The goal of nonmem2rx
is to convert a NONMEM control stream to rxode2 for easy
clinical trial simulation in R.
Here is a quick example of a conversion:
library(nonmem2rx)
# First we need the location of the nonmem control stream Since we are running an example, we will use one of the built-in examples in `nonmem2rx`
ctlFile <- system.file("mods/cpt/runODE032.ctl", package="nonmem2rx")
# You can use a control stream or other file. With the development
# version of `babelmixr2`, you can simply point to the listing file
mod <- nonmem2rx(ctlFile, lst=".res", save=FALSE, determineError=FALSE)
#> ℹ getting information from '/tmp/RtmpnH2sTe/Rinst2117d6bb73c/nonmem2rx/mods/cpt/runODE032.ctl'
#> ℹ reading in xml file
#> ℹ done
#> ℹ reading in ext file
#> ℹ done
#> ℹ reading in phi file
#> ℹ done
#> ℹ reading in lst file
#> ℹ abbreviated list parsing
#> ℹ done
#> ℹ done
#> ℹ splitting control stream by records
#> ℹ done
#> ℹ Processing record $INPUT
#> ℹ Processing record $MODEL
#> ℹ Processing record $gTHETA
#> ℹ Processing record $OMEGA
#> ℹ Processing record $SIGMA
#> ℹ Processing record $PROBLEM
#> ℹ Processing record $DATA
#> ℹ Processing record $SUBROUTINES
#> ℹ Processing record $PK
#> ℹ Processing record $DES
#> ℹ Processing record $ERROR
#> ℹ Processing record $ESTIMATION
#> ℹ Ignore record $ESTIMATION
#> ℹ Processing record $COVARIANCE
#> ℹ Ignore record $COVARIANCE
#> ℹ Processing record $TABLE
#> ℹ change initial estimate of `theta1` to `1.37034036528946`
#> ℹ change initial estimate of `theta2` to `4.19814911033061`
#> ℹ change initial estimate of `theta3` to `1.38003493562413`
#> ℹ change initial estimate of `theta4` to `3.87657341967489`
#> ℹ change initial estimate of `theta5` to `0.196446108190896`
#> ℹ change initial estimate of `eta1` to `0.101251418415006`
#> ℹ change initial estimate of `eta2` to `0.0993872449483344`
#> ℹ change initial estimate of `eta3` to `0.101302674763154`
#> ℹ change initial estimate of `eta4` to `0.0730497519364148`
#> ℹ read in nonmem input data (for model validation): /tmp/RtmpnH2sTe/Rinst2117d6bb73c/nonmem2rx/mods/cpt/Bolus_2CPT.csv
#> ℹ ignoring lines that begin with a letter (IGNORE=@)'
#> ℹ applying names specified by $INPUT
#> ℹ subsetting accept/ignore filters code: .data[-which((.data$SD == 0)),]
#> ℹ done
#> Setting r-universe rmarkdown theme...
#> using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
#> ℹ read in nonmem IPRED data (for model validation): /tmp/RtmpnH2sTe/Rinst2117d6bb73c/nonmem2rx/mods/cpt/runODE032.csv
#> ℹ done
#> ℹ changing most variables to lower case
#> ℹ done
#> ℹ replace theta names
#> ℹ done
#> ℹ replace eta names
#> ℹ done (no labels)
#> ℹ renaming compartments
#> ℹ done
#> Setting r-universe rmarkdown theme...
#> using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
mod
#> ── rxode2-based free-form 2-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> theta1 theta2 theta3 theta4 RSV
#> 1.3703404 4.1981491 1.3800349 3.8765734 0.1964461
#>
#> Omega ($omega):
#> eta1 eta2 eta3 eta4
#> eta1 0.1012514 0.00000000 0.0000000 0.00000000
#> eta2 0.0000000 0.09938724 0.0000000 0.00000000
#> eta3 0.0000000 0.00000000 0.1013027 0.00000000
#> eta4 0.0000000 0.00000000 0.0000000 0.07304975
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 CENTRAL
#> 2 2 PERI
#> ── μ-referencing ($muRefTable): ──
#> theta eta level
#> 1 theta1 eta1 id
#> 2 theta2 eta2 id
#> 3 theta3 eta3 id
#> 4 theta4 eta4 id
#>
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- "BOLUS_2CPT_CLV1QV2 SINGLE DOSE FOCEI (120 Ind/2280 Obs) runODE032"
#> dfObs <- 2280
#> dfSub <- 120
#> sigma <- lotri({
#> eps1 ~ 1
#> })
#> thetaMat <- lotri({
#> theta1 ~ c(theta1 = 0.000887681)
#> theta2 ~ c(theta1 = -0.00010551, theta2 = 0.000871409)
#> theta3 ~ c(theta1 = 0.000184416, theta2 = -0.000106195,
#> theta3 = 0.00299336)
#> theta4 ~ c(theta1 = -0.000120234, theta2 = -5.06663e-05,
#> theta3 = 0.000165252, theta4 = 0.00121347)
#> RSV ~ c(theta1 = 5.2783e-08, theta2 = -1.56562e-05, theta3 = 5.99331e-06,
#> theta4 = -2.53991e-05, RSV = 9.94218e-06)
#> eps1 ~ c(theta1 = 0, theta2 = 0, theta3 = 0, theta4 = 0,
#> RSV = 0, eps1 = 0)
#> eta1 ~ c(theta1 = -4.71273e-05, theta2 = 4.69667e-05,
#> theta3 = -3.64271e-05, theta4 = 2.54796e-05, RSV = -8.16885e-06,
#> eps1 = 0, eta1 = 0.000169296)
#> omega.2.1 ~ c(theta1 = 0, theta2 = 0, theta3 = 0, theta4 = 0,
#> RSV = 0, eps1 = 0, eta1 = 0, omega.2.1 = 0)
#> eta2 ~ c(theta1 = -7.37156e-05, theta2 = 2.56634e-05,
#> theta3 = -8.08349e-05, theta4 = 1.37e-05, RSV = -4.36564e-06,
#> eps1 = 0, eta1 = 8.75181e-06, omega.2.1 = 0, eta2 = 0.00015125)
#> omega.3.1 ~ c(theta1 = 0, theta2 = 0, theta3 = 0, theta4 = 0,
#> RSV = 0, eps1 = 0, eta1 = 0, omega.2.1 = 0, eta2 = 0,
#> omega.3.1 = 0)
#> omega.3.2 ~ c(theta1 = 0, theta2 = 0, theta3 = 0, theta4 = 0,
#> RSV = 0, eps1 = 0, eta1 = 0, omega.2.1 = 0, eta2 = 0,
#> omega.3.1 = 0, omega.3.2 = 0)
#> eta3 ~ c(theta1 = 6.63383e-05, theta2 = -8.19002e-05,
#> theta3 = 0.000548985, theta4 = 0.000168356, RSV = 1.59122e-06,
#> eps1 = 0, eta1 = 3.48714e-05, omega.2.1 = 0, eta2 = 4.31593e-07,
#> omega.3.1 = 0, omega.3.2 = 0, eta3 = 0.000959029)
#> omega.4.1 ~ c(theta1 = 0, theta2 = 0, theta3 = 0, theta4 = 0,
#> RSV = 0, eps1 = 0, eta1 = 0, omega.2.1 = 0, eta2 = 0,
#> omega.3.1 = 0, omega.3.2 = 0, eta3 = 0, omega.4.1 = 0)
#> omega.4.2 ~ c(theta1 = 0, theta2 = 0, theta3 = 0, theta4 = 0,
#> RSV = 0, eps1 = 0, eta1 = 0, omega.2.1 = 0, eta2 = 0,
#> omega.3.1 = 0, omega.3.2 = 0, eta3 = 0, omega.4.1 = 0,
#> omega.4.2 = 0)
#> omega.4.3 ~ c(theta1 = 0, theta2 = 0, theta3 = 0, theta4 = 0,
#> RSV = 0, eps1 = 0, eta1 = 0, omega.2.1 = 0, eta2 = 0,
#> omega.3.1 = 0, omega.3.2 = 0, eta3 = 0, omega.4.1 = 0,
#> omega.4.2 = 0, omega.4.3 = 0)
#> eta4 ~ c(theta1 = -9.49661e-06, theta2 = 0.000110108,
#> theta3 = -0.000306537, theta4 = -9.12897e-05, RSV = 3.1877e-06,
#> eps1 = 0, eta1 = 1.36628e-05, omega.2.1 = 0, eta2 = -1.95096e-05,
#> omega.3.1 = 0, omega.3.2 = 0, eta3 = -0.00012977,
#> omega.4.1 = 0, omega.4.2 = 0, omega.4.3 = 0, eta4 = 0.00051019)
#> })
#> validation <- c("IPRED relative difference compared to Nonmem IPRED: 0%; 95% percentile: (0%,0%); rtol=6.43e-06",
#> "IPRED absolute difference compared to Nonmem IPRED: 95% percentile: (2.19e-05, 0.0418); atol=0.00167",
#> "IWRES relative difference compared to Nonmem IWRES: 0%; 95% percentile: (0%,0.01%); rtol=8.99e-06",
#> "IWRES absolute difference compared to Nonmem IWRES: 95% percentile: (1.82e-07, 4.63e-05); atol=3.65e-06",
#> "PRED relative difference compared to Nonmem PRED: 0%; 95% percentile: (0%,0%); rtol=6.41e-06",
#> "PRED absolute difference compared to Nonmem PRED: 95% percentile: (1.41e-07,0.00382) atol=6.41e-06")
#> ini({
#> theta1 <- 1.37034036528946
#> label("log Cl")
#> theta2 <- 4.19814911033061
#> label("log Vc")
#> theta3 <- 1.38003493562413
#> label("log Q")
#> theta4 <- 3.87657341967489
#> label("log Vp")
#> RSV <- c(0, 0.196446108190896, 1)
#> label("RSV")
#> eta1 ~ 0.101251418415006
#> eta2 ~ 0.0993872449483344
#> eta3 ~ 0.101302674763154
#> eta4 ~ 0.0730497519364148
#> })
#> model({
#> cmt(CENTRAL)
#> cmt(PERI)
#> cl <- exp(theta1 + eta1)
#> v <- exp(theta2 + eta2)
#> q <- exp(theta3 + eta3)
#> v2 <- exp(theta4 + eta4)
#> 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
#> ipred <- f
#> rescv <- RSV
#> w <- ipred * rescv
#> ires <- DV - ipred
#> iwres <- ires/w
#> y <- ipred + w * eps1
#> })
#> }
#> ── nonmem2rx translation notes ($notes): ──
#> • there are duplicate eta names, not renaming duplicate parameters
#> • there are duplicate theta names, not renaming duplicate parameters
#> ── nonmem2rx extra properties: ──
#>
#> Sigma ($sigma):
#> eps1
#> eps1 1
#>
#> other properties include: $nonmemData, $etaData
#> captured NONMEM table outputs: $predData, $ipredData
#> NONMEM/rxode2 comparison data: $iwresCompare, $predCompare, $ipredCompare
#> NONMEM/rxode2 composite comparison: $predAtol, $predRtol, $ipredAtol, $ipredRtol, $iwresAtol, $iwresRtolnonmem2rx for your modelSome common options that you may want to change when importing NONMEM control stream are:
The default NONMEM output extension; By default it is
.lst. You can set it to something else, like
.res, using the following option:
options(nonmem2rx.lst=".res").
Turn on extended
control stream support. You can turn it on by
options(nonmem2rx.extended=TRUE)
You probably also want to change the name of parameters and compartments. The easiest way to name the parameters whatever you want is to pre-specify the names. For example:
mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"), lst=".res", save=FALSE,
thetaNames=c("lcl", "lvc", "lq", "lvp", "prop.sd"),
etaNames=c("eta.cl", "eta.vc", "eta.q","eta.vp"),
cmtNames = c("central", "perip"))
#> ℹ getting information from '/tmp/RtmpnH2sTe/Rinst2117d6bb73c/nonmem2rx/mods/cpt/runODE032.ctl'
#> ℹ reading in xml file
#> ℹ done
#> ℹ reading in ext file
#> ℹ done
#> ℹ reading in phi file
#> ℹ done
#> ℹ reading in lst file
#> ℹ abbreviated list parsing
#> ℹ done
#> ℹ done
#> ℹ splitting control stream by records
#> ℹ done
#> ℹ Processing record $INPUT
#> ℹ Processing record $MODEL
#> ℹ Processing record $gTHETA
#> ℹ Processing record $OMEGA
#> ℹ Processing record $SIGMA
#> ℹ Processing record $PROBLEM
#> ℹ Processing record $DATA
#> ℹ Processing record $SUBROUTINES
#> ℹ Processing record $PK
#> ℹ Processing record $DES
#> ℹ Processing record $ERROR
#> ℹ Processing record $ESTIMATION
#> ℹ Ignore record $ESTIMATION
#> ℹ Processing record $COVARIANCE
#> ℹ Ignore record $COVARIANCE
#> ℹ Processing record $TABLE
#> ℹ change initial estimate of `theta1` to `1.37034036528946`
#> ℹ change initial estimate of `theta2` to `4.19814911033061`
#> ℹ change initial estimate of `theta3` to `1.38003493562413`
#> ℹ change initial estimate of `theta4` to `3.87657341967489`
#> ℹ change initial estimate of `theta5` to `0.196446108190896`
#> ℹ change initial estimate of `eta1` to `0.101251418415006`
#> ℹ change initial estimate of `eta2` to `0.0993872449483344`
#> ℹ change initial estimate of `eta3` to `0.101302674763154`
#> ℹ change initial estimate of `eta4` to `0.0730497519364148`
#> ℹ read in nonmem input data (for model validation): /tmp/RtmpnH2sTe/Rinst2117d6bb73c/nonmem2rx/mods/cpt/Bolus_2CPT.csv
#> ℹ ignoring lines that begin with a letter (IGNORE=@)'
#> ℹ applying names specified by $INPUT
#> ℹ subsetting accept/ignore filters code: .data[-which((.data$SD == 0)),]
#> ℹ done
#> Setting r-universe rmarkdown theme...
#> using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
#> ℹ read in nonmem IPRED data (for model validation): /tmp/RtmpnH2sTe/Rinst2117d6bb73c/nonmem2rx/mods/cpt/runODE032.csv
#> ℹ done
#> ℹ changing most variables to lower case
#> ℹ done
#> ℹ replace theta names
#> ℹ done
#> ℹ replace eta names
#> ℹ done
#> ℹ renaming compartments
#> ℹ done
#> Setting r-universe rmarkdown theme...
#> using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
mod
#> ── rxode2-based free-form 2-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lcl lvc lq lvp prop.sd
#> 1.3703404 4.1981491 1.3800349 3.8765734 0.1964461
#>
#> Omega ($omega):
#> eta.cl eta.vc eta.q eta.vp
#> eta.cl 0.1012514 0.00000000 0.0000000 0.00000000
#> eta.vc 0.0000000 0.09938724 0.0000000 0.00000000
#> eta.q 0.0000000 0.00000000 0.1013027 0.00000000
#> eta.vp 0.0000000 0.00000000 0.0000000 0.07304975
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 central
#> 2 2 perip
#> ── μ-referencing ($muRefTable): ──
#> theta eta level
#> 1 lcl eta.cl id
#> 2 lvc eta.vc id
#> 3 lq eta.q id
#> 4 lvp eta.vp id
#>
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- "BOLUS_2CPT_CLV1QV2 SINGLE DOSE FOCEI (120 Ind/2280 Obs) runODE032"
#> dfObs <- 2280
#> dfSub <- 120
#> sigma <- lotri({
#> eps1 ~ 1
#> })
#> thetaMat <- lotri({
#> lcl ~ c(lcl = 0.000887681)
#> lvc ~ c(lcl = -0.00010551, lvc = 0.000871409)
#> lq ~ c(lcl = 0.000184416, lvc = -0.000106195, lq = 0.00299336)
#> lvp ~ c(lcl = -0.000120234, lvc = -5.06663e-05, lq = 0.000165252,
#> lvp = 0.00121347)
#> prop.sd ~ c(lcl = 5.2783e-08, lvc = -1.56562e-05, lq = 5.99331e-06,
#> lvp = -2.53991e-05, prop.sd = 9.94218e-06)
#> eps1 ~ c(lcl = 0, lvc = 0, lq = 0, lvp = 0, prop.sd = 0,
#> eps1 = 0)
#> eta.cl ~ c(lcl = -4.71273e-05, lvc = 4.69667e-05, lq = -3.64271e-05,
#> lvp = 2.54796e-05, prop.sd = -8.16885e-06, eps1 = 0,
#> eta.cl = 0.000169296)
#> omega.2.1 ~ c(lcl = 0, lvc = 0, lq = 0, lvp = 0, prop.sd = 0,
#> eps1 = 0, eta.cl = 0, omega.2.1 = 0)
#> eta.vc ~ c(lcl = -7.37156e-05, lvc = 2.56634e-05, lq = -8.08349e-05,
#> lvp = 1.37e-05, prop.sd = -4.36564e-06, eps1 = 0,
#> eta.cl = 8.75181e-06, omega.2.1 = 0, eta.vc = 0.00015125)
#> omega.3.1 ~ c(lcl = 0, lvc = 0, lq = 0, lvp = 0, prop.sd = 0,
#> eps1 = 0, eta.cl = 0, omega.2.1 = 0, eta.vc = 0,
#> omega.3.1 = 0)
#> omega.3.2 ~ c(lcl = 0, lvc = 0, lq = 0, lvp = 0, prop.sd = 0,
#> eps1 = 0, eta.cl = 0, omega.2.1 = 0, eta.vc = 0,
#> omega.3.1 = 0, omega.3.2 = 0)
#> eta.q ~ c(lcl = 6.63383e-05, lvc = -8.19002e-05, lq = 0.000548985,
#> lvp = 0.000168356, prop.sd = 1.59122e-06, eps1 = 0,
#> eta.cl = 3.48714e-05, omega.2.1 = 0, eta.vc = 4.31593e-07,
#> omega.3.1 = 0, omega.3.2 = 0, eta.q = 0.000959029)
#> omega.4.1 ~ c(lcl = 0, lvc = 0, lq = 0, lvp = 0, prop.sd = 0,
#> eps1 = 0, eta.cl = 0, omega.2.1 = 0, eta.vc = 0,
#> omega.3.1 = 0, omega.3.2 = 0, eta.q = 0, omega.4.1 = 0)
#> omega.4.2 ~ c(lcl = 0, lvc = 0, lq = 0, lvp = 0, prop.sd = 0,
#> eps1 = 0, eta.cl = 0, omega.2.1 = 0, eta.vc = 0,
#> omega.3.1 = 0, omega.3.2 = 0, eta.q = 0, omega.4.1 = 0,
#> omega.4.2 = 0)
#> omega.4.3 ~ c(lcl = 0, lvc = 0, lq = 0, lvp = 0, prop.sd = 0,
#> eps1 = 0, eta.cl = 0, omega.2.1 = 0, eta.vc = 0,
#> omega.3.1 = 0, omega.3.2 = 0, eta.q = 0, omega.4.1 = 0,
#> omega.4.2 = 0, omega.4.3 = 0)
#> eta.vp ~ c(lcl = -9.49661e-06, lvc = 0.000110108, lq = -0.000306537,
#> lvp = -9.12897e-05, prop.sd = 3.1877e-06, eps1 = 0,
#> eta.cl = 1.36628e-05, omega.2.1 = 0, eta.vc = -1.95096e-05,
#> omega.3.1 = 0, omega.3.2 = 0, eta.q = -0.00012977,
#> omega.4.1 = 0, omega.4.2 = 0, omega.4.3 = 0, eta.vp = 0.00051019)
#> })
#> validation <- c("IPRED relative difference compared to Nonmem IPRED: 0%; 95% percentile: (0%,0%); rtol=6.43e-06",
#> "IPRED absolute difference compared to Nonmem IPRED: 95% percentile: (2.19e-05, 0.0418); atol=0.00167",
#> "IWRES relative difference compared to Nonmem IWRES: 0%; 95% percentile: (0%,0.01%); rtol=8.99e-06",
#> "IWRES absolute difference compared to Nonmem IWRES: 95% percentile: (1.82e-07, 4.63e-05); atol=3.65e-06",
#> "PRED relative difference compared to Nonmem PRED: 0%; 95% percentile: (0%,0%); rtol=6.41e-06",
#> "PRED absolute difference compared to Nonmem PRED: 95% percentile: (1.41e-07,0.00382) atol=6.41e-06")
#> ini({
#> lcl <- 1.37034036528946
#> label("log Cl")
#> lvc <- 4.19814911033061
#> label("log Vc")
#> lq <- 1.38003493562413
#> label("log Q")
#> lvp <- 3.87657341967489
#> label("log Vp")
#> prop.sd <- c(0, 0.196446108190896, 1)
#> label("RSV")
#> eta.cl ~ 0.101251418415006
#> eta.vc ~ 0.0993872449483344
#> eta.q ~ 0.101302674763154
#> eta.vp ~ 0.0730497519364148
#> })
#> model({
#> cmt(central)
#> cmt(perip)
#> cl <- exp(lcl + eta.cl)
#> v <- exp(lvc + eta.vc)
#> q <- exp(lq + eta.q)
#> v2 <- exp(lvp + eta.vp)
#> v1 <- v
#> scale1 <- v
#> k21 <- q/v2
#> k12 <- q/v
#> d/dt(central) <- k21 * perip - k12 * central - cl * central/v1
#> d/dt(perip) <- -k21 * perip + k12 * central
#> f <- central/scale1
#> ipred <- f
#> rescv <- prop.sd
#> ipred ~ prop(prop.sd)
#> })
#> }
#> ── nonmem2rx extra properties: ──
#> other properties include: $nonmemData, $etaData
#> captured NONMEM table outputs: $predData, $ipredData
#> NONMEM/rxode2 comparison data: $iwresCompare, $predCompare, $ipredCompare
#> NONMEM/rxode2 composite comparison: $predAtol, $predRtol, $ipredAtol, $ipredRtol, $iwresAtol, $iwresRtolThis checks the parameter names to make sure they are the same length
as the input names, if they are not, the model will skip parameter
renaming and keep the default translation names theta# and
eta#.
As a note, sigma parameters are not currently renamed;
So for the following model (which grabs the parameter automatically
labels to generate variables), sigma is simply
eps#.
mod <- nonmem2rx(system.file("Theopd.ctl", package="nonmem2rx"), save=FALSE)
#> ℹ getting information from '/tmp/RtmpnH2sTe/Rinst2117d6bb73c/nonmem2rx/Theopd.ctl'
#> ℹ reading in lst file
#> ℹ seeing if file argument is actually lst file
#> ℹ not list file, control stream
#> ℹ done
#> ℹ splitting control stream by records
#> ℹ done
#> ℹ Processing record $INPUT
#> ℹ Processing record $gTHETA
#> ℹ Processing record $OMEGA
#> ℹ Processing record $SIGMA
#> ℹ Processing record $PROBLEM
#> ℹ Processing record $DATA
#> ℹ Processing record $ESTIMATION
#> ℹ Ignore record $ESTIMATION
#> ℹ Processing record $COVARIANCE
#> ℹ Ignore record $COVARIANCE
#> ℹ Processing record $PRED
#> ℹ Processing record $TABLE
#> ℹ final parameters not updated, will skip validation
#> ℹ changing most variables to lower case
#> ℹ done
#> ℹ replace theta names
#> ℹ done
#> ℹ replace eta names
#> ℹ done
mod
#> ── rxode2-based Pred model ─────────────────────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> POP_E0 POP_EMAX POP_C50
#> 150 200 10
#>
#> Omega ($omega):
#> PPV_E0 PPV_EMAX PPV_C50
#> PPV_E0 0.5 0.0 0.0
#> PPV_EMAX 0.0 0.5 0.0
#> PPV_C50 0.0 0.0 0.5
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- "theophylline pharmacodynamics standard control stream"
#> sigma <- lotri({
#> eps1 ~ 100
#> })
#> validation <- "final parameters not updated, validation skipped"
#> ini({
#> POP_E0 <- c(0, 150)
#> label("POP_E0 1")
#> POP_EMAX <- c(0, 200)
#> label("POP_EMAX 2")
#> POP_C50 <- c(0.001, 10)
#> label("POP_C50 3")
#> PPV_E0 ~ 0.5
#> PPV_EMAX ~ 0.5
#> PPV_C50 ~ 0.5
#> })
#> model({
#> e0 <- POP_E0 * exp(PPV_E0)
#> emax <- POP_EMAX * exp(PPV_EMAX)
#> ec50 <- POP_C50 * exp(PPV_C50)
#> y <- e0 + emax * THEO/(THEO + ec50) + eps1
#> })
#> }
#> ── nonmem2rx extra properties: ──
#>
#> Sigma ($sigma):
#> eps1
#> eps1 100
#>
#> other properties include: $etaData
#> captured NONMEM table outputs: $predData, $ipredData
#> NONMEM/rxode2 comparison data: $iwresCompare, $predCompare, $ipredCompare
#> NONMEM/rxode2 composite comparison: $predAtol, $predRtol, $ipredAtol, $ipredRtol, $iwresAtol, $iwresRtolYou can still rename however you wish, though, using model piping
(rxRename() or dplyr::rename() would both
work):
mod <- mod %>% rxRename(add.var=eps1)
mod
#> ── rxode2-based Pred model ─────────────────────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> POP_E0 POP_EMAX POP_C50
#> 150 200 10
#>
#> Omega ($omega):
#> PPV_E0 PPV_EMAX PPV_C50
#> PPV_E0 0.5 0.0 0.0
#> PPV_EMAX 0.0 0.5 0.0
#> PPV_C50 0.0 0.0 0.5
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- "theophylline pharmacodynamics standard control stream"
#> sigma <- lotri({
#> add.var ~ 100
#> })
#> validation <- "final parameters not updated, validation skipped"
#> ini({
#> POP_E0 <- c(0, 150)
#> label("POP_E0 1")
#> POP_EMAX <- c(0, 200)
#> label("POP_EMAX 2")
#> POP_C50 <- c(0.001, 10)
#> label("POP_C50 3")
#> PPV_E0 ~ 0.5
#> PPV_EMAX ~ 0.5
#> PPV_C50 ~ 0.5
#> })
#> model({
#> e0 <- POP_E0 * exp(PPV_E0)
#> emax <- POP_EMAX * exp(PPV_EMAX)
#> ec50 <- POP_C50 * exp(PPV_C50)
#> y <- e0 + emax * THEO/(THEO + ec50) + add.var
#> })
#> }
#> ── nonmem2rx extra properties: ──
#>
#> Sigma ($sigma):
#> add.var
#> add.var 100
#>
#> other properties include: $etaData
#> captured NONMEM table outputs: $predData, $ipredData
#> NONMEM/rxode2 comparison data: $iwresCompare, $predCompare, $ipredCompare
#> NONMEM/rxode2 composite comparison: $predAtol, $predRtol, $ipredAtol, $ipredRtol, $iwresAtol, $iwresRtolThis model does not specify the residuals in a way that makes sense
to nlmixr2. If you want, you can still convert
the rxode2 model to a nlmixr2 fit.
The key files to import are the NONMEM control stream (or related
file) and the NONMEM output (often with a .lst or
.res extension).
The import process steps are below:
Read in the nonmem control stream and convert the model to a
rxode2 ui function.
Try to determine an endpoint/residual specification in the model
(if possible), and convert to a fully qualified ui model that can be
used in nlmixr2 and rxode2. If it cannot be
determined automatically, you
can manually fix this and still convert to a nlmixr2
object (if the data/estimates are available of course).
If available, nonmem2rx will read the final
parameter estimates and update the model.
The converter will read in the nonmem input dataset, and search
for the output files with IPRED, PRED and the
ETA values. The translated rxode2 model is run
for the population parameters and the individual parameters. This will
then compare the results between NONMEM and
rxode2 to make sure the translation makes sense. This only
works when nonmem2rx has access to the input data and the
output with the IWRES, IPRED,
PRED and the ETA values.
Converts the upper case NONMEM variables to lower case (can be
turned off with nonmem2rx(..., toLowerLhs=FALSE)))
Replaces the NONMEM theta / eta names with the label-based names
like an extended control stream (can be turned off with
nonmem2rx(thetaNames=FALSE, etaNames=FALSE))
Replaces the compartment names with the defined compartment names
in the control stream (ie COMP=(compartmenName))