Progress bar • campsis

This vignette explains how you can track the simulation progress thanks to the package progressr.

Track the simulation progress in an R script

Load package progressr as follows:

library(progressr)

The easiest way to track the progress is to add the following snippet once for all in your script. By doing so, any call to the simulate method of campsis will display the progress bar.

handlers(global=TRUE)

By default, the progress bar will only give the progress as a percentage. Any user-custom handler may be provided. Please have a look at the official documentation (Vignette progressr: An Introduction / ‘Customizing how progress is reported’).

If you want to use the default handler from campsis, which gives you more details about what’s being simulated and what’s the remaining time (ETA), you can write:

handlers(campsis_handler())

If you don’t want your handler(s) to be global, you can also explicitly call the method with_progress. The snippet below is an example of simulation where this method is called.

dataset <- Dataset(1000) %>%
  add(Infusion(time=0, amount=1000, compartment=1, ii=24, addl=6)) %>%
  add(Observations(seq(0, 7*24)))

model <- model_suite$pk$`1cpt_fo`
results <- with_progress(simulate(model=model, dataset=dataset, dest="mrgsolve", seed=1, replicates=3))
shadedPlot(results, "CONC", "replicate")

Any handler may be provided as well:

results <- with_progress(simulate(model=model, dataset=dataset, dest="mrgsolve", seed=1, replicates=3), handlers=campsis_handler())

Track the simulation progress in a targets project

The targets package is a Make-like pipeline tool for Statistics and data science in R. With targets, you can maintain a reproducible workflow without repeating yourself. It is the ideal pipeline tool to use for medium to large simulation projects with Campsis.

The following script (_targets.R) gives you a brief overview of what you can achieve with targets and how the progress bar can be enabled. It is important to mention that handlers(global=TRUE) can’t be used in such a script. If you try to do so, an error message will pop up.

library(targets)

source("R/my_script.R")

# Packages loaded by targets
packages <- c("campsis", "progressr")
tar_option_set(packages=packages)

# Enable progress bar
options(progressr.enable=TRUE)
progressr::handlers(campsis::campsis_handler())

list(
  tar_target(
    model,
    model_suite$pk$`1cpt_fo`
  ),
  tar_target(
    dataset,
    makeDataset(subjects=1000, dose=1000)
  ),
  tar_target(
    results,
    runSimulation(model=model, dataset=dataset, replicates=3)
  )
)

The R folder contains as much as possible of the code (or logic) being executed, in the form of R functions. The snippet below shows the content of my_script.R. An explicit call to with_progress will make the progress bar appear when executing the target results.

makeDataset <- function(subjects, dose) {
  dataset <- Dataset(subjects=subjects) %>%
    add(Infusion(time=0, amount=dose, compartment=1, ii=24, addl=6)) %>%
    add(Observations(seq(0, 7*24)))
  return(dataset)
}

runSimulation <- function(model, dataset, replicates) {
  results <- with_progress(simulate(model=model, dataset=dataset, dest="mrgsolve",
                                    seed=1, replicates=replicates))
  return(results)
}

This small project can be downloaded by clicking the link below.

Download targets squeletton

To run this project, simply open an R console within your targets folder and type:

library(targets)
tar_make()