Converting model from lincmt to an ODE model fails due to missing parameter in the ini block

[billdenney]

The example below indicates that peripheral1 should be in the ini block, but it shouldn't. This is likely a sequencing issue with append. I can try to look at it in a few days.

library(nlmixr2lib)
library(nlmixr2)
#> Warning: package 'nlmixr2' was built under R version 4.2.3
#> Loading required package: nlmixr2data
#> Warning: package 'nlmixr2data' was built under R version 4.2.3

readModelDb("Soehoel_2022_tralokinumab") %>%
  model(-f(depot), -cp) %>%
  model(
    {
      kel <- cl/vc
      k12 <- q/vc
      k21 <- q/vp
      
      d/dt(depot) <- -ka*depot
      d/dt(central) <-  ka*depot - kel*central - k12*central + k21*peripheral1
      d/dt(peripheral1) <- k12*central - k21*peripheral1
      cp <- central / vc
      
      f(depot) <- fdepot
      cp ~ add(cpaddSd) + prop(cppropSd)
    },
    append = TRUE
  )
#> ! remove population parameter `cpaddSd`
#> ! remove population parameter `cppropSd`
#> ℹ promote `peripheral1` to population parameter with initial estimate 1
#> ℹ add residual parameter `cpaddSd` and set estimate to 1
#> ℹ add residual parameter `cppropSd` and set estimate to 1
#> Error: syntax/parsing errors:
#> the following parameter(s) were in the ini block but not in the model block: peripheral1

^{Created on 2023-04-19 with reprex v2.0.2}

[mattfidler]

This seems to work for me now.

library(rxode2)
#> rxode2 2.0.14.9000 using 8 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`
library(nlmixr2lib)
readModelDb("Soehoel_2022_tralokinumab") %>%
model(-f(depot), -cp) %>%
model(
      {
      kel <- cl/vc
      k12 <- q/vc
      k21 <- q/vp
      
      d/dt(depot) <- -ka*depot
      d/dt(central) <-  ka*depot - kel*central - k12*central + k21*peripheral1
      d/dt(peripheral1) <- k12*central - k21*peripheral1
      cp <- central / vc
      
      f(depot) <- fdepot
      cp ~ add(cpaddSd) + prop(cppropSd)
      },
      append = TRUE
      )
#> ! remove population parameter `cpaddSd`
#> ! remove population parameter `cppropSd`
#> ℹ add residual parameter `cpaddSd` and set estimate to 1
#> ℹ add residual parameter `cppropSd` and set estimate to 1
#>  ── rxode2-based free-form 3-cmt ODE model ────────────────────────────────────── 
#>  ── Initalization: ──  
#> Fixed Effects ($theta): 
#>            lka            lvc            lcl            lvp             lq 
#>     -1.6928195      0.9969486     -1.9038090      0.3646431     -1.8388511 
#>        lfdepot      e_wt_vcvp       e_wt_clq e_nonECZTRA_cl e_nonECZTRA_vc 
#>     -0.2731219      0.7930000      0.8730000      0.3440000      0.2580000 
#>   e_f_dilution  e_ka_dilution        cpaddSd       cppropSd 
#>      0.3540000     -0.5190000      1.0000000      1.0000000 
#> 
#> Omega ($omega): 
#>           etavc     etacl
#> etavc 0.3861480 0.2683494
#> etacl 0.2683494 0.3057157
#> 
#> States ($state or $stateDf): 
#>   Compartment Number Compartment Name
#> 1                  1            depot
#> 2                  2          central
#> 3                  3      peripheral1
#>  ── μ-referencing ($muRefTable): ──  
#>   theta   eta level
#> 1   lcl etacl    id
#> 2   lvc etavc    id
#> 
#>  ── Model (Normalized Syntax): ── 
#> function() {
#>     covariateData <- list(nonECZTRA = "1 = any study other than ECZTRA; 0 = ECZTRA study", 
#>         WT = "Body weight in kg", dilution = "Was the drug diluted as it was in study D2213C00001? 1 = yes, 0 = no (0 is typical)")
#>     reference <- "Soehoel A, Larsen MS, Timmermann S. Population Pharmacokinetics of Tralokinumab in Adult Subjects With Moderate to Severe Atopic Dermatitis. Clinical Pharmacology in Drug Development. 2022;11(8):910-921. doi:10.1002/cpdd.1113"
#>     ini({
#>         lka <- -1.69281952137315
#>         label("Absorption rate (1/day)")
#>         lvc <- 0.99694863489161
#>         label("Central volume of distribution (L)")
#>         lcl <- -1.90380897303668
#>         label("Clearance (L/day)")
#>         lvp <- 0.364643113587909
#>         label("Peripheral volume of distribution (L)")
#>         lq <- -1.83885107676191
#>         label("Intercompartmental clearance (L/day)")
#>         lfdepot <- -0.273121921120451
#>         label("Subcutaneous bioavailability (fraction)")
#>         e_wt_vcvp <- 0.793
#>         label("Effect of body weight on central and peripheral volumes (unitless)")
#>         e_wt_clq <- 0.873
#>         label("Effect of body weight on clearance and intercompartmental clearance (unitless)")
#>         e_nonECZTRA_cl <- 0.344
#>         label("Effect of non-ECZTRA trials on clearance (unitless)")
#>         e_nonECZTRA_vc <- 0.258
#>         label("Effect of non-ECZTRA trials on central volume (unitless)")
#>         e_f_dilution <- 0.354
#>         label("Effect of dilution on bioavailability (unitless)")
#>         e_ka_dilution <- -0.519
#>         label("Effect of dilution trials on absorption rate (unitless)")
#>         cpaddSd <- c(0, 1)
#>         cppropSd <- c(0, 1)
#>         etavc + etacl ~ c(0.386148, 0.2683494, 0.3057157)
#>     })
#>     model({
#>         fdepot <- exp(lfdepot) * (1 + e_f_dilution * dilution)
#>         ka <- exp(lka) * (1 + e_ka_dilution * dilution)
#>         cl <- exp(lcl + etacl) * (WT/75)^e_wt_clq * (1 + e_nonECZTRA_cl * 
#>             nonECZTRA)
#>         vc <- exp(lvc + etavc) * (WT/75)^e_wt_vcvp * (1 + e_nonECZTRA_vc * 
#>             nonECZTRA)
#>         q <- exp(lq) * (WT/75)^e_wt_clq
#>         vp <- exp(lvp) * (WT/75)^e_wt_vcvp
#>         kel <- cl/vc
#>         k12 <- q/vc
#>         k21 <- q/vp
#>         d/dt(depot) <- -ka * depot
#>         d/dt(central) <- ka * depot - kel * central - k12 * central + 
#>             k21 * peripheral1
#>         d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#>         cp <- central/vc
#>         f(depot) <- fdepot
#>         cp ~ add(cpaddSd) + prop(cppropSd)
#>     })
#> }

^{Created on 2023-11-30 with reprex v2.0.2}

At least with #610 applied