:orphan:

.. The content of this file was generated
.. automatically by the popy.conf.fio.rstdoc_writer module


.. _mtut_spec:



.. _mtut-method_options_spec:

METHOD_OPTIONS
**************

Type: :term:`dict_record <dict_record>`

method options for mtut_script

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: mtut
        rand_seed: 12345
        float_format: default


.. _mtut-method_options-py_module_spec:

py_module
=========

Type: :term:`one_of(mtut) <one_of>`

Python module required to process this script file

Example:-

.. code-block:: pyml

    py_module: mtut


.. _mtut-method_options-rand_seed_spec:

rand_seed
=========

Type: :term:`int <int>` / :term:`auto <auto>`

Option to set seed to make run result
reproducible -e.g. when debugging.

Example:-

.. code-block:: pyml

    rand_seed: 12345


.. _mtut-method_options-float_format_spec:

float_format
============

Type: :term:`str <str>`

Format string for numerical output

Example:-

.. code-block:: pyml

    float_format: default


.. _mtut-parallel_spec:

PARALLEL
********

Type: :term:`one_of_record <one_of_record>`

one of many possible servers

Example:-

.. code-block:: pyml

    PARALLEL:
        SINGLE: {}


.. _mtut-parallel-single_spec:

SINGLE
======

Type: :term:`dict_record <dict_record>`

single process server spec.

Example:-

.. code-block:: pyml

    SINGLE: {}


.. _mtut-parallel-mpi_workers_spec:

MPI_WORKERS
===========

Type: :term:`dict_record <dict_record>`

MPI local server spec.

Example:-

.. code-block:: pyml

    MPI_WORKERS:
        n_workers: auto


.. _mtut-parallel-mpi_workers-n_workers_spec:

n_workers
---------

Type: :term:`int <int>` / :term:`auto <auto>`

Number of workers to use on this machine, defaults to number of processors, but could be more or fewer.

Example:-

.. code-block:: pyml

    n_workers: auto


.. _mtut-description_spec:

DESCRIPTION
***********

Type: :term:`dict_record <dict_record>`

Description fields for script.

Example:-

.. code-block:: pyml

    DESCRIPTION:
        name: pk_first_order
        title: First order absorption model with peripheral compartment
        author: J.R. Hartley
        abstract: |
            A two compartment PK model with bolus dose and
            first order absorption, similar to a nonmem advan4trans4 model.
        keywords: ['tutorial', 'pk', 'advan4', 'dep_two_cmp', 'first order']


.. _mtut-description-name_spec:

name
====

Type: :term:`str <str>`

Unique name used to distinguish script

Example:-

.. code-block:: pyml

    name: pk_first_order


.. _mtut-description-title_spec:

title
=====

Type: :term:`str <str>`

A longer text string that could serve as a title

Example:-

.. code-block:: pyml

    title: First order absorption model with peripheral compartment


.. _mtut-description-author_spec:

author
======

Type: :term:`str <str>`

Author of the model

Example:-

.. code-block:: pyml

    author: J.R. Hartley


.. _mtut-description-abstract_spec:

abstract
========

Type: :term:`verbatim <verbatim>`

Abstract paragraph describing model

Example:-

.. code-block:: pyml

    abstract: |
        A two compartment PK model with bolus dose and
        first order absorption, similar to a nonmem advan4trans4 model.


.. _mtut-description-keywords_spec:

keywords
========

Type: :term:`list <list>`

Keywords list used to categorise models.

Example:-

.. code-block:: pyml

    keywords: ['tutorial', 'pk', 'advan4', 'dep_two_cmp', 'first order']


.. _mtut-file_paths_spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

file paths

Example:-

.. code-block:: pyml

    FILE_PATHS:
        output_folder: auto
        log_folder: auto
        output_file_ext: ['svg']
        output_iteration_results: True


.. _mtut-file_paths-output_folder_spec:

output_folder
=============

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Output folder - results of computation stored here

Example:-

.. code-block:: pyml

    output_folder: auto


.. _mtut-file_paths-log_folder_spec:

log_folder
==========

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Log folder - log files stored here

Example:-

.. code-block:: pyml

    log_folder: auto


.. _mtut-file_paths-output_file_ext_spec:

output_file_ext
===============

Type: :term:`list_of(pdf,png,svg) <list_of>`

Output file extension - determines graphical output file format.

Example:-

.. code-block:: pyml

    output_file_ext: ['svg']


.. _mtut-file_paths-output_iteration_results_spec:

output_iteration_results
========================

Type: :term:`bool <bool>`

Option to output iteration-by-iteration values.

Example:-

.. code-block:: pyml

    output_iteration_results: True


.. _mtut-data_fields_spec:

DATA_FIELDS
***********

Type: :term:`dict_record <dict_record>`

data fields for popy.dat.fields object

Example:-

.. code-block:: pyml

    DATA_FIELDS:
        type_field: TYPE
        id_field: ID
        time_field: TIME


.. _mtut-data_fields-type_field_spec:

type_field
==========

Type: :term:`str <str>`

Field name in data file that contains row type info, e.g. obs/dose etc

Example:-

.. code-block:: pyml

    type_field: TYPE


.. _mtut-data_fields-id_field_spec:

id_field
========

Type: :term:`str <str>`

Field name in data file that contains identity string for each data row e.g. obs/dose etc

Example:-

.. code-block:: pyml

    id_field: ID


.. _mtut-data_fields-time_field_spec:

time_field
==========

Type: :term:`str <str>`

Field name in data file that contains time or event for each data row

Example:-

.. code-block:: pyml

    time_field: TIME


.. _mtut-gen_effects_spec:

GEN_EFFECTS
***********

Type: :term:`repeat_verb_record <repeat_verb_record>`

GEN_EFFECT params to define hierarchical population model

Example:-

.. code-block:: pyml

    GEN_EFFECTS:
        POP: |
            c[AMT] = 100.0
            f[KA] = 0.2
            f[CL] = 2.0
            f[V1] = 50
            f[Q] = 1.0
            f[V2] = 80
            f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv] = [
                [0.1],
                [0.01, 0.03],
                [0.01, -0.01, 0.09],
                [0.01, 0.02, 0.01, 0.07],
                [0.01, 0.02, 0.01, 0.01, 0.05],
            ]
            f[PNOISE] = 0.15

        ID: |
            c[ID] = sequential(50)
            t[DOSE] = 2.0
            t[OBS] ~ unif(1.0, 50.0; 5)
            # t[OBS] = range(1.0, 50.0; 5)
            r[KA, CL, V1, Q, V2] ~ mnorm([0,0,0,0,0], f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv])


.. _mtut-fit_effects_spec:

FIT_EFFECTS
***********

Type: :term:`repeat_verb_record <repeat_verb_record>`

FIT_EFFECT params to define hierarchical population model

Example:-

.. code-block:: pyml

    FIT_EFFECTS:
        POP: |
            f[KA] ~ P1.0
            f[CL] ~ P1.0
            f[V1] ~ P20
            f[Q] ~ P0.5
            f[V2] ~ P100
            f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv] ~ spd_matrix() [
                [0.05],
                [0.01, 0.05],
                [0.01, 0.01, 0.05],
                [0.01, 0.01, 0.01, 0.05],
                [0.01, 0.01, 0.01, 0.01, 0.05],
            ]
            f[PNOISE] ~ P0.1

        ID: |
            r[KA, CL, V1, Q, V2] ~ mnorm([0,0,0,0,0], f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv])


.. _mtut-preprocess_spec:

PREPROCESS
**********

Type: :term:`verbatim <verbatim>`

Code that preprocesses the input data.
Use this to filter rows and create derived covariates.

Example:-

.. code-block:: pyml

    PREPROCESS: |


.. _mtut-model_params_spec:

MODEL_PARAMS
************

Type: :term:`verbatim <verbatim>`

Defines the mapping from c[X], f[X] and r[X] variables to individual model m[X] parameters.

Example:-

.. code-block:: pyml

    MODEL_PARAMS: |
        m[KA] = f[KA] * exp(r[KA])
        m[CL] = f[CL] * exp(r[CL])
        m[V1] = f[V1] * exp(r[V1])
        m[Q] = f[Q] * exp(r[Q])
        m[V2] = f[V2] * exp(r[V2])
        m[ANOISE] = 0.001
        m[PNOISE] = f[PNOISE]


.. _mtut-states_spec:

STATES
******

Type: :term:`verbatim <verbatim>`

Optional section for setting initial values of s[X] variables
can also set slabel[X] text labels.

Example:-

.. code-block:: pyml

    STATES: |


.. _mtut-derivatives_spec:

DERIVATIVES
***********

Type: :term:`verbatim <verbatim>`

Define how the covariates and effects determine flows
between compartments.

Example:-

.. code-block:: pyml

    DERIVATIVES: |
        # s[DEPOT,CENTRAL,PERI] = @dep_two_cmp_cl{dose:@bolus{amt:c[AMT]}}
        d[DEPOT] = @bolus{amt:c[AMT]} - m[KA]*s[DEPOT]
        d[CENTRAL] = m[KA]*s[DEPOT] - s[CENTRAL]*m[CL]/m[V1] - s[CENTRAL]*m[Q]/m[V1]  + s[PERI]*m[Q]/m[V2]
        d[PERI] = s[CENTRAL]*m[Q]/m[V1] - s[PERI]*m[Q]/m[V2]


.. _mtut-predictions_spec:

PREDICTIONS
***********

Type: :term:`verbatim <verbatim>`

Define the final predicted m[X] variables to be output
by the compartment model system.

Example:-

.. code-block:: pyml

    PREDICTIONS: |
        p[DV_CENTRAL] = s[CENTRAL]/m[V1]
        var = m[ANOISE]**2 + m[PNOISE]**2 * p[DV_CENTRAL]**2
        c[DV_CENTRAL] ~ norm(p[DV_CENTRAL], var)


.. _mtut-ode_solver_spec:

ODE_SOLVER
**********

Type: :term:`one_of_record <one_of_record>`

one of many possible solvers

Example:-

.. code-block:: pyml

    ODE_SOLVER:
        SCIPY_ODEINT:
            atol: 1e-06
            rtol: 1e-06
            max_nsteps: 10000000
            use_supersections: True
            use_jacobian: False
            use_sens: False
            use_tcrit: False


.. _mtut-ode_solver-no_solver_spec:

NO_SOLVER
=========

Type: :term:`dict_record <dict_record>`

Null method for blank derivatives.

Example:-

.. code-block:: pyml

    NO_SOLVER: {}


.. _mtut-ode_solver-analytic_spec:

ANALYTIC
========

Type: :term:`dict_record <dict_record>`

Analytic method for solving ODE

Example:-

.. code-block:: pyml

    ANALYTIC:
        use_supersections: True
        use_sens: True


.. _mtut-ode_solver-analytic-use_supersections_spec:

use_supersections
-----------------

Type: :term:`bool <bool>`

Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).

Example:-

.. code-block:: pyml

    use_supersections: True


.. _mtut-ode_solver-analytic-use_sens_spec:

use_sens
--------

Type: :term:`bool <bool>`

Option to use sensitivity equations in ode solver.

Example:-

.. code-block:: pyml

    use_sens: True


.. _mtut-ode_solver-scipy_odeint_spec:

SCIPY_ODEINT
============

Type: :term:`dict_record <dict_record>`

odeint solver record

Example:-

.. code-block:: pyml

    SCIPY_ODEINT:
        atol: 1e-06
        rtol: 1e-06
        max_nsteps: 10000000
        use_supersections: True
        use_jacobian: False
        use_sens: False
        use_tcrit: False


.. _mtut-ode_solver-scipy_odeint-atol_spec:

atol
----

Type: :term:`float <float>`

Absolute tolerance of ode solver.

Example:-

.. code-block:: pyml

    atol: 1e-06


.. _mtut-ode_solver-scipy_odeint-rtol_spec:

rtol
----

Type: :term:`float <float>`

Relative tolerance of ode solver.

Example:-

.. code-block:: pyml

    rtol: 1e-06


.. _mtut-ode_solver-scipy_odeint-max_nsteps_spec:

max_nsteps
----------

Type: :term:`int <int>`

Maximum number of steps allowed in ode solver.

Example:-

.. code-block:: pyml

    max_nsteps: 10000000


.. _mtut-ode_solver-scipy_odeint-use_supersections_spec:

use_supersections
-----------------

Type: :term:`bool <bool>`

Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).

Example:-

.. code-block:: pyml

    use_supersections: True


.. _mtut-ode_solver-scipy_odeint-use_jacobian_spec:

use_jacobian
------------

Type: :term:`bool <bool>`

Option to use jacobian in ode solver.

Example:-

.. code-block:: pyml

    use_jacobian: False


.. _mtut-ode_solver-scipy_odeint-use_sens_spec:

use_sens
--------

Type: :term:`bool <bool>`

Option to use sensitivity equations in ode solver.

Example:-

.. code-block:: pyml

    use_sens: False


.. _mtut-ode_solver-scipy_odeint-use_tcrit_spec:

use_tcrit
---------

Type: :term:`bool <bool>`

Option to set lsoda tcrit to start and end of subsection. Note this is an experimental option.

Example:-

.. code-block:: pyml

    use_tcrit: False


.. _mtut-ode_solver-cppode_spec:

CPPODE
======

Type: :term:`dict_record <dict_record>`

C++ version of original cvode c library.

Example:-

.. code-block:: pyml

    CPPODE:
        atol: 1e-06
        rtol: 1e-06
        max_nsteps: 10000000
        use_supersections: True
        use_sens: False


.. _mtut-ode_solver-cppode-atol_spec:

atol
----

Type: :term:`float <float>`

Absolute tolerance of ode solver.

Example:-

.. code-block:: pyml

    atol: 1e-06


.. _mtut-ode_solver-cppode-rtol_spec:

rtol
----

Type: :term:`float <float>`

Relative tolerance of ode solver.

Example:-

.. code-block:: pyml

    rtol: 1e-06


.. _mtut-ode_solver-cppode-max_nsteps_spec:

max_nsteps
----------

Type: :term:`int <int>`

Maximum number of steps allowed in ode solver.

Example:-

.. code-block:: pyml

    max_nsteps: 10000000


.. _mtut-ode_solver-cppode-use_supersections_spec:

use_supersections
-----------------

Type: :term:`bool <bool>`

Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).

Example:-

.. code-block:: pyml

    use_supersections: True


.. _mtut-ode_solver-cppode-use_sens_spec:

use_sens
--------

Type: :term:`bool <bool>`

Option to use sensitivity equations in ode solver.

Example:-

.. code-block:: pyml

    use_sens: False


.. _mtut-ode_solver-cpplsoda_spec:

CPPLSODA
========

Type: :term:`dict_record <dict_record>`

C++ version of original cvode c library.

Example:-

.. code-block:: pyml

    CPPLSODA:
        atol: 1e-06
        rtol: 1e-06
        max_nsteps: 10000000
        use_supersections: True
        use_sens: False
        hmin: 1e-12


.. _mtut-ode_solver-cpplsoda-atol_spec:

atol
----

Type: :term:`float <float>`

Absolute tolerance of ode solver.

Example:-

.. code-block:: pyml

    atol: 1e-06


.. _mtut-ode_solver-cpplsoda-rtol_spec:

rtol
----

Type: :term:`float <float>`

Relative tolerance of ode solver.

Example:-

.. code-block:: pyml

    rtol: 1e-06


.. _mtut-ode_solver-cpplsoda-max_nsteps_spec:

max_nsteps
----------

Type: :term:`int <int>`

Maximum number of steps allowed in ode solver.

Example:-

.. code-block:: pyml

    max_nsteps: 10000000


.. _mtut-ode_solver-cpplsoda-use_supersections_spec:

use_supersections
-----------------

Type: :term:`bool <bool>`

Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).

Example:-

.. code-block:: pyml

    use_supersections: True


.. _mtut-ode_solver-cpplsoda-use_sens_spec:

use_sens
--------

Type: :term:`bool <bool>`

Option to use sensitivity equations in ode solver.

Example:-

.. code-block:: pyml

    use_sens: False


.. _mtut-ode_solver-cpplsoda-hmin_spec:

hmin
----

Type: :term:`float <float>`

Minimum step size of ode solver.

Example:-

.. code-block:: pyml

    hmin: 1e-12


.. _mtut-fit_methods_spec:

FIT_METHODS
***********

Type: :term:`list_record <list_record>`

one of many possible fitters

Example:-

.. code-block:: pyml

    FIT_METHODS:
        - JOE:
            ODE_SOLVER: {INHERIT: {}}
            output_timing_flag: False
            output_warning_detail_flag: True
            max_n_main_iterations: 30
            CONVERGER: {OBJ_INC: {}}
            recompute_jacobians_flag: False
            use_laplacian: False
            use_chain: True
            use_lm_jac: True
            reset_re_flag: True


.. _mtut-fit_methods-joe_spec:

JOE
===

Type: :term:`dict_record <dict_record>`

Joint Optimisation and Estimation method

Example:-

.. code-block:: pyml

    JOE:
        ODE_SOLVER: {INHERIT: {}}
        output_timing_flag: False
        output_warning_detail_flag: True
        max_n_main_iterations: 50
        CONVERGER: {OBJ_INC: {}}
        recompute_jacobians_flag: False
        use_laplacian: False
        use_chain: True
        use_lm_jac: True
        reset_re_flag: True


.. _mtut-fit_methods-joe-output_timing_flag_spec:

output_timing_flag
------------------

Type: :term:`bool <bool>`

Option to output timing info.

Example:-

.. code-block:: pyml

    output_timing_flag: False


.. _mtut-fit_methods-joe-output_warning_detail_flag_spec:

output_warning_detail_flag
--------------------------

Type: :term:`bool <bool>`

Option to output warning detail.

Example:-

.. code-block:: pyml

    output_warning_detail_flag: True


.. _mtut-fit_methods-joe-max_n_main_iterations_spec:

max_n_main_iterations
---------------------

Type: :term:`int <int>`

Maximum number of iterations

Example:-

.. code-block:: pyml

    max_n_main_iterations: 50


.. _mtut-fit_methods-joe-converger_spec:

CONVERGER
---------

Type: :term:`one_of_record <one_of_record>`

Convergence methods.

Example:-

.. code-block:: pyml

    CONVERGER:
        OBJ_INC: {}


.. _mtut-fit_methods-joe-converger-none_spec:

NONE
^^^^

Type: :term:`dict_record <dict_record>`

No convergence testing.

Example:-

.. code-block:: pyml

    NONE: {}


.. _mtut-fit_methods-joe-converger-obj_inc_spec:

OBJ_INC
^^^^^^^

Type: :term:`dict_record <dict_record>`

Objective function increase converger.

Example:-

.. code-block:: pyml

    OBJ_INC: {}


.. _mtut-fit_methods-joe-converger-obj_sim_spec:

OBJ_SIM
^^^^^^^

Type: :term:`dict_record <dict_record>`

Objective function similar converger.

Example:-

.. code-block:: pyml

    OBJ_SIM: {}


.. _mtut-fit_methods-joe-recompute_jacobians_flag_spec:

recompute_jacobians_flag
------------------------

Type: :term:`bool <bool>`

Option to recompute jacobians more often, e.g in noise optimiser.

Example:-

.. code-block:: pyml

    recompute_jacobians_flag: False


.. _mtut-fit_methods-joe-use_laplacian_spec:

use_laplacian
-------------

Type: :term:`bool <bool>`

Option to use full laplacian to compute hessian in objective function term4, this is much slower than using the expectation of the outer product of the jacobian

Example:-

.. code-block:: pyml

    use_laplacian: False


.. _mtut-fit_methods-joe-use_chain_spec:

use_chain
---------

Type: :term:`bool <bool>`

Option to use chain rule when computing derivatives.

Example:-

.. code-block:: pyml

    use_chain: True


.. _mtut-fit_methods-joe-use_lm_jac_spec:

use_lm_jac
----------

Type: :term:`bool <bool>`

Option to use custom jacobian when optimising r[X] using L-M.

Example:-

.. code-block:: pyml

    use_lm_jac: True


.. _mtut-fit_methods-joe-reset_re_flag_spec:

reset_re_flag
-------------

Type: :term:`bool <bool>`

Reset r[X]=0.0 before each r[X] optimisation

Example:-

.. code-block:: pyml

    reset_re_flag: True


.. _mtut-fit_methods-bo_spec:

BO
==

Type: :term:`dict_record <dict_record>`

Bayesian Optimisation FOCE method

Example:-

.. code-block:: pyml

    BO:
        ODE_SOLVER: {INHERIT: {}}
        output_timing_flag: False
        output_warning_detail_flag: True
        max_n_main_iterations: 50
        CONVERGER: {OBJ_INC: {}}
        recompute_jacobians_flag: False
        use_laplacian: False
        use_chain: True
        use_lm_jac: True
        reset_re_flag: True
        objv_quantile: 0.5
        n_prev_objv: 100


.. _mtut-fit_methods-bo-output_timing_flag_spec:

output_timing_flag
------------------

Type: :term:`bool <bool>`

Option to output timing info.

Example:-

.. code-block:: pyml

    output_timing_flag: False


.. _mtut-fit_methods-bo-output_warning_detail_flag_spec:

output_warning_detail_flag
--------------------------

Type: :term:`bool <bool>`

Option to output warning detail.

Example:-

.. code-block:: pyml

    output_warning_detail_flag: True


.. _mtut-fit_methods-bo-max_n_main_iterations_spec:

max_n_main_iterations
---------------------

Type: :term:`int <int>`

Maximum number of iterations

Example:-

.. code-block:: pyml

    max_n_main_iterations: 50


.. _mtut-fit_methods-bo-converger_spec:

CONVERGER
---------

Type: :term:`one_of_record <one_of_record>`

Convergence methods.

Example:-

.. code-block:: pyml

    CONVERGER:
        OBJ_INC: {}


.. _mtut-fit_methods-bo-converger-none_spec:

NONE
^^^^

Type: :term:`dict_record <dict_record>`

No convergence testing.

Example:-

.. code-block:: pyml

    NONE: {}


.. _mtut-fit_methods-bo-converger-obj_inc_spec:

OBJ_INC
^^^^^^^

Type: :term:`dict_record <dict_record>`

Objective function increase converger.

Example:-

.. code-block:: pyml

    OBJ_INC: {}


.. _mtut-fit_methods-bo-converger-obj_sim_spec:

OBJ_SIM
^^^^^^^

Type: :term:`dict_record <dict_record>`

Objective function similar converger.

Example:-

.. code-block:: pyml

    OBJ_SIM: {}


.. _mtut-fit_methods-bo-recompute_jacobians_flag_spec:

recompute_jacobians_flag
------------------------

Type: :term:`bool <bool>`

Option to recompute jacobians more often, e.g in noise optimiser.

Example:-

.. code-block:: pyml

    recompute_jacobians_flag: False


.. _mtut-fit_methods-bo-use_laplacian_spec:

use_laplacian
-------------

Type: :term:`bool <bool>`

Option to use full laplacian to compute hessian in objective function term4, this is much slower than using the expectation of the outer product of the jacobian

Example:-

.. code-block:: pyml

    use_laplacian: False


.. _mtut-fit_methods-bo-use_chain_spec:

use_chain
---------

Type: :term:`bool <bool>`

Option to use chain rule when computing derivatives.

Example:-

.. code-block:: pyml

    use_chain: True


.. _mtut-fit_methods-bo-use_lm_jac_spec:

use_lm_jac
----------

Type: :term:`bool <bool>`

Option to use custom jacobian when optimising r[X] using L-M.

Example:-

.. code-block:: pyml

    use_lm_jac: True


.. _mtut-fit_methods-bo-reset_re_flag_spec:

reset_re_flag
-------------

Type: :term:`bool <bool>`

Reset r[X]=0.0 before each r[X] optimisation

Example:-

.. code-block:: pyml

    reset_re_flag: True


.. _mtut-fit_methods-bo-objv_quantile_spec:

objv_quantile
-------------

Type: :term:`float <float>`

Objective value quantile, in range[0.0,1.0]

Example:-

.. code-block:: pyml

    objv_quantile: 0.5


.. _mtut-fit_methods-bo-n_prev_objv_spec:

n_prev_objv
-----------

Type: :term:`int <int>`

Number of previous objective values to use for limit

Example:-

.. code-block:: pyml

    n_prev_objv: 100


.. _mtut-fit_methods-foce_spec:

FOCE
====

Type: :term:`dict_record <dict_record>`

First order conditional estimation method

Example:-

.. code-block:: pyml

    FOCE:
        ODE_SOLVER: {INHERIT: {}}
        output_timing_flag: False
        output_warning_detail_flag: True
        max_n_main_iterations: 50
        CONVERGER: {OBJ_INC: {}}
        recompute_jacobians_flag: False
        use_laplacian: False
        use_chain: True
        use_central_diffs_from_start: False
        use_lm_jac: True
        reset_re_flag: True
        central_diff_switch_flag: True


.. _mtut-fit_methods-foce-output_timing_flag_spec:

output_timing_flag
------------------

Type: :term:`bool <bool>`

Option to output timing info.

Example:-

.. code-block:: pyml

    output_timing_flag: False


.. _mtut-fit_methods-foce-output_warning_detail_flag_spec:

output_warning_detail_flag
--------------------------

Type: :term:`bool <bool>`

Option to output warning detail.

Example:-

.. code-block:: pyml

    output_warning_detail_flag: True


.. _mtut-fit_methods-foce-max_n_main_iterations_spec:

max_n_main_iterations
---------------------

Type: :term:`int <int>`

Maximum number of iterations

Example:-

.. code-block:: pyml

    max_n_main_iterations: 50


.. _mtut-fit_methods-foce-converger_spec:

CONVERGER
---------

Type: :term:`one_of_record <one_of_record>`

Convergence methods.

Example:-

.. code-block:: pyml

    CONVERGER:
        OBJ_INC: {}


.. _mtut-fit_methods-foce-converger-none_spec:

NONE
^^^^

Type: :term:`dict_record <dict_record>`

No convergence testing.

Example:-

.. code-block:: pyml

    NONE: {}


.. _mtut-fit_methods-foce-converger-obj_inc_spec:

OBJ_INC
^^^^^^^

Type: :term:`dict_record <dict_record>`

Objective function increase converger.

Example:-

.. code-block:: pyml

    OBJ_INC: {}


.. _mtut-fit_methods-foce-converger-obj_sim_spec:

OBJ_SIM
^^^^^^^

Type: :term:`dict_record <dict_record>`

Objective function similar converger.

Example:-

.. code-block:: pyml

    OBJ_SIM: {}


.. _mtut-fit_methods-foce-recompute_jacobians_flag_spec:

recompute_jacobians_flag
------------------------

Type: :term:`bool <bool>`

Option to recompute jacobians more often, e.g in noise optimiser.

Example:-

.. code-block:: pyml

    recompute_jacobians_flag: False


.. _mtut-fit_methods-foce-use_laplacian_spec:

use_laplacian
-------------

Type: :term:`bool <bool>`

Option to use full laplacian to compute hessian in objective function term4, this is much slower than using the expectation of the outer product of the jacobian

Example:-

.. code-block:: pyml

    use_laplacian: False


.. _mtut-fit_methods-foce-use_chain_spec:

use_chain
---------

Type: :term:`bool <bool>`

Option to use chain rule when computing derivatives.

Example:-

.. code-block:: pyml

    use_chain: True


.. _mtut-fit_methods-foce-use_central_diffs_from_start_spec:

use_central_diffs_from_start
----------------------------

Type: :term:`bool <bool>`

Use central differencing from the start.

Example:-

.. code-block:: pyml

    use_central_diffs_from_start: False


.. _mtut-fit_methods-foce-use_lm_jac_spec:

use_lm_jac
----------

Type: :term:`bool <bool>`

Option to use custom jacobian when optimising r[X] using L-M.

Example:-

.. code-block:: pyml

    use_lm_jac: True


.. _mtut-fit_methods-foce-reset_re_flag_spec:

reset_re_flag
-------------

Type: :term:`bool <bool>`

Reset r[X]=0.0 before each r[X] optimisation

Example:-

.. code-block:: pyml

    reset_re_flag: True


.. _mtut-fit_methods-foce-central_diff_switch_flag_spec:

central_diff_switch_flag
------------------------

Type: :term:`bool <bool>`

Allow switch to central differences, instead of forward diff

Example:-

.. code-block:: pyml

    central_diff_switch_flag: True


.. _mtut-covariance_spec:

COVARIANCE
**********

Type: :term:`one_of_record <one_of_record>`

Covariance methods used to estimate standard errors.

Example:-

.. code-block:: pyml

    COVARIANCE:
        NO_COVARIANCE: {}


.. _mtut-covariance-no_covariance_spec:

NO_COVARIANCE
=============

Type: :term:`dict_record <dict_record>`

Do NOT compute covariance matrix and standard errors.

Example:-

.. code-block:: pyml

    NO_COVARIANCE: {}


.. _mtut-covariance-sandwich_spec:

SANDWICH
========

Type: :term:`dict_record <dict_record>`

Use sandwich operator to estimate covariance matrix.

Example:-

.. code-block:: pyml

    SANDWICH:
        var_covariance_flag: False
        inv_hessian_flag: False


.. _mtut-covariance-sandwich-var_covariance_flag_spec:

var_covariance_flag
-------------------

Type: :term:`bool <bool>`

Optionally compute standard errors for f[X] covariance elements this could take a long time for large covariance matrices. Note the results of the standard error computation for the main f[X] parameters combined with the variances will be different.

Example:-

.. code-block:: pyml

    var_covariance_flag: False


.. _mtut-covariance-sandwich-inv_hessian_flag_spec:

inv_hessian_flag
----------------

Type: :term:`bool <bool>`

Optionally invert the hessian and output results to disk. this is mainly to generate PoPy documentation output.

Example:-

.. code-block:: pyml

    inv_hessian_flag: False


.. _mtut-covariance-nonmem_spec:

NONMEM
======

Type: :term:`dict_record <dict_record>`

Use sandwich operator to estimate covariance matrix.

Example:-

.. code-block:: pyml

    NONMEM:
        var_covariance_flag: False
        inv_hessian_flag: False


.. _mtut-covariance-nonmem-var_covariance_flag_spec:

var_covariance_flag
-------------------

Type: :term:`bool <bool>`

Optionally compute standard errors for f[X] covariance elements this could take a long time for large covariance matrices. Note the results of the standard error computation for the main f[X] parameters combined with the variances will be different.

Example:-

.. code-block:: pyml

    var_covariance_flag: False


.. _mtut-covariance-nonmem-inv_hessian_flag_spec:

inv_hessian_flag
----------------

Type: :term:`bool <bool>`

Optionally invert the hessian and output results to disk. this is mainly to generate PoPy documentation output.

Example:-

.. code-block:: pyml

    inv_hessian_flag: False


.. _mtut-output_options_spec:

OUTPUT_OPTIONS
**************

Type: :term:`dict_record <dict_record>`

Output options

Example:-

.. code-block:: pyml

    OUTPUT_OPTIONS:
        n_pop_samples: 100


.. _mtut-output_options-n_pop_samples_spec:

n_pop_samples
=============

Type: :term:`int <int>`

Number of new populations to sample.

Example:-

.. code-block:: pyml

    n_pop_samples: 100


.. _mtut-output_scripts_spec:

OUTPUT_SCRIPTS
**************

Type: :term:`dict_record <dict_record>`

Scripts to output for further processing.

Example:-

.. code-block:: pyml

    OUTPUT_SCRIPTS:
        MGEN: {output_mode: run}
        MFIT: {output_mode: run}
        MCOMP: {output_mode: run, dot_size: 12}


.. _mtut-output_scripts-mgen_spec:

MGEN
====

Type: :term:`dict_record <dict_record>`

options to pass to mgen_script.

Example:-

.. code-block:: pyml

    MGEN:
        output_mode: none


.. _mtut-output_scripts-mgen-output_mode_spec:

output_mode
-----------

Type: :term:`one_of(none,create,run) <one_of>`

Output options.

Example:-

.. code-block:: pyml

    output_mode: none


.. _mtut-output_scripts-mfit_spec:

MFIT
====

Type: :term:`dict_record <dict_record>`

options to pass to mfit_script.

Example:-

.. code-block:: pyml

    MFIT:
        output_mode: none


.. _mtut-output_scripts-mfit-output_mode_spec:

output_mode
-----------

Type: :term:`one_of(none,create,run) <one_of>`

Output options.

Example:-

.. code-block:: pyml

    output_mode: none


.. _mtut-output_scripts-mcomp_spec:

MCOMP
=====

Type: :term:`dict_record <dict_record>`

options to pass to mcomp script.

Example:-

.. code-block:: pyml

    MCOMP:
        output_mode: none
        dot_size: 12


.. _mtut-output_scripts-mcomp-output_mode_spec:

output_mode
-----------

Type: :term:`one_of(none,create,run) <one_of>`

Output options.

Example:-

.. code-block:: pyml

    output_mode: none


.. _mtut-output_scripts-mcomp-dot_size_spec:

dot_size
--------

Type: :term:`int <int>`

Size of dots appearing in scatter plots

Example:-

.. code-block:: pyml

    dot_size: 12



