determineError = TRUE, validate = getOption("nonmem2rx.validate", TRUE), nonmemData = FALSE, strictLst = FALSE, unintFixed = FALSE, extended = getOption("nonmem2rx.extended", FALSE), nLinesPro = 20L, delta = 1e-04, usePhi = TRUE, useExt = TRUE, useCov = TRUE, useXml = TRUE, useLst = TRUE, mod = ".mod", cov = ".cov", phi = ".phi", lst = getOption("nonmem2rx.lst", ".lst"), xml = ".xml", ext = ".ext", scanLines = getOption("nonmem2rx.scanLines", 50L), save = getOption("nonmem2rx.save", NA), saveTime = getOption("nonmem2rx.saveTime", 15), overwrite = getOption("nonmem2rx.overwrite", TRUE), load = getOption("nonmem2rx.load", TRUE), compress = getOption("nonmem2rx.compress", TRUE), keep = getOption("nonmem2rx.keep", c("dfSub", "dfObs", "thetaMat", "sigma")) )
nonmem2rx( file, inputData = NULL, nonmemOutputDir = NULL, rename = NULL, tolowerLhs = TRUE, thetaNames = TRUE, etaNames = TRUE, cmtNames = TRUE, updateFinal = TRUE, determineError = TRUE, validate = getOption("nonmem2rx.validate", TRUE), nonmemData = FALSE, strictLst = FALSE, unintFixed = FALSE, extended = getOption("nonmem2rx.extended", FALSE), nLinesPro = 20L, delta = 1e-04, usePhi = TRUE, useExt = TRUE, useCov = TRUE, useXml = TRUE, useLst = TRUE, mod = ".mod", cov = ".cov", phi = ".phi", lst = getOption("nonmem2rx.lst", ".lst"), xml = ".xml", ext = ".ext", scanLines = getOption("nonmem2rx.scanLines", 50L), save = getOption("nonmem2rx.save", NA), saveTime = getOption("nonmem2rx.saveTime", 15), overwrite = getOption("nonmem2rx.overwrite", TRUE), load = getOption("nonmem2rx.load", TRUE), compress = getOption("nonmem2rx.compress", TRUE), keep = getOption("nonmem2rx.keep", c("dfSub", "dfObs", "thetaMat", "sigma")) )
file |
NONMEM run file, like an |
inputData |
this is a path to the input dataset (or |
nonmemOutputDir |
This is a path the the nonmem output
directory. When not |
rename |
When not |
tolowerLhs |
Boolean to change the lhs to lower case (default:
|
thetaNames |
this could be a boolean indicating that the theta
names should be changed to the comment-labeled names (default:
|
etaNames |
this could be a boolean indicating that the eta
names should be changed to the comment-labeled names (default:
|
cmtNames |
this could be a boolean indicating that the
compartment names should be changed to the named compartments in
the |
updateFinal |
Update the parsed model with the model estimates
from the |
determineError |
Boolean to try to determine the |
validate |
Boolean that this tool will attempt to "validate" the model by solving the derived model under pred conditions (etas are zero and eps values are zero) |
nonmemData |
Boolean that tells |
strictLst |
The list parsing needs to be correct for a
successful load (default |
unintFixed |
Treat uninteresting values as fixed parameters (default |
extended |
Translate extended control streams from tools like wings for NONMEM |
nLinesPro |
The number of lines to check for the $PROBLEM statement. |
delta |
this is the offset for NONMEM times that are tied |
usePhi |
if present, use the NONMEM phi file to extract etas
(default |
useExt |
if present, use the NONMEM ext file to extract
parameter estimates (default |
useCov |
if present, use the NONMEM cov file to import the covariance, otherwise import the covariance with list file |
useXml |
if present, use the NONMEM xml file to import much of the NONMEM information |
useLst |
if present, use the NONMEM lst file to extract NONMEM information |
mod |
the NONMEM output extension, defaults to |
cov |
the NONMEM covariance file extension, defaults to |
phi |
the NONMEM eta/phi file extension, defaults to |
lst |
the NONMEM output extension, defaults to |
xml |
the NONMEM xml file extension , defaults to |
ext |
the NONMEM ext file extension, defaults to |
scanLines |
number of lines to scan for comment chars when
|
save |
This can be:
|
saveTime |
The time that the translation/validation needs (in secs) before it will save to avoid having to rerun the model (default 15 for 15 seconds) |
overwrite |
is a boolean to allow overwriting the save file
(see |
load |
a boolean that says to load the save file (if it
exists) instead of re-running the translation and validation.
Note if |
compress |
a boolean indicating if the UI should be a
compressed UI. If you are using this for simulation with old
versions of rxode2, the compressed ui is not supported, so this
should be |
keep |
is a character vector of imported model items that are kept in the model itself; The defaults is "sigma" which keeps the sigma matrix in the model itself. You can add rxode2 solving options that are imported from NONMEM to keep in the model. |
Since some of these options you may want to set per project, the following options are queried:
nonmem2rx.validate
- boolean to validate the model (default: TRUE
)
nonmem2rx.lst
- default extension for output (default: .lst
)
nonmem2rx.save
- should nonmem2rx save the model output?
nonmem2rx.overwrite
- should nonmem2rx save output be
overwritten (default TRUE
)
nonmem2rx.load
- should nonmem2rx load a saved model instead of
translating and validating again? (default TRUE
)
nonmem2rx.extended
- should nonmem2rx support extended control
streams? (default FALSE
)
nonmem2rx.compress
- should the ui be compressed or
uncompressed (default: TRUE
)
rxode2 function
# You can run a translation without validating the input. This is # a faster way to import a dataset (and allows the CRAN machines to # run a quick example) mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res", save=FALSE, validate=FALSE, compress=FALSE) # Though by default you likely wish to validate the input mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res", save=FALSE) mod # you can plot to compare the pred/ipred differences plot(mod) # if you want to see the individual differences # you can by plotting by page of plots plot(mod, nrow=2, ncol=2, page=1, log="y") # or select which pages you want to print plot(mod, nrow=2, ncol=2, page=c(1,3), log="y") #' or even all the individuals with # plot(page=TRUE) plot(mod, nrow=5, ncol=5, page=TRUE, log="y") # you can also convert to a nlmixr2 object, but need babelmixr2 for # that conversion
# You can run a translation without validating the input. This is # a faster way to import a dataset (and allows the CRAN machines to # run a quick example) mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res", save=FALSE, validate=FALSE, compress=FALSE) # Though by default you likely wish to validate the input mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res", save=FALSE) mod # you can plot to compare the pred/ipred differences plot(mod) # if you want to see the individual differences # you can by plotting by page of plots plot(mod, nrow=2, ncol=2, page=1, log="y") # or select which pages you want to print plot(mod, nrow=2, ncol=2, page=c(1,3), log="y") #' or even all the individuals with # plot(page=TRUE) plot(mod, nrow=5, ncol=5, page=TRUE, log="y") # you can also convert to a nlmixr2 object, but need babelmixr2 for # that conversion