Converting a NONMEM fit to a nlmixr2 object
Source:vignettes/articles/convert-nlmixr2.Rmd
convert-nlmixr2.RmdCreating a nlmixr2 compatible model
Depending on the model, not all the residual specifications are
translated to the nlmixr2 style residuals. This means the
model cannot be immediately used for either nlmixr2()
estimation or creating a nlmixr2 fit object (though you can
simulate with and without certainty without any modifications)
For example you could have something like:
y <- ipred*(1+eps1)For a model that can do nlmixr2 estimation instead of
simply simulation the residual needs to be changed to something
like:
cp ~ prop(prop.sd)Since the model when import has most of the translation done already, you can easily tweak the model to have this form.
Here is the same example where the residual errors are not
automatically translated to the nlmixr2 parameter style (in
this case because of the option determineError=FALSE)
Example – no error determined
library(nonmem2rx)
library(babelmixr2)
#> Loading required package: nlmixr2
#> Loading required package: nlmixr2data
# 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 '/home/runner/work/_temp/Library/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): /home/runner/work/_temp/Library/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
#> ℹ read in nonmem IPRED data (for model validation): /home/runner/work/_temp/Library/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
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
print(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, $iwresRtolOne approach to get a nlmixr2 compatible model is to copy the printed model above and then modify it as needed.
In this case, I will name the parameters to something a bit more meaningful while keeping the estimates the same:
mod2 <-function() {
ini({
lcl <- 1.37034036528946
lvc <- 4.19814911033061
lq <- 1.38003493562413
lvp <- 3.87657341967489
RSV <- c(0, 0.196446108190896, 1)
eta.cl ~ 0.101251418415006
eta.v ~ 0.0993872449483344
eta.q ~ 0.101302674763154
eta.v2 ~ 0.0730497519364148
})
model({
cmt(CENTRAL)
cmt(PERI)
cl <- exp(lcl + eta.cl)
v <- exp(lvc + eta.v)
q <- exp(lq + eta.q)
v2 <- exp(lvp + eta.v2)
v1 <- v
scale1 <- v
k21 <- q/v2
k12 <- q/v
d/dt(CENTRAL) <- k21 * PERI - k12 * CENTRAL - cl * CENTRAL/v1
d/dt(PERI) <- -k21 * PERI + k12 * CENTRAL
f <- CENTRAL/scale1
f ~ prop(RSV)
})
}The as.nonmem2rx() function will compare the already
imported rxode2 model function with the model you made some manual
tweaks to:
new <- as.nonmem2rx(mod2, mod)
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> ℹ copy 'dfSub' to nonmem2rx model
#> ℹ copy 'thetaMat' to nonmem2rx model
#> ℹ copy 'dfObs' to nonmem2rx model
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
print(new)
#> ── rxode2-based free-form 2-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lcl lvc lq lvp RSV
#> 1.3703404 4.1981491 1.3800349 3.8765734 0.1964461
#>
#> Omega ($omega):
#> eta.cl eta.v eta.q eta.v2
#> eta.cl 0.1012514 0.00000000 0.0000000 0.00000000
#> eta.v 0.0000000 0.09938724 0.0000000 0.00000000
#> eta.q 0.0000000 0.00000000 0.1013027 0.00000000
#> eta.v2 0.0000000 0.00000000 0.0000000 0.07304975
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 CENTRAL
#> 2 2 PERI
#> ── μ-referencing ($muRefTable): ──
#> theta eta level
#> 1 lcl eta.cl id
#> 2 lvc eta.v id
#> 3 lq eta.q id
#> 4 lvp eta.v2 id
#>
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- "BOLUS_2CPT_CLV1QV2 SINGLE DOSE FOCEI (120 Ind/2280 Obs) runODE032"
#> dfObs <- 2280
#> dfSub <- 120
#> 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)
#> RSV ~ c(lcl = 5.2783e-08, lvc = -1.56562e-05, lq = 5.99331e-06,
#> lvp = -2.53991e-05, RSV = 9.94218e-06)
#> eta.cl ~ c(lcl = -4.71273e-05, lvc = 4.69667e-05, lq = -3.64271e-05,
#> lvp = 2.54796e-05, RSV = -8.16885e-06, eta.cl = 0.000169296)
#> eta.v ~ c(lcl = -7.37156e-05, lvc = 2.56634e-05, lq = -8.08349e-05,
#> lvp = 1.37e-05, RSV = -4.36564e-06, eta.cl = 8.75181e-06,
#> eta.v = 0.00015125)
#> eta.q ~ c(lcl = 6.63383e-05, lvc = -8.19002e-05, lq = 0.000548985,
#> lvp = 0.000168356, RSV = 1.59122e-06, eta.cl = 3.48714e-05,
#> eta.v = 4.31593e-07, eta.q = 0.000959029)
#> eta.v2 ~ c(lcl = -9.49661e-06, lvc = 0.000110108, lq = -0.000306537,
#> lvp = -9.12897e-05, RSV = 3.1877e-06, eta.cl = 1.36628e-05,
#> eta.v = -1.95096e-05, eta.q = -0.00012977, eta.v2 = 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
#> 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)
#> })
#> }
#> ── 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, $iwresRtolIn this case the new model qualifies and now has all the
information from the imported nonmem2rx model.
This means you can estimate from the new model knowing it was the same model specified in NONMEM.
Since iwres is affected by how your specify your
residuals, pay special attention to that validation. If it does not
validate, you may have forgot to translate the NONMEM variance estimate
to the standard deviation estimate required by many estimation
methods.
Converting the model to a nlmixr2 fit
Once you have a rxode2() model that:
Qualifies against the NONMEM model,
Has
nlmixr2compatible residuals
You can then convert it to a nlmixr2 fit object with
babelmixr2:
library(babelmixr2)
fit <- as.nlmixr2(new)
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of full model...
#> ✔ done
#> → finding duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → compiling EBE model...
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ✔ done
#> rxode2 3.0.2.9000 using 2 threads (see ?getRxThreads)
#> no cache: create with `rxCreateCache()`
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 204016
#> → compress parHistData in nlmixr2 object, save 2176
fit
#> ── nlmixr² nonmem2rx reading NONMEM ver 7.4.3 ──
#>
#> OBJF AIC BIC Log-likelihood Condition#(Cov)
#> nonmem2rx 15977.28 20185.64 20237.23 -10083.82 335.4129
#> Condition#(Cor)
#> nonmem2rx 2.096559
#>
#> ── Time (sec fit$time): ──
#>
#> setup table compress NONMEM as.nlmixr2
#> elapsed 0.038768 0.124 0.012 100.95 2.778
#>
#> ── Population Parameters (fit$parFixed or fit$parFixedDf): ──
#>
#> Est. SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)%
#> lcl 1.37 0.0298 2.17 3.94 (3.71, 4.17) 32.6 1.94%
#> lvc 4.2 0.0295 0.703 66.6 (62.8, 70.5) 32.3 2.46%
#> lq 1.38 0.0547 3.96 3.98 (3.57, 4.42) 32.7 40.5%
#> lvp 3.88 0.0348 0.899 48.3 (45.1, 51.7) 27.5 28.4%
#> RSV 0.196 0.196
#>
#> Covariance Type (fit$covMethod): nonmem2rx
#> No correlations in between subject variability (BSV) matrix
#> Full BSV covariance (fit$omega) or correlation (fit$omegaR; diagonals=SDs)
#> Distribution stats (mean/skewness/kurtosis/p-value) available in fit$shrink
#> Censoring (fit$censInformation): No censoring
#> Minimization message (fit$message):
#>
#>
#> WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1
#>
#> (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
#>
#>
#> 0MINIMIZATION SUCCESSFUL
#> NO. OF FUNCTION EVALUATIONS USED: 320
#> NO. OF SIG. DIGITS IN FINAL EST.: 2.5
#>
#> IPRED relative difference compared to Nonmem IPRED: 0%; 95% percentile: (0%,0%); rtol=6.43e-06
#> PRED relative difference compared to Nonmem PRED: 0%; 95% percentile: (0%,0%); rtol=6.41e-06
#> IPRED absolute difference compared to Nonmem IPRED: 95% percentile: (2.25e-05, 0.0418); atol=0.00167
#> PRED absolute difference compared to Nonmem PRED: 95% percentile: (1.41e-07,0.00382); atol=6.41e-06
#> nonmem2rx model file: '/home/runner/work/_temp/Library/nonmem2rx/mods/cpt/runODE032.ctl'
#>
#> ── Fit Data (object fit is a modified tibble): ──
#> # A tibble: 2,280 × 25
#> ID TIME DV PRED RES IPRED IRES IWRES eta.cl eta.v eta.q eta.v2
#> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 0.25 1041. 1750. -710. 1215. -175. -0.732 -0.144 0.375 0.0650 0.241
#> 2 1 0.5 1629 1700. -70.8 1192. 437. 1.87 -0.144 0.375 0.0650 0.241
#> 3 1 0.75 878. 1651. -774. 1169. -291. -1.27 -0.144 0.375 0.0650 0.241
#> # ℹ 2,277 more rows
#> # ℹ 13 more variables: f <dbl>, CENTRAL <dbl>, PERI <dbl>, cl <dbl>, v <dbl>,
#> # q <dbl>, v2 <dbl>, v1 <dbl>, scale1 <dbl>, k21 <dbl>, k12 <dbl>, tad <dbl>,
#> # dosenum <dbl>