Convert a model to a nonmem2rx model
Examples
# \donttest{
mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"),
determineError=FALSE, lst=".res", save=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 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 $THETA
#> 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
#>
#>
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> 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
#>
#>
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
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))
#>
#>
#> ℹ copy 'dfSub' to nonmem2rx model
#> ℹ copy 'thetaMat' to nonmem2rx model
#> ℹ copy 'dfObs' to nonmem2rx model
#>
#>
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
if (!inherits(new, "try-error")) print(new, page=1)
#> ── 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 + lvc + lq + lvp + RSV + eta.cl + eta.v + eta.q +
#> eta.v2 ~ c(0.000887681, -0.00010551, 0.000871409,
#> 0.000184416, -0.000106195, 0.00299336, -0.000120234,
#> -5.06663e-05, 0.000165252, 0.00121347, 5.2783e-08,
#> -1.56562e-05, 5.99331e-06, -2.53991e-05, 9.94218e-06,
#> -4.71273e-05, 4.69667e-05, -3.64271e-05, 2.54796e-05,
#> -8.16885e-06, 0.000169296, -7.37156e-05, 2.56634e-05,
#> -8.08349e-05, 1.37e-05, -4.36564e-06, 8.75181e-06,
#> 0.00015125, 6.63383e-05, -8.19002e-05, 0.000548985,
#> 0.000168356, 1.59122e-06, 3.48714e-05, 4.31593e-07,
#> 0.000959029, -9.49661e-06, 0.000110108, -0.000306537,
#> -9.12897e-05, 3.1877e-06, 1.36628e-05, -1.95096e-05,
#> -0.00012977, 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, $iwresRtol
# }