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Validation

We run a simulation study to verify the models in pmrm are implemented correctly. For each simulation scenario (model type and disease progression trajectory), we:

  1. Simulate 1000 datasets from the model using independent non-RTMB R code.
  2. Fit the model to each simulated dataset using the RTMB-powered implementation.

Around half of the 50% confidence intervals from (2) should cover the true data-generating parameter values in (1). Likewise, around 95% of the 95% confidence intervals from (2) should cover the truth. In addition, we expect all models to converge.

Implementation

library(dplyr)
library(ggplot2)
library(knitr)
library(readr)
library(scales)

This simulation study is a targets pipeline in the vignettes/validation/ directory of the source code of pmrm. To run the pipeline, change to that working directory and call targets::tar_make(). Due to the computational cost, we only run this pipeline once per release.

Last run

We last ran the simulation pipeline with pmrm version 0.0.1 with GitHub commit hash .

Convergence

The following table shows the percentage of fitted models that converged for each scenario.

read_csv(file.path("validation", "convergence.csv")) |>
  mutate(convergence = label_percent()(convergence)) |>
  kable()
scenario convergence
exponential_decline_nonproportional 100%
exponential_decline_proportional 100%
exponential_slowing_nonproportional 100%
exponential_slowing_proportional 100%
linear_decline_nonproportional 100%
linear_decline_proportional 100%
linear_slowing_nonproportional 100%
linear_slowing_proportional 100%

Parameter coverage

The following plot shows the percentage of confidence intervals that covered the true parameter values. Coverage is shown separately for each parameter in each scenario. For reference, the expected coverage rate is shown as a horizontal solid in each facet.

include_graphics(file.path("validation", "coverage.png"))

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.