PoPy
1.0.3
Getting Started Guide
Principles of Pharmacokinetics
Population Models in PoPy
PoPy Example Models
PoPy for Nonmem Users
PoPy Reference Guide
Appendices
PoPy
Docs
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PoPy Contents Page
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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