object 'lag(depot2)' not found - When trying to create NONMEM export

[john-harrold]

In the example below I'm trying to convert a model from the nlmixr2lib model library into NONMEM. It's giving me an error that suggests it doesn't understand the lag portion of the model. Is there something I'm doing wrong?

rm(list=ls())
library(rxode2)
#> rxode2 3.0.3 using 1 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`
#> ========================================
#> rxode2 has not detected OpenMP support and will run in single-threaded mode
#> This is a Mac. Please read https://mac.r-project.org/openmp/
#> ========================================
library(nlmixr2)
#> Loading required package: nlmixr2data

rx_fun = function() {
    description <- "PK double absorption model with simultaneous zero order and first order absorptions"
    ini({
        tk01 <- 0.4
        label("Zero order absorption rate from first site (K01)")
        lka2 <- 0.45
        label("First order Absorption rate (Ka)")
        lcl <- 1
        label("Clearance (CL)")
        lvc <- 3
        label("Central volume of distribution (V)")
        propSd <- c(0, 0.5)
        label("Proportional residual error (fraction)")
        lgfdepot1 <- 1.38629436111989
        lalag <- 2.19722457733622
        TV_PAR <- 0.1
        ETA.PAR ~ 1
    })
    model({
        POP_PAR <- exp(TV_PAR + ETA.PAR)
        k01 <- exp(tk01)
        ka2 <- exp(lka2)
        cl <- exp(lcl)
        vc <- exp(lvc)
        fdepot1 <- expit(lgfdepot1, 0, 1)
        alag <- exp(lalag)
        kel <- cl/vc
        d/dt(depot1) <- -k01
        f(depot1) <- fdepot1
        d/dt(depot2) <- -ka2 * depot2
        lag(depot2) <- alag
        f(depot2) <- 1 - fdepot1
        d/dt(central) <- k01 + ka2 * depot2 - kel * central
        Cc <- central/vc
        Cc ~ prop(propSd)
    })
}

rx_obj = rxode2::rxode2(rx_fun)
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
dataset = data.frame(
  id = c(1L, 1L, 2L, 2L), 
  time = c(0, 1, 0, 1),      
  cmt = c("Cc", "Cc", "Cc", "Cc"), 
  evid = c(0L, 0L, 0L, 0L),      
  dv = c(0, 0, 0, 0))

res = nlmixr2::nlmixr2(rx_obj, dataset, "nonmem", babelmixr2::nonmemControl(modelName="test_nm", runCommand=NA))
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of full model...
#> ✔ done
#> Error in get(.tmp, envir = rxUiGetNonememModelEnv$rxS) : 
#>   object 'lag(depot2)' not found
#> Error: object 'lag(depot2)' not found




sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Sonoma 14.7.1
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: America/Los_Angeles
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] nlmixr2_3.0.1.9000 nlmixr2data_2.0.9  rxode2_3.0.3      
#> 
#> loaded via a namespace (and not attached):
#>  [1] generics_0.1.3        lattice_0.22-6        digest_0.6.37        
#>  [4] magrittr_2.0.3        nonmem2rx_0.1.6       evaluate_1.0.1       
#>  [7] grid_4.4.1            fastmap_1.2.0         lotri_1.0.0          
#> [10] backports_1.5.0       nlmixr2est_3.0.2      scales_1.3.0         
#> [13] lazyeval_0.2.2        RApiSerialize_0.1.4   cli_3.6.3            
#> [16] crayon_1.5.3          symengine_0.2.6       rlang_1.1.4          
#> [19] units_0.8-5           monolix2rx_0.0.4      munsell_0.5.1        
#> [22] reprex_2.1.1          withr_3.0.2           cachem_1.1.0         
#> [25] yaml_2.3.10           tools_4.4.1           qs_0.27.2            
#> [28] nlmixr2plot_3.0.0     lbfgsb3c_2024-3.5     memoise_2.0.1        
#> [31] checkmate_2.3.2       dplyr_1.1.4           colorspace_2.1-1     
#> [34] ggplot2_3.5.1         n1qn1_6.0.1-12        vctrs_0.6.5          
#> [37] R6_2.5.1              lifecycle_1.0.4       fs_1.6.5             
#> [40] stringfish_0.16.0     PreciseSums_0.7       pkgconfig_2.0.3      
#> [43] rex_1.2.1             RcppParallel_5.1.9    pillar_1.10.0        
#> [46] gtable_0.3.6          data.table_1.16.4     glue_1.8.0           
#> [49] Rcpp_1.0.13-1         xfun_0.49             tibble_3.2.1         
#> [52] tidyselect_1.2.1      sys_3.4.3             knitr_1.49           
#> [55] babelmixr2_0.1.5.9000 dparser_1.3.1-13      htmltools_0.5.8.1    
#> [58] nlme_3.1-166          rmarkdown_2.29        compiler_4.4.1

[mattfidler]

Probably an error

…

On Fri, Dec 20, 2024, 5:47 PM John Harrold ***@***.***> wrote: In the example below I'm trying to convert a model from the nlmixr2lib model library into NONMEM. It's giving me an error that suggests it doesn't understand the lag portion of the model. Is there something I'm doing wrong? rm(list=ls()) library(rxode2)#> rxode2 3.0.3 using 1 threads (see ?getRxThreads)#> no cache: create with `rxCreateCache()`#> ========================================#> rxode2 has not detected OpenMP support and will run in single-threaded mode#> This is a Mac. Please read https://mac.r-project.org/openmp/#> ======================================== library(nlmixr2)#> Loading required package: nlmixr2data rx_fun = function() { description <- "PK double absorption model with simultaneous zero order and first order absorptions" ini({ tk01 <- 0.4 label("Zero order absorption rate from first site (K01)") lka2 <- 0.45 label("First order Absorption rate (Ka)") lcl <- 1 label("Clearance (CL)") lvc <- 3 label("Central volume of distribution (V)") propSd <- c(0, 0.5) label("Proportional residual error (fraction)") lgfdepot1 <- 1.38629436111989 lalag <- 2.19722457733622 TV_PAR <- 0.1 ETA.PAR ~ 1 }) model({ POP_PAR <- exp(TV_PAR + ETA.PAR) k01 <- exp(tk01) ka2 <- exp(lka2) cl <- exp(lcl) vc <- exp(lvc) fdepot1 <- expit(lgfdepot1, 0, 1) alag <- exp(lalag) kel <- cl/vc d/dt(depot1) <- -k01 f(depot1) <- fdepot1 d/dt(depot2) <- -ka2 * depot2 lag(depot2) <- alag f(depot2) <- 1 - fdepot1 d/dt(central) <- k01 + ka2 * depot2 - kel * central Cc <- central/vc Cc ~ prop(propSd) }) } rx_obj = rxode2::rxode2(rx_fun)#> ℹ parameter labels from comments are typically ignored in non-interactive mode#> ℹ Need to run with the source intact to parse commentsdataset = data.frame( id = c(1L, 1L, 2L, 2L), time = c(0, 1, 0, 1), cmt = c("Cc", "Cc", "Cc", "Cc"), evid = c(0L, 0L, 0L, 0L), dv = c(0, 0, 0, 0)) res = nlmixr2::nlmixr2(rx_obj, dataset, "nonmem", babelmixr2::nonmemControl(modelName="test_nm", runCommand=NA))#> → loading into symengine environment...#> → pruning branches (`if`/`else`) of full model...#> ✔ done#> Error in get(.tmp, envir = rxUiGetNonememModelEnv$rxS) : #> object 'lag(depot2)' not found#> Error: object 'lag(depot2)' not found sessionInfo()#> R version 4.4.1 (2024-06-14)#> Platform: aarch64-apple-darwin20#> Running under: macOS Sonoma 14.7.1#> #> Matrix products: default#> BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib #> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0#> #> locale:#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8#> #> time zone: America/Los_Angeles#> tzcode source: internal#> #> attached base packages:#> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages:#> [1] nlmixr2_3.0.1.9000 nlmixr2data_2.0.9 rxode2_3.0.3 #> #> loaded via a namespace (and not attached):#> [1] generics_0.1.3 lattice_0.22-6 digest_0.6.37 #> [4] magrittr_2.0.3 nonmem2rx_0.1.6 evaluate_1.0.1 #> [7] grid_4.4.1 fastmap_1.2.0 lotri_1.0.0 #> [10] backports_1.5.0 nlmixr2est_3.0.2 scales_1.3.0 #> [13] lazyeval_0.2.2 RApiSerialize_0.1.4 cli_3.6.3 #> [16] crayon_1.5.3 symengine_0.2.6 rlang_1.1.4 #> [19] units_0.8-5 monolix2rx_0.0.4 munsell_0.5.1 #> [22] reprex_2.1.1 withr_3.0.2 cachem_1.1.0 #> [25] yaml_2.3.10 tools_4.4.1 qs_0.27.2 #> [28] nlmixr2plot_3.0.0 lbfgsb3c_2024-3.5 memoise_2.0.1 #> [31] checkmate_2.3.2 dplyr_1.1.4 colorspace_2.1-1 #> [34] ggplot2_3.5.1 n1qn1_6.0.1-12 vctrs_0.6.5 #> [37] R6_2.5.1 lifecycle_1.0.4 fs_1.6.5 #> [40] stringfish_0.16.0 PreciseSums_0.7 pkgconfig_2.0.3 #> [43] rex_1.2.1 RcppParallel_5.1.9 pillar_1.10.0 #> [46] gtable_0.3.6 data.table_1.16.4 glue_1.8.0 #> [49] Rcpp_1.0.13-1 xfun_0.49 tibble_3.2.1 #> [52] tidyselect_1.2.1 sys_3.4.3 knitr_1.49 #> [55] babelmixr2_0.1.5.9000 dparser_1.3.1-13 htmltools_0.5.8.1 #> [58] nlme_3.1-166 rmarkdown_2.29 compiler_4.4.1 — Reply to this email directly, view it on GitHub <#149>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAD5VWQF34QRHVNNLEMJWGT2GST73AVCNFSM6AAAAABUAAPTR6VHI2DSMVQWIX3LMV43ASLTON2WKOZSG42TGNRUGAYTSOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>