Tools

A tool in Pharmpy is an implementation of a pharmacometric method. The Pharmpy tools typically create multiple candidate models according to the tool selected, estimate those, and make some sort of selection of the best model. If possible, Pharmpy will parallelize the runs. All tools are independent of the estimation software chosen, the only part of the tool that is software specific is the estimation.

The tools can be split into two sections: Pharmpy tools and tools connected to PsN. Pharmpy tools are implemented in Pharmpy, while the tools connected to PsN allows for parsing and presenting results from PsN tools. Documentation of PsN tools can be found here.

Tools in Pharmpy

Note

In order to run any of the tools you need to have a configuration file set up with a path to NONMEM, instructions can be found here.

• General
  • Common features
  • Model Feature Language (MFL)
  • Strictness
• AMD - automatic model development
  • Supported model types
  • Running
  • Arguments
  • Input
  • Search space
  • Strategy for running AMD
  • Retries
  • Strategy components
  • Results
  • Examples
• Modelsearch - search for best structural model for a PK model
  • Running
  • The search space
  • Algorithms
  • Adding IIV to the candidate models during search
  • Comparing and ranking candidates
  • The Modelsearch results
• Structsearch - search for best structural model for PKPD, drug metabolite and TMDD models
  • PKPD
  • TMDD
  • Drug Metabolite
  • Running
  • The model types
  • The search space
  • Results
• IIVsearch - search for best IIV structure (both variance and covariance)
  • Running
  • Arguments
  • Algorithms
  • Adding IIV to the start model
  • Comparing and ranking candidates
  • The IIVsearch results
• IOVsearch - search for best IOV structure and trim IIV
  • Running
  • Arguments
  • Algorithm
  • Distribution of new IOVs
  • Comparing and ranking candidates
  • Results
• COVsearch - identify covariates that explain some of the IIV
  • Running
  • Arguments
  • Search space
  • Algorithm
  • Results
• RUVsearch - search for best residual error model
  • Running
  • Arguments
  • Models
  • Procedure
  • The RUVsearch results
• allometry - add allometric scaling
  • Running
  • Arguments
  • Procedure
  • The allometry results
• estmethod - compare estimation methods and/or solvers
  • Running
  • Algorithms
  • Estimation methods
  • Solvers
  • Parameter uncertainty methods
  • The Estmethod results
• Retries - Rerun a model with tweaked initial estimates
  • Running
  • Scales
  • The Retries results
• Simulation - Run a simulation
  • Running
  • Examples
  • The Simulation results
• Linearize - Linearize a model
  • Running
  • Arguments
  • De-linearization
  • The linearize results

Common options

In addition to the tool specific options, there are some options that all tools have in common.

Argument	Description
path	Path to create (or resume in) tool database
resume	Flag whether to resume an existing tool run