.. _introducing_popy:

Introducing |popy|
#####################

.. _overview:

Overview
==========

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    this text below only appears in the pdf+epub, similar text appears in the index page in the html+json 

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    |popy| (pronounced pop-eye, as in the sailor man) is new software to support population modelling of |pkpd| (pharmacokinetic/pharmacodynamic) data using the |python| Programming Language.

    |popy|’s intuitive interface and automated visualization make it perfect for people who are new to |pkpd|. For experienced analysts, |popy| contains all of the features that are required for modern |pkpd| modelling.

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    |popy| is a |python| based |pkpd| (pharmacokinetic/pharmacodynamic) modelling system. 

|popy|'s features include:-

* Nonlinear :ref:`mixed-effect<more_detailed_explanation_of_fit_script>` models
* :ref:`Bolus<@bolus>` and :ref:`infusion <@inf_rate>` dosing regimens
* :ref:`Inter-occasion variability<inter_occasion_variation>`
* :ref:`Continuous<norm_dist_lik_example>` and :ref:`categorical<poisson_dist_example>` likelihoods
* :ref:`PK<example_derivatives_pk>` and :ref:`PD<example_derivatives_pd>` models

|popy| consists of a powerful set of :ref:`popy_tools` and :ref:`script files <script_formats>`, to enable you to analyse a :ref:`PK/PD data file<input_data_format>` quickly and efficiently, whilst minisimising errors due to an elegant and intuitive syntax.

|popy| makes it easy to :ref:`fit models<simple_fit_example>` to data, but also has the ability to :ref:`generate new data<simple_tut_example>` to test hypothetical scenarios.

.. _doc_structure:

Documentation Structure
===========================

See :numref:`tab_doc_structure` for layout of this documentation:-

.. _tab_doc_structure:

.. list-table:: |popy| Documentation Structure
    :header-rows: 1
    
    * - Section
      - Contents
    
    * - :ref:`user_guide_index`
      - Read this first to get familiar with |popy|

    * - :ref:`indiv_pkpd_index`
      - A summary of **individual** |pkpd| models using |popy| syntax
      
    * - :ref:`pop_pkpd_index`
      - A summary of **population** |pk| models using |popy| syntax

    * - :ref:`examples_index`
      - Examples of using |popy| for |pkpd| analysis
      
    * - :ref:`nonmem_index`
      - Guidance for converting |nonmem| examples to |popy|
      
    * - :ref:`popy_reference_index`
      - A comprehensive reference on |popy| tools and scripts

    * - :ref:`appendices_index`
      - Links to |pkpd| terms used throughout this guide.
      
.. _system_requirements:

System Requirements
=====================

|popy| is currently available as a 64 bit |windoze| binary. See  :numref:`tab_system_requirements`:-

.. _tab_system_requirements:

.. list-table:: System Requirements for |popy|
  
    * - Operating System
      - |windoze| 7.0/8.0/10.0

    * - Disk Space Required
      - 1.5Gb
      
    * - Bit Size
      - 64
      
    * - Processor
      - Intel Core i3 and better recommended
    
    * - Binary Installer Size
      - ~250Mb

.. _abbreviations:

Abbreviations
================
                
.. glossary::
    :sorted:
    
    FOCE
        :term:`first order conditional estimation`
    
    IMP
        :term:`importance sampling`
    
    ITS
        :term:`iterative two stage`
    
    JOE
        :term:`joint optimisation and estimation`
    
    LAPLACE
        :term:`Laplace approximation`
    
    SAEM
        :term:`stochastic approximation expectation maximisation`
        
    OBJV
        :term:`objective function` value
    
    ODEs
        :term:`ordinary differential equations`

    PK/PD
        Pharmacokinetic/Pharmacodynamic 
            
    TSLD
        Time since last dose
            
    VPC 
        :term:`visual predictive check`
  
    wrt 
        With respect to - usually defines rate of change variable in an |ode|
        
    IV 
        Intra-venous, |ie| injected directly into a vein
    
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    .. _overview_next:
       
    Next Steps
    ============

    See :ref:`install_popy`.   
