Changelog
-
Version 0.89
- 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.
- Changed
-
Version 0.88
- 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.
- Added
-
Version 0.87
- 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
inmake/local
. -
Support
RATE
as parameter inpmx_solve_rk45/bdf/adams
functions.
-
- Changed
- Some fixes on steady-state solvers
- Update to rstan version 2.19.2.
- Added
-
Version 0.86
- 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 inpmx_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.
-
- Added
-
Version 0.85
- Added
- Dosing rate as parameter
- Changed
- Update to Stan version 2.18.0.
- Added
-
Version 0.84
- Added
- Piecewise linear interpolation function.
- Univariate integral functions.
- Changed
- Update to Stan version 2.17.1.
- Minor revisions to User Manual.
- Bugfixes.
- Added
-
Version 0.83
- Added
- Work with TorstenHeaders
- Each chain has a different initial estimate
- Changed
- User manual
- Fix misspecification in ODE system for TwoCpt example.
- Other bugfixes
- Added
-
Version 0.82
- 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
- Split the parameter argument into three arguments: pMatrix
(parameters for the ODEs – note: for
- Added
-
Version 0.81
- Added
- linCptModel (linear compartmental model) function
- Added
-
Version 0.80a
- Added
- check_finite statements in pred_1 and pred_2 to reject metropolis proposal if initial conditions are not finite
- Added