PoPy Contents Page

• Preliminaries
  • Motivation
  • About PoPy
    • System Requirements
    • Bug Reporting
    • Acknowledgements
  • About This Book
    • Book Structure
    • Abbreviations
  • Setting Up PoPy
    • Installation
    • Configure Editor
    • Configure PoPy
• Operating Instructions
  • PoPy Terminal
  • Checking The PoPy Installation
    • PoPy Validation
  • Activating a PoPy Licence
    • Deactivating a PoPy Licence
  • Creating Your First PoPy Scripts
    • Creating a fit Script
    • Message Logging
    • Creating a tut Script
  • Running Your First tut Script
    • Script Hierarchies
    • The gen Subscript
    • The fit Subscript
    • The comp and tutsum Subscripts
  • PoPy Data Format
    • Required Fields
    • Dosing Fields
    • Observation Fields
    • User-Defined Fields
• Simulating A Single Individual
  • Dose Administration
    • Bolus Dose
    • Infusion
    • Gamma Dose
    • Weibull Dose
  • Elimination, Clearance and Volume of Distribution
    • Volume of Distribution
    • Clearance
  • Compartment Models
    • One Compartment Model
    • Two Compartment Model
    • Three Compartment Model
  • Residual Error Model
    • Controlling Randomness in Simulations
    • Error Models for Continuous Data
  • Pharmacodynamic Models
    • Time Delay
    • Direct Effect Models
    • Indirect Effect Models
    • Linear Effect Model
    • Circadian Models
    • Emax Models
    • Other Stuff
    • PD Parameter Fitting
• Simulating A Population Of Individuals
  • Inter-Subject Variability (ISV)
    • Data Synthesis with ISV
    • Naïve ISV Fit
    • Mixed Effect ISV Fit
  • Inter-Occasion Variability (IOV)
    • Data Synthesis with IOV
    • Naïve IOV Fit
    • Mixed Effect IOV Fit
  • Modelling Correlation in Random Effects
    • Uncorrelated Effects
    • Correlated Effects
  • Covariates
    • Continuous Covariates
    • Discrete Covariates
• Estimating Population Parameters
  • Estimating Model Parameters
    • Likelihood and the Objective Function
    • Minimization Algorithm
    • Initial Values and Convergence
  • Uncertainty and Standard Errors
    • Likelihood Hessian
    • Confidence Intervals
    • Standard Errors
  • Diagnostics
    • Residuals
    • Weighted Residuals (WRES)
    • Conditional Weighted Residuals (CWRES)
  • Generate BLQ observations and fit different error models
    • Generating BLQ observations
    • Fitting BLQ observations using rectnorm (correct error model)
    • Fitting BLQ observations using norm (incorrect error model)
    • Fitting BLQ observations using half LLQ (approx error model)
    • Fit to non-BLQ observations only (reduced data model)
• Working With Many Populations
  • Generate multiple data sets and Fit using Simple PopPK Model
    • Running the MTut Script
    • Syntax of MTut Script
    • Summary of MTut Results
• PoPy for Nonmem Users
  • Nonmem control file to PoPy Fit Script
    • $PROBLEM
    • $DATA
    • $INPUT
    • $SUBROUTINES
    • $MODEL
    • $THETA
    • $OMEGA
    • $SIGMA
    • $PK
    • $DES
    • $ERROR
    • $ESTIMATION
  • Nonmem Advan1,2,3,4,11,12 to PoPy analytic compartment models
    • ADVAN1
    • ADVAN1 TRANS2
    • ADVAN2
    • ADVAN2 TRANS2
    • ADVAN3
    • ADVAN3 TRANS4
    • ADVAN4
    • ADVAN4 TRANS4
    • ADVAN11
    • ADVAN11 TRANS4
    • ADVAN12
    • ADVAN12 TRANS4
  • Nonmem Data to PoPy Data File
    • EVID
    • ID
    • TIME
    • CMT
    • AMT
    • DV
    • MDV
  • DDMoRe0061 Conversion Example
    • Data Source
    • Data Preprocessing
    • Fixed/Random Effects Specification
    • PK Model Parameters Specification
    • ODEs Specification
    • Likelihood Error Specification
    • Parameter Fitting Methods Specification
  • DDMoRe0093 Conversion Example
    • Data Source & Preprocessing
    • Fixed/Random Effects Specification
    • PK Model Parameters Specification
    • ODEs Specification
    • Likelihood Error Specification
    • Parameter Fitting Methods Specification
  • DDMoRe0238 Conversion Example
    • Data Source
    • Data Preprocessing
    • Fixed/Random Effects Specification
    • PK Model Parameters Specification
    • Initial State Specification
    • ODEs Specification
    • Likelihood Error Specification
    • Parameter Fitting Methods Specification
• PoPy Reference Guide
  • PoPy Quick Reference Guide
  • Command Line Tools
  • Script File Formats
  • Script File Sections
  • Script File Elements
  • Script File Outputs
  • Glossary
  • HTML Summary Links
    • Example Summaries
    • Individual Model Summaries
    • Population Model Summaries
  • Release Notes
    • PoPy v1.3.0
    • PoPy v1.2.3
    • PoPy v1.2.2
    • PoPy v1.2.1
    • PoPy v1.2.0
    • PoPy v1.1.2
    • PoPy v1.1.1
    • PoPy v1.1.0
    • PoPy v1.0.5
    • PoPy v1.0.4
    • PoPy v1.0.3
    • PoPy v1.0.2
    • PoPy v1.0.1
    • PoPy v1.0.0
  • Notepad++
    • Install Notepad++
    • Configure Notepad++ Tabs for Indentation
    • Configure Notepad++ Colouring
  • Validation Examples
  • Troubleshooting
    • Win10 Increase max path length
  • Bibliography