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
    • Glossary
    • HTML Summary Links
      • Example Summaries
        • Simple Fit Example
        • Simple Tut Example
        • First order absorption model with peripheral compartment
        • First order absorption model with peripheral compartment
        • First order absorption model with peripheral compartment
      • Individual Model Summaries
        • Elimination Example with KE parameter
        • Elimination Example with Volume of Distribution
        • Elimination Example with Clearance
        • One Compartment Model with Intravenous Dosing
        • One Compartment Model with Absorption
        • Two Compartment Model with Intravenous Dosing
        • Two Compartment Model with Absorption
        • Three Compartment Model with Intravenous Dosing
        • Three Compartment Model with Absorption
        • Bolus Dose with no elimination.
        • Infusion Duration Dose with no elimination.
        • Infusion Rate Dose with no elimination.
        • Gamma Dose with no elimination.
        • Weibull Dose with no elimination.
        • Repeated Bolus Dose with first order elimination.
        • Repeated Infusion Duration Dose with first order elimination.
        • Repeated Infusion Rate Dose with first order elimination.
        • Repeated Gamma Dose with first order elimination.
        • Repeated Weibull Dose with first order elimination.
        • Model containing additive error only and additive error only input data
        • Model containing proportional error only, with proportional only data
        • Model containing both proportional and additive error
        • Mixed error model fitted to mixed error data, but with incorrect variance definition
        • Sine circadian model
        • Direct PD Model
        • Direct PD Model Simultaneous PK/PD Parameter fit
        • One Compartment Model with Absorption estimating KA
        • One Compartment Model with Absorption estimating KA and V
        • One Compartment Model with Absorption estimating KA and CL
        • One Compartment Model with Absorption estimating V and CL
        • One Compartment Model with Absorption estimating KA, V and CL
      • Population Model Summaries
        • One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.2
        • One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.01
        • One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.5
        • One Compartment Model with Absorption and no inter-subject Variance f[CL_isv]=0
        • One Compartment Model with Absorption and Inter-occasion Variance f[CL_isv]=0.2
        • One Compartment Model with Absorption and Inter-occasion Variance f[CL_isv]=0.5
        • One Compartment Model with Absorption and no inter-occasion Variance f[CL_iov]=0
        • Diagonal matrix generation diagonal matrix fit using separate univariate normals
        • Diagonal matrix generation diagonal matrix fit
        • Diagonal matrix generation full matrix fit
        • Full matrix generation diagonal matrix fit
        • Full matrix generation full matrix fit
        • Body Weight Covariate
        • Depot + One compartment PK with BLQ
        • Depot One Comp PK with BLQ observations set to LLQ
        • Depot One Comp PK with BLQ observations set to 0.5*LLQ
        • Depot One Comp PK ignoring BLQ observations.
    • Troubleshooting
    • Bug Reporting
    • Credits
    • Release Notes
    • Bibliography
PoPy
  • Docs »
  • Appendices »
  • HTML Summary Links
  • View page source

HTML Summary Links¶

PoPy outputs HTML summaries of fit_scripts, gen_scripts and tut_scripts.

This page lists the summary outputs for all example scripts used in this documentation. Browse this list to see the variety of PK/PD modelling available in PoPy.

Note, each summary contains a link to the original script. e.g. A tut summary contains a link to the original Tut Script, so you can download each script and re-run all of the examples on this page using your own installation of PoPy. You can also adapt each example script to your own PK/PD modelling requirements.

Example Summaries¶

Simple Fit Example¶

Used in Fitting a Simple PopPK Model using PoPy to demonstrate running a Fit Script.

Note

Summary file: Simple Fit Example

Simple Tut Example¶

Used in Generate data and Fit using Simple PopPK Model to demonstrate running a Tut Script.

Note

Summary file: Simple Tut Example

First order absorption model with peripheral compartment¶

Used in Fitting a Two Compartment PopPK Model to demonstrate running a Fit Script.

Note

Summary file: First order absorption model with peripheral compartment

First order absorption model with peripheral compartment¶

Used in Generate a Two Compartment PopPK Data Set to demonstrate running a Gen Script.

Note

Summary file: First order absorption model with peripheral compartment

Note

Example Data: synthetic_data.csv

First order absorption model with peripheral compartment¶

Used in Generate data and Fit using a Two Compartment Model to demonstrate running a Tut Script.

Note

Summary file: First order absorption model with peripheral compartment

Individual Model Summaries¶

Elimination Example with KE parameter¶

Used in Elimination, Clearance and Volume of Distribution to demonstrate elimination with the elimination rate constant, KE.

Note

Summary file: Elimination Example with KE parameter

Elimination Example with Volume of Distribution¶

Used in Volume of Distribution to demonstrate elimination with the apparent volume of distribution, V.

Note

Summary file: Elimination Example with Volume of Distribution

Elimination Example with Clearance¶

Used in Clearance to demonstrate elimination with clearance, CL.

Note

Summary file: Elimination Example with Clearance

One Compartment Model with Intravenous Dosing¶

Used in One Compartment Model with Intravenous Dosing to demonstrate a one compartment model with intravenous dosing.

Note

Summary file: One Compartment Model with Intravenous Dosing

One Compartment Model with Absorption¶

Used in One Compartment Model with Absorption to demonstrate a one compartment model with absorption.

Note

Summary file: One Compartment Model with Absorption

Two Compartment Model with Intravenous Dosing¶

Used in Two Compartment Model with Intravenous Dosing to demonstrate a two compartment model with intravenous dosing.

Note

Summary file: Two Compartment Model with Intravenous Dosing

Two Compartment Model with Absorption¶

Used in Two Compartment Model with Absorption to demonstrate a two compartment model with absorption.

Note

Summary file: Two Compartment Model with Absorption

Three Compartment Model with Intravenous Dosing¶

Used in Three Compartment Model with Intravenous Dosing to demonstrate a three compartment model with intravenous dosing.

Note

Summary file: Three Compartment Model with Intravenous Dosing

Three Compartment Model with Absorption¶

Used in Three Compartment Model with Absorption to demonstrate a three compartment model with absorption.

Note

Summary file: Three Compartment Model with Absorption

Bolus Dose with no elimination.¶

Used in Bolus Dose to demonstrate a single bolus dose with no elimination.

Note

Summary file: Bolus Dose with no elimination.

Infusion Duration Dose with no elimination.¶

Used in Infusion Duration to demonstrate a single infusion dose parametrised by duration, with no elimination.

Note

Summary file: Infusion Duration Dose with no elimination.

Infusion Rate Dose with no elimination.¶

Used in Infusion Rate to demonstrate a single infusion dose parametrised by rate, with no elimination.

Note

Summary file: Infusion Rate Dose with no elimination.

Gamma Dose with no elimination.¶

Used in Gamma Dose to demonstrate a single gamma dose with no elimination.

Note

Summary file: Gamma Dose with no elimination.

Weibull Dose with no elimination.¶

Used in Weibull Dose to demonstrate a single weibull dose with no elimination.

Note

Summary file: Weibull Dose with no elimination.

Repeated Bolus Dose with first order elimination.¶

Used in Repeated Dosing to demonstrate a repeated bolus dose with first order elimination.

Note

Summary file: Repeated Bolus Dose with first order elimination.

Repeated Infusion Duration Dose with first order elimination.¶

Used in Repeated Dosing to demonstrate a repeated infusion duration dose with first order elimination.

Note

Summary file: Repeated Infusion Duration Dose with first order elimination.

Repeated Infusion Rate Dose with first order elimination.¶

Used in Repeated Dosing to demonstrate a repeated infusion rate dose with first order elimination.

Note

Summary file: Repeated Infusion Rate Dose with first order elimination.

Repeated Gamma Dose with first order elimination.¶

Used in Repeated Dosing to demonstrate a repeated gamma dose with first order elimination.

Note

Summary file: Repeated Gamma Dose with first order elimination.

Repeated Weibull Dose with first order elimination.¶

Used in Repeated Dosing to demonstrate a repeated weibull dose with first order elimination.

Note

Summary file: Repeated Weibull Dose with first order elimination.

Model containing additive error only and additive error only input data¶

Tut script used in Residual Error Model to demonstrate additive noise only model.

Note

Summary file: Model containing additive error only and additive error only input data

Model containing proportional error only, with proportional only data¶

Tut script used in Residual Error Model to demonstrate proportional noise only model.

Note

Summary file: Model containing proportional error only, with proportional only data

Model containing both proportional and additive error¶

Tut script used in Residual Error Model to demonstrate proportional and additive noise model.

Note

Summary file: Model containing both proportional and additive error

Mixed error model fitted to mixed error data, but with incorrect variance definition¶

Fit script used in Residual Error Model to demonstrate fitting mis-specified proportional and additive noise model to proportional and additive noise synthetic data.

Note

Summary file: Mixed error model fitted to mixed error data, but with incorrect variance definition

Sine circadian model¶

Used in Example DERIVATIVES using x[TIME] to demonstrate a PK/PD model with a circadian input function for a single individual.

Note

Summary file: Sine circadian model

Direct PD Model¶

Used in Example DERIVATIVES for PD Model to demonstrate an individual PK/PD model with a bolus dose, one compartment PK and single PD compartment.

Note

Summary file: Direct PD Model

Direct PD Model Simultaneous PK/PD Parameter fit¶

Used in Example PREDICTIONS for PD Model to demonstrate an individual PK/PD model with a bolus dose, one compartment PK and single PD compartment.

Note

Summary file: Direct PD Model Simultaneous PK/PD Parameter fit

One Compartment Model with Absorption estimating KA¶

Used in Uncertainty and Standard Errors to show how we estimate confidence in a single parameter problem.

Note

Summary file: One Compartment Model with Absorption estimating KA

One Compartment Model with Absorption estimating KA and V¶

Used in Uncertainty and Standard Errors to show how we estimate confidence in a two parameter problem.

Note

Summary file: One Compartment Model with Absorption estimating KA and V

One Compartment Model with Absorption estimating KA and CL¶

Used in Uncertainty and Standard Errors to show how we estimate confidence in a two parameter problem.

Note

Summary file: One Compartment Model with Absorption estimating KA and CL

One Compartment Model with Absorption estimating V and CL¶

Used in Uncertainty and Standard Errors to show how we estimate confidence in a two parameter problem.

Note

Summary file: One Compartment Model with Absorption estimating V and CL

One Compartment Model with Absorption estimating KA, V and CL¶

Used in Uncertainty and Standard Errors to show how we estimate confidence in a three parameter problem.

Note

Summary file: One Compartment Model with Absorption estimating KA, V and CL

Population Model Summaries¶

One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.2¶

Used in Inter-Subject Variation (ISV) to demonstrate inter-subject (or between-subject) variability.

Note

Summary file: One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.2

One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.01¶

Used in Inter-Subject Variation (ISV) to demonstrate inter-subject (or between-subject) variability.

Note

Summary file: One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.01

One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.5¶

Used in Inter-Subject Variation (ISV) to demonstrate inter-subject (or between-subject) variability.

Note

Summary file: One Compartment Model with Absorption and Inter-subject Variance f[CL_isv]=0.5

One Compartment Model with Absorption and no inter-subject Variance f[CL_isv]=0¶

Used in Inter-Subject Variation (ISV) to demonstrate inter-subject (or between-subject) variability.

Note

Summary file: One Compartment Model with Absorption and no inter-subject Variance f[CL_isv]=0

One Compartment Model with Absorption and Inter-occasion Variance f[CL_isv]=0.2¶

Used in Inter-Occasion Variation (IOV) to demonstrate inter-occasion (or between-occasion) variability.

Note

Summary file: One Compartment Model with Absorption and Inter-occasion Variance f[CL_isv]=0.2

One Compartment Model with Absorption and Inter-occasion Variance f[CL_isv]=0.5¶

Used in Inter-Occasion Variation (IOV) to demonstrate inter-occasion (or between-occasion) variability.

Note

Summary file: One Compartment Model with Absorption and Inter-occasion Variance f[CL_isv]=0.5

One Compartment Model with Absorption and no inter-occasion Variance f[CL_iov]=0¶

Used in Inter-Occasion Variation (IOV) to demonstrate inter-occasion (or between-occasion) variability.

Note

Summary file: One Compartment Model with Absorption and no inter-occasion Variance f[CL_iov]=0

Diagonal matrix generation diagonal matrix fit using separate univariate normals¶

Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.

Note

Summary file: Diagonal matrix generation diagonal matrix fit using separate univariate normals

Diagonal matrix generation diagonal matrix fit¶

Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.

Note

Summary file: Diagonal matrix generation diagonal matrix fit

Diagonal matrix generation full matrix fit¶

Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.

Note

Summary file: Diagonal matrix generation full matrix fit

Full matrix generation diagonal matrix fit¶

Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.

Note

Summary file: Full matrix generation diagonal matrix fit

Full matrix generation full matrix fit¶

Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.

Note

Summary file: Full matrix generation full matrix fit

Body Weight Covariate¶

Used in Covariates to demonstrate using weight as a covariate.

Note

Summary file: Body Weight Covariate

Depot + One compartment PK with BLQ¶

Used in Generate BLQ observations and fit different error models to demonstrate using ~rectnorm() distribution to model observations below LLQ.

Note

Summary file: Depot + One compartment PK with BLQ

Depot One Comp PK with BLQ observations set to LLQ¶

Used in Generate BLQ observations and fit different error models to demonstrate replacing BLQ observations with LLQ.

Note

Summary file: Depot One Comp PK with BLQ observations set to LLQ

Depot One Comp PK with BLQ observations set to 0.5*LLQ¶

Used in Generate BLQ observations and fit different error models to demonstrate replacing BLQ observations with 0.5*|llq|.

Note

Summary file: Depot One Comp PK with BLQ observations set to 0.5*LLQ

Depot One Comp PK ignoring BLQ observations.¶

Used in Generate BLQ observations and fit different error models to demonstrate removing BLQ observations from data set.

Note

Summary file: Depot One Comp PK ignoring BLQ observations.

Next Previous

© Copyright 2020, David Cristinacce/Phil Tresadern/Andrew Cristinacce/James Wright.

Built with Sphinx using a theme provided by Read the Docs.