sim_blq read in correctly for Monolix 2019R2, 2020R1 and 2022R2 but not used in any of the plots

[biencan1]

In Monolix 2019R2, 2020R1 and 2022R2 there are no issues with reading in sim_blq data, but they are not used in plotting to substitute DV values for censored data.

Example code run after creating controller:

ctr %>% pmx_plot_iwres_ipred (bloq=pmx_bloq(cens="BLOQ",colour="blue",size=1),
                              strat.facet = ~TRT,
                              use.abbrev = TRUE,
                              is.draft=FALSE,
                              facets=list(scales="free_x",nrow=1),
                              labels = list(title = "IWRES vs IPRED by dose"))

Produces following plot:

While the plot should look more like this:

When checking the controller the simulated values seem to be loaded fine but under “bloq”: type NULL and value reads “Pairlist of length 0” (see snapshot below). Is that correct?

ggPMX 1.2.8 was used using following R-module: R 4.1.0 Base.

Monolix run outputs and R scripts available to recreate the issue

[tynsci]

• it has been possible to reproduce the bug
• debugging in progress

[tynsci]

@biencan1

Data substition for simulated BLOQ

• data substition for IWRES vs IPRED plot would be based on the following logic:
  • IWRES=ifelse(as.logical(BLOQ), iwRes_mode_simBlq, IWRES)

Resulting Plot

Next

• implement code change in a pull request

[tynsci]

@biencan1

• see above pull request Use simulated BLOQ data for iwRes, pwRes and npde in sim_blq #285 which addresses the issue

Assumptions

• npde, iwres and pwres data are the data types which may need to be copied from simulations
• these data types are available with "_mode" suffix
  • should "mean" ever be used, or would it be available, if so, how should a choice between mean and mode be made: a new parameter?

Challenges

• there appears to be no data in the package under inst which allows this to be tested (no [iwRes,pwRes,npde]_mode_simBlq columns)

[biencan1]

I suggest to use the mode_simBlq only (without giving the choice between the mean and the mode). However, it should be made clear in the documentation that the mode_simBlq is used.

[baltcir1]

sim_blq still doesn't work.

[mattfidler]

Not fixed by #365

[mattfidler]

First issue with BLQ

This is hard coded in the yaml file:

ggPMX/inst/templates/mlx18/standing.ipmx

Line 10 in ee9a72d

y_simBlq_mode: y_simBlq_mode

It shouldn't be. It is based on endpoint, and should match what you are pulling in for the endpoint. The default should be y which is the typical endpoint for monolix single endpoint models (though in truth this can be arbitrary and is for models coming from other sources like babelmixr2 or edited manually).

Second issue with BLQ

Currently the DVs are not replaced with the simulated values; Currently it actually replaces the DV with nothing. The default DV is still the LLOQ value which was in the input dataset, and doesn't match the simulated BLQ dataset from the monolix files.

[mattfidler]

@tynesjo if you need to have some screen sharing we can show you what the issue is and which columns you need to grab.