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.