PoPy Contents Page

• Getting Started Guide
  • Introducing PoPy
    • Overview
    • Documentation Structure
    • System Requirements
    • Abbreviations
    • Next Steps
  • Install PoPy
    • Downloading PoPy
    • Installing PoPy
    • Checking your new PoPy Installation
    • First Steps after Install
  • Configure Editor
    • Notepad++
    • Next Steps
  • Fitting a Simple PopPK Model using PoPy
    • Run the Fit Script
    • Summary of Fit Results
    • Syntax of Fit Script
    • Visual Predictive Check for Simple PopPK Model
    • Next Steps
  • PoPy Data Format
    • Required Fields
    • Dosing Fields
    • Observation Fields
    • Extra Fields
    • Next Steps
  • Generate data and Fit using Simple PopPK Model
    • Running the Tutorial Script
    • Syntax of Tut Script
    • Summary of Tut Results
    • Generate multiple data sets and Fit using Simple PopPK Model
    • Next Steps
  • Typical Workflows
    • Developing a PK/PD model for a real life Data Set
    • Investigate a PK/PD model using synthetic data
    • Compare PoPy with a previous Nonmem model
    • Next Steps
• Principles of Pharmacokinetics
  • Elimination, Clearance and Volume of Distribution
    • Volume of Distribution
    • Clearance
  • Compartment Models
    • One Compartment Model
    • Two Compartment Model
    • Three Compartment Model
  • Dose Administration
    • Bolus Dose
    • Infusion
    • Gamma Dose
    • Weibull Dose
    • Repeated Dosing
  • Residual Error Model
    • Error Models for Continuous Data
  • Estimating Model Parameters
    • Likelihood and the Objective Function
    • Minimization Algorithm
    • Initial Values and Convergence
  • Uncertainty and Standard Errors
    • Likelihood Hessian
    • Confidence Intervals
    • Standard Errors
• Population Models in PoPy
  • Inter-Subject Variation (ISV)
    • Data Synthesis with ISV
    • Naïve ISV Fit
    • Mixed Effect ISV Fit
  • Inter-Occasion Variation (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
• PoPy Example Models
  • Creating Example Scripts
    • Creating an example Fit Script
    • Creating an example Tut Script
  • Fitting a Two Compartment PopPK Model
    • Run the Fit Script
    • Summary of Fit Results
    • Syntax of Fit Script
    • Visual Predictive Check for Two Compartment PopPK Model
  • Generate a Two Compartment PopPK Data Set
    • Running the Gen Script
    • Summary of Gen Results
    • Syntax in the Gen Script
    • Structure of output synthetic data file
    • Controlling Random Seed in PoPy scripts
  • Generate data and Fit using a Two Compartment Model
    • Running the Tutorial Script
    • Syntax of Tut Script
    • Summary of Tut Results
    • Re-run the tutorial
  • Generate multiple data sets and Fit using a Two Compartment Model
    • Running the MTut Script
    • Syntax of MTut Script
    • Summary of MTut Results
    • Re-run the MTut Script
    • Convert Tut to MTut
  • 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)
• PoPy for Nonmem Users
  • Nonmem Data to PoPy Data File
    • EVID
    • ID
    • TIME
    • CMT
    • AMT
    • DV
    • MDV
  • Nonmem to PoPy Data conversions using P2NDAT and N2PDAT Scripts
    • P2NDAT Example
    • N2PDAT Example
    • Compare original PoPy data with P2NDAT/N2PDAT version
  • 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
  • DDMoRe0061 Conversion Example
    • Overview
    • Data Conversion
    • Script Conversion
  • DDMoRe0093 Conversion Example
    • Overview
    • Data Conversion
    • Script Conversion
  • DDMoRe0238 Conversion Example
    • Overview
    • Data Conversion
    • Script Conversion
• PoPy Reference Guide
  • Open a PoPy Command Prompt
    • Desktop Shortcut Method
    • Terminal popy_env Method
    • Copy popy_cmd.exe Method
    • Verify PoPy Environment
  • PoPy Activation
    • Activation Status
    • Activate PoPy
    • Deactivate PoPy
    • Transfer Product Key Between Machines
    • Licensing
  • Configure PoPy
    • PoPy Config File
    • Configuration Options
    • Factory Reset Options
    • Inkscape
    • Uninstall PoPy
  • PoPy Website
    • PoPy introductory site
    • PoPy product website
    • Obtain a website account
    • Website Structure
  • Validate PoPy
    • Check the PoPy Configuration
    • Run the Validator
    • Validation Examples
    • Troubleshoot
  • Command Line Tools
  • Script File Formats
  • Script File Sections
  • Script File Elements
  • Script File Outputs
  • PoPy Quick Reference Guide
• Appendices
  • Glossary
  • HTML Summary Links
    • Example Summaries
    • Individual Model Summaries
    • Population Model Summaries
  • Troubleshooting
    • ‘popy_run’ is not recognized
    • The term ‘popy_run’ is not recognized as the name of a cmdlet
    • ‘popy_env’ is not recognized
    • The term ‘popy_env’ is not recognized as the name of a cmdlet
    • ‘popy_env’ permission error
  • Bug Reporting
    • Check you have a bug!
    • Bug Report Advice
    • Reporting the bug
  • Credits
    • Authors
    • Sponsor
    • Python Libraries
  • Release Notes
    • PoPy v1.0.3
    • PoPy v1.0.2
    • PoPy v1.0.1
    • PoPy v1.0.0
  • Bibliography