Missing endpoint

[mattfidler]

In the example below I'm trying to extract the endpoint from the rxode2 object. I believe the model should have one endpoint and it should be tumorVol. However it's not being found/discovered. Instead it just gives me character(0).

library(rxode2)
library(nlmixr2)

oncology_sdm_lobo_2002 <- function() {
  description <- "Signal transduction model for delayed concentration effects on cancer cell growth"
  reference <- "Lobo ED, Balthasar JP. Pharmacodynamic modeling of chemotherapeutic effects: Application of a transit compartment model to characterize methotrexate effects in vitro. AAPS J. 2002;4(4):212-222. doi:10.1208/ps040442"
  depends<-"Cc"
  units<-list(time="hr")
  # Values for lkng, ltau, lec50, and kmax are for methotrexate from Lobo 2002,
  # Table 2.  propErr and addErr are added as reasonable values though not from
  # Lobo 2002 where no value is apparent in the paper.
  ini({
    lkng <- log(0.02) ; label("Cell net growth rate (growth minus death) (1/hr)")
    ltau <- log(34.1) ; label("Mean transit time of each transit compartment (hr)")
    lec50 <- log(0.1) ; label("Drug concentration reducing the cell growth by 50% (ug/mL)")
    kmax <- 0.29 ; label("Maximum drug-related reduction in cell growth (1/hr)")

    tumorVolpropSd <- c(0, 0.3) ; label("Proportional residual error (fraction)")
    tumorVoladdSd <- c(0, 50, 1000) ; label("Additive residual error (tumor volume units)")
  })
  model({
    # Cc is the drug concentration
    kng <- exp(lkng)
    tau <- exp(ltau)
    ec50 <- exp(lec50)

    drugEffectTumorVol <- kmax*Cc/(ec50 + Cc)

    tumorVol(0) <- tumorVol0
    d/dt(tumorVol) <- kng*tumorVol - transit4*tumorVol
    d/dt(transit1) <- (drugEffectTumorVol - transit1)/tau
    d/dt(transit2) <- (transit1 - transit2)/tau
    d/dt(transit3) <- (transit2 - transit3)/tau
    d/dt(transit4) <- (transit3 - transit4)/tau
    tumorVol ~ prop(tumorVolpropSd) + add(tumorVoladdSd)
  })
}

rx_obj = rxode2::rxode2(oncology_sdm_lobo_2002)

rx_obj$params$output$endpoint

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

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_2.1.2     nlmixr2data_2.0.9 rxode2_2.1.3     

loaded via a namespace (and not attached):
 [1] utf8_1.2.4          generics_0.1.3      lattice_0.22-6     
 [4] digest_0.6.36       magrittr_2.0.3      grid_4.4.0         
 [7] rxode2random_2.1.1  fastmap_1.2.0       lotri_0.4.3        
[10] backports_1.5.0     nlmixr2est_2.2.2    fansi_1.0.6        
[13] scales_1.3.0        lazyeval_0.2.2      RApiSerialize_0.1.3
[16] cli_3.6.3           crayon_1.5.3        rlang_1.1.4        
[19] symengine_0.2.6     munsell_0.5.1       cachem_1.1.0       
[22] rxode2et_2.0.13     qs_0.26.3           tools_4.4.0        
[25] rxode2parse_2.0.19  nlmixr2plot_2.0.9   lbfgsb3c_2024-3.4  
[28] memoise_2.0.1       checkmate_2.3.1     dplyr_1.1.4        
[31] colorspace_2.1-0    ggplot2_3.5.1       n1qn1_6.0.1-11     
[34] vctrs_0.6.5         R6_2.5.1            lifecycle_1.0.4    
[37] stringfish_0.16.0   PreciseSums_0.6     pkgconfig_2.0.3    
[40] RcppParallel_5.1.7  rex_1.2.1           pillar_1.9.0       
[43] gtable_0.3.5        data.table_1.15.4   glue_1.7.0         
[46] Rcpp_1.0.12         xfun_0.45           tibble_3.2.1       
[49] tidyselect_1.2.1    sys_3.4.2           knitr_1.47         
[52] dparser_1.3.1-11    nlme_3.1-164        compiler_4.4.0 

[mattfidler]

@john-harrold as far as I know you are the only one who uses this interface (and I don't think it has been released publicly yet).

With that being said there is an unfortunate collision between this property and the low level $params which has a totally different meaning.

This is moving to props with this change.

[mattfidler]

I'm unsure why changing the issue to a pull request changes the author.

Anyway, this should fix the issue. Once there is a successful check I will merge.

[john-harrold]

I'm pretty sure I'm using the one on CRAN so I think it's live, but I'm probably the only one who really knows its there. And I'm also probably one of the few people dong this kind of thing. I wrapped most of this in a function because I thought it might change. So I will only have update in a few places :).

[mattfidler]

That is good 😄 thank you for your understanding