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library of C++ functions that support applications of Stan in Pharmacometrics
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README.md

Torsten

Overview

Torsten is a collection of Stan functions to facilitate analysis of pharmacometric data using Stan. The current version includes:

  • Specific linear compartment models:
    • One compartment model with first order absorption.
    • Two compartment model with elimination from and first order absorption into central compartment
  • General linear compartment model described by a system of first-order \underline{linear} Ordinary Differential Equations (ODEs).
  • General compartment model described by a system of first order ODEs.
  • Mix compartment model with PK forcing function described by a linear one or two compartment model.

The models and data format are based on NONMEM\textregistered{}1/NMTRAN/PREDPP conventions including:

  • Recursive calculation of model predictions
    • This permits piecewise constant covariate values
  • Bolus or constant rate inputs into any compartment
  • Handles single dose and multiple dose histories
  • Handles steady state dosing histories
    • Note: The infusion time must be shorter than the inter-dose interval.
  • Implemented NMTRAN data items include: TIME, EVID, CMT, AMT, RATE, ADDL, II, SS

In general, all real variables may be passed as Stan parameters. A few exceptions apply /to functions which use a numerical integrator/(i.e. the general and the mix compartment models). The below listed cases present technical difficulties, which we expect to overcome in Torsten's next release:

  • In the case of a multiple truncated infusion rate dosing regimen:
    • The bioavailability (F) and the amount (AMT) must be fixed.

This library provides Stan language functions that calculate amounts in each compartment, given an event schedule and an ODE system.

Installation

We are working with Stan development team to create a system to add and share Stan packages. In the mean time, the current repo contains forked version of Stan with Torsten. The latest version of Torsten (v0.86) is compatible with Stan v2.19.1. Torsten is agnostic to which Stan interface you use. Here we provide command line and R interfaces.

Command line interface

After downloading the project

The command line interface cmdstan is available to use without installation. The following command builds a Torsten model model_name in model_path

cd $TORSTEN_PATH/cmdstan; make model_path/model_name

Currently MPI support is only available through cmdstan interface. To use MPI-supported population/group solvers, add/edit make/local

TORSTEN_MPI=1
CXXFLAGS += -isystem /usr/local/include # path to MPI headers

Note that currently TORSTEN_MPI and STAN_MPI flags conflict on processes management and cannot be used in a same Stan model.

R interface

The R interface is based on rstan, the Stan's interface for R. To install R version of Torsten, at $TORSTEN_PATH, in R

source('install.R')

Please ensure the R toolchain includes a C++ compiler with C++14 support. In particular, R 3.4.0 and later is recommended as it contains toolchain based on gcc 4.9.3. On Windows platform, such a toolchain can be found in Rtools34 and later.

Please ensure .R/Makevars constains the following flags

CXX14 = g++ -fPIC               # or CXX14 = clang++ -fPIC

CXXFLAGS=-O3 -std=c++1y -mtune=native -march=native -Wno-unused-variable -Wno-unused-function
CXXFLAGS += -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30

CXX14FLAGS=-O3 -std=c++1y -mtune=native -march=native -Wno-unused-variable -Wno-unused-function
CXX14FLAGS += -DBOOST_MPL_CFG_NO_PREPROCESSED_HEADERS -DBOOST_MPL_LIMIT_LIST_SIZE=30

Fore more information of setting up makevar and its functionality, see

For more information of installation troubleshooting, please consult rstan wiki.

Testing

With project in torsten_path, set the envionment variable TORSTEN_PATH as

# in bash
export TORSTEN_PATH=torsten_path
# in csh
setenv TORSTEN_PATH torsten_path

To test the installation, run

./test-torsten.sh --unit        # math unit test
./test-torsten.sh --signature   # stan function # signature test
./test-torsten.sh --model       # R model test, takes long time to finish

Development plans

Our current plans for future development of Torsten include the following:

  • Build a system to easily share packages of Stan functions (written in C++ or in the Stan language)
  • Allow numerical methods to handle bioavailability fraction (F) as parameters in all cases.
  • Optimize Matrix exponential functions
    • Function for the action of Matrix Exponential on a vector
    • Hand-coded gradients
    • Special algorithm for matrices with special properties
  • Fix issue that arises when computing the adjoint of the lag time parameter (in a dosing compartment) evaluated at (t_{\text{lag}} = 0).
  • Extend formal tests
    • We want more C++ Google unit tests to address cases users may encounter
    • Comparison with simulations from the R package mrgsolve and the software NONMEM\textregistered{}
    • Recruit non-developer users to conduct beta testing

Changelog

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

      • PKModelOneCptpmx_solve_onecpt
      • PKModelTwoCptpmx_solve_onecpt
      • linOdeModelpmx_solve_linode
      • generalOdeModel_adamspmx_solve_adams
      • generalOdeModel_bdfpmx_solve_bdf
      • generalOdeModel_rk45pmx_solve_rk45
      • mixOde1CptModel_bdfpmx_solve_onecpt_bdf
      • mixOde1CptModel_rk45pmx_solve_onecpt_rk45
      • mixOde2CptModel_bdfpmx_solve_twocpt_bdf
      • mixOde2CptModel_rk45pmx_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.

0.85 <2018-12-04 Tue>

  • Added

    • Dosing rate as parameter
  • Changed

    • Update to Stan version 2.18.0.

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.

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

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

0.81 <2016-09-27 Tue>

  • Added

    linCptModel (linear compartmental model) function

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

    \bibliography{./doc/torsten}

Footnotes

1 NONMEM\textregistered{} is licensed and distributed by ICON Development Solutions.

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