# 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.

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Summary file: Simple Fit Example

### Simple Tut Example¶

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

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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.

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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.

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Summary file: First order absorption model with peripheral compartment

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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.

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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*.

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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*.

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Summary file: Elimination Example with Volume of Distribution

### Elimination Example with Clearance¶

Used in Clearance to demonstrate elimination with clearance, *CL*.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

### 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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

### 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.

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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.

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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.

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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.

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Summary file: Full matrix generation full matrix fit

### Body Weight Covariate¶

Used in Covariates to demonstrate using weight as a covariate.

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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.

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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**.

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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|.

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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.

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Summary file: Depot One Comp PK ignoring BLQ observations.