Release Notes for Pumas 2.7.1

Pumas

Documentation and error messages

  • Fix typo in fit docstring where optim_options was not passed correctly as a named tuple.
  • Fix docstring for Central1Periph2 that referred to two compartment structure even though it's a three compartment model.
  • Fix several small grammatical errors in docstrings
  • Fix an incorrect description of how obstimes affects the time points present in the output of predict. The correct behavior is now reflected in the docstring.
  • Throw better error messages when left-hand sides (variable names) are malformed in the model macro (for example tv-a ∈ RealDomain() is not allowed but tv_a ∈ RealDomain() is).

Bugs

  • Fix a bug where time-varying covariates that were used in @dynamics or @derived would caused an error to be thrown stating that the covariate was not in @pre. The covariates are now correctly handled.
  • Fix a bug where a vpc call would fail if there were censored derived variables mixed with uncensored variables.
  • Fix calls to ϵshrinkage when there are non-Gaussian derived variables in the model. Such dependent variables are now filtered away to avoid throwing an error and only Gaussian variable shrinkages are returned.
  • Fix the handling of reset events (evid 3 and evid 4) with negative time points. In Pumas, reset events lead to time offsets being added to maintain monotone time. Previously, the calculation was wrong if the time at a reset event was negative. The behavior is now fixed to correctly offset based on the negative time.
  • Upgrade ForwardDiff.jl to include a fix of a bug that would cause stiff solvers to fail during fitting.
  • Upgrade LinearSolve.jl to include a fix of a bug that would cause stiff solvers to fail during fitting.
  • Upgrade julia to v1.11.7 from v1.11.6 to fix a bug when running distributed computing (for example through the use of EnsembleDistributed()).

AlgebraOfGraphics

Bugs

  • When faceting a plot empty plots would still have visible axes. They are now completely hidden. For example, a 3x3 panel of plots with 8 plots will have the plot at index (3,3) completely blank instead of an axis with no content.

PumasReports

Bugs

  • coefficients_table and metrics_table had RawTypst in some cells. This has been fixed and now the cells simply have Strings as before.

Julia

Pumas now ships with the Julia v1.11.7 runtime.