gunhanb / titepk_sequential Goto Github PK

After a discussion with Burak Günhan, a question about the data attached to the code for the TITE-PK model remained unanswered. Why are there lines in the data file that actually correspond to the dose administration data for each patient at time t=0 and lines with "strange" log dose and compartment number values at time t=+2 weeks between the previous lines? I can't understand the meaning and usefulness of this in the code, when there is obviously one.

You can find below a screenshot of the data for the file dat_RAD_daily to illustrate the question:

While trying to run the available code on the main executing R file (TITEPK_run.R), I wasn't able to run the expose_stan_functions line command to import functions written on Stan files into the R environment using R version 4.2.3 (2023-03-15) and rstan version 2.21.8 (StanHeaders_2.26.27). Instead of executing correctly, I got the following error :

Error: $ operator is invalid for atomic vectors

After discussing directly with Burak Günhan, it became clear that the problem was coming from the version of rstan and its dependencies and a solution was find using online ressource that already faced this problem : https://discourse.mc-stan.org/t/expose-stan-functions-not-working-after-updating-rstan-and-r/25569/20

The solution used to solve the issue was to run the following code lines to install another rstan version in which the issue is solved:
remove.packages(c("rstan", "StanHeaders"))
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))