Torsten

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Torsten is a collection of Stan functions to facilitate analysis of pharmacometric data. See the user guide for more details. A slightly outdated web version can be found at https://metrumresearchgroup.github.io/Torsten/.

Changelog

• Version 0.91.0 <2024-03-18 Sun>

  • Changed
    • Update model examples according to new array syntax.
    • Update to Stan version 2.33.1.
    • Removed experimental cross-chain feature.
    • Deprecation of old Torsten functions not using 'pmx\_' prefix.
    • Minor bug fixes.

• Version 0.90.0 <2022-05-18 Wed>

  • Changed
    • Update model examples according to new array syntax.
    • Update to Stan version 2.29.2.

• Version 0.89 <2021-06-15 Tue>

  • Changed
    • New backend for ODE events solvers.
    • Use vector instead of array as ODE function state & return type.
    • Simplified ODE integrator naming, e.g. pmx_ode_bdf[_ctrl].
    • Update to Stan version 2.27.0.

• Version 0.88 <2020-12-18 Fri>

  • Added

    • Bioavailability, lag time, ODE real & integer data are optional in PMX function signatures.
    • Support all EVID options from NM-TRAN and mrgsolve.
    • Support steady-state infusion through multiple interdose intervals.

  • Changed

    • More efficient memory management of COVDES implenmentation.
    • Update of MPI framework to adapt multilevel paralleism.
    • Update to Stan version 2.25.0.
    • Use cmdstanr as R interface.
    • Stop supporting rstan as R interface.

• Version 0.87 <2019-07-26 Fri>

  • Added

    • MPI dynamic load balance for Torsten's population ODE integrators

      • pmx_integrate_ode_group_adams
      • pmx_integrate_ode_group_bdf
      • pmx_integrate_ode_group_rk45

      To invoke dynamic load balance instead of default static balance for MPI, issue TORSTEN_MPI=2 in make/local.

    • Support RATE as parameter in pmx_solve_rk45/bdf/adams functions.

  • Changed
    • Some fixes on steady-state solvers
    • Update to rstan version 2.19.2.

• Version 0.86 <2019-05-15 Wed>

  • Added

    • Torsten's ODE integrator functions

      • pmx_integrate_ode_adams
      • pmx_integrate_ode_bdf
      • pmx_integrate_ode_rk45

      and their counterparts to solve a population/group of subjects governed by an ODE

      • pmx_integrate_ode_group_adams
      • pmx_integrate_ode_group_bdf
      • pmx_integrate_ode_group_rk45

    • Torsten's population PMX solver functions for general ODE models

      • pmx_solve_group_adams
      • pmx_solve_group_bdf
      • pmx_solve_group_rk45

    • Support time step ts as parameter in pmx_integrate_ode_xxx solvers.

  • Changed

    • Renaming Torsten functions in previous releases, the old-new name mapping is

      • PKModelOneCpt → pmx_solve_onecpt
      • PKModelTwoCpt → pmx_solve_onecpt
      • linOdeModel → pmx_solve_linode
      • generalOdeModel_adams → pmx_solve_adams
      • generalOdeModel_bdf → pmx_solve_bdf
      • generalOdeModel_rk45 → pmx_solve_rk45
      • mixOde1CptModel_bdf → pmx_solve_onecpt_bdf
      • mixOde1CptModel_rk45 → pmx_solve_onecpt_rk45
      • mixOde2CptModel_bdf → pmx_solve_twocpt_bdf
      • mixOde2CptModel_rk45 → pmx_solve_twocpt_rk45

      Note that the new version of the above functions return the transpose of the matrix returned by the old versions, in order to improve memory efficiency. The old version are retained but will be deprecated in the future.

    • Update to Stan version 2.19.1.

• Version 0.85 <2018-12-04 Tue>

  • Added
    • Dosing rate as parameter
  • Changed
  • Update to Stan version 2.18.0.

• Version 0.84 <2018-02-24 Sat>

  • Added
    • Piecewise linear interpolation function.
    • Univariate integral functions.
  • Changed
    • Update to Stan version 2.17.1.
    • Minor revisions to User Manual.
    • Bugfixes.

• Version 0.83 <2017-08-02 Wed>

  • Added
    • Work with TorstenHeaders
    • Each chain has a different initial estimate
  • Changed
    • User manual
    • Fix misspecification in ODE system for TwoCpt example.
    • Other bugfixes

• Version 0.82 <2017-01-29 Sun>

  • Added
    • Allow parameter arguments to be passed as 1D or 2D arrays
    • More unit tests
    • Unit tests check automatic differentiation against finite differentiation.
  • Changed
    • Split the parameter argument into three arguments: pMatrix (parameters for the ODEs – note: for linOdeModel, pMatrix is replaced by the constant rate matrix K), biovar (parameters for the biovariability), and tlag (parameters for the lag time).
    • bugfixes

• Version 0.81 <2016-09-27 Tue>

  • Added
    • linCptModel (linear compartmental model) function

• Version 0.80a <2016-09-21 Wed>

  • Added
    • check_finite statements in pred_1 and pred_2 to reject metropolis proposal if initial conditions are not finite