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.
Simple Tut Example
Used in Generate data and Fit using Simple PopPK Model to demonstrate running a Tut Script.
First order absorption model with peripheral compartment
Used in Fitting a Two Compartment PopPK Model to demonstrate running a Fit Script.
First order absorption model with peripheral compartment
Used in Generate a Two Compartment PopPK Data Set to demonstrate running a Gen Script.
First order absorption model with peripheral compartment
Used in Generate data and Fit using a Two Compartment Model to demonstrate running a Tut Script.
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.
Elimination Example with Volume of Distribution
Used in Volume of Distribution to demonstrate elimination with the apparent volume of distribution, V.
Elimination Example with Clearance
Used in Clearance to demonstrate elimination with clearance, CL.
One Compartment Model with Intravenous Dosing
Used in One Compartment Model with Intravenous Dosing to demonstrate a 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.
Two Compartment Model with Intravenous Dosing
Used in Two Compartment Model with Intravenous Dosing to demonstrate a 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.
Three Compartment Model with Intravenous Dosing
Used in Three Compartment Model with Intravenous Dosing to demonstrate a 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.
Bolus Dose with no elimination.
Used in Bolus Dose to demonstrate a single 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.
Infusion Rate Dose with no elimination.
Used in Infusion Rate to demonstrate a single infusion dose parametrised by rate, with no elimination.
Gamma Dose with no elimination.
Used in Gamma Dose to demonstrate a single gamma dose with no elimination.
Weibull Dose with no elimination.
Used in Weibull Dose to demonstrate a single 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.
Repeated Infusion Duration Dose with first order elimination.
Used in Repeated Dosing to demonstrate a 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.
Repeated Gamma Dose with first order elimination.
Used in Repeated Dosing to demonstrate a 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.
Model containing additive error only and additive error only input data
Tut script used in Residual Error Model to demonstrate additive noise only model.
Model containing proportional error only, with proportional only data
Tut script used in Residual Error Model to demonstrate proportional noise only model.
Model containing both proportional and additive error
Tut script used in Residual Error Model to demonstrate proportional and additive noise model.
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.
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.
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.
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.
One Compartment Model with Absorption estimating KA
Used in Uncertainty and Standard Errors to show how we estimate confidence in a single parameter problem.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Diagonal matrix generation diagonal matrix fit using separate univariate normals
Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.
Diagonal matrix generation diagonal matrix fit
Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.
Diagonal matrix generation full matrix fit
Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.
Full matrix generation diagonal matrix fit
Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.
Full matrix generation full matrix fit
Used in Modelling Correlation in Random Effects to demonstrate correlation between random effects.
Body Weight Covariate
Used in Covariates to demonstrate using weight as a 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.
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.
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|.
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.