Options#

Running a tool requires the user to specify the input to the tool and in many cases to give options that can change the beahviour of the run. These options are either specific to the particular tool or general options that can be given to any tool. There are three categories of options a tool can take:

Type

Description

tool_options

Options specific to one tool

common_options

Options common to all tools

dispatching_options

Options affecting how a tool is dispatched. These shouldn’t directly affect what the tool does.

The values of all types of options can be found in the metadata-file for each tool and subtool run.

Tool options#

Since the tool options are specific for each tool their documentation can be found under the user guides for the separate tools.

Common options#

Common options are options that can directly affect the execution of a tool and not only the environment in which the tool is run (see the dispatching options).

Option

Description

esttool

The external tool to use for model estimation and evaluation. The options are nonmem, nlmixr and dummy. The dummy estimation tool doesn’t do estimation, but instead randomizes the results. Since this is very fast it can be used for testing and demonstration purposes. nonmem is the default

Dipatching options#

Dipatching options are technical options telling Pharmpy something about how a workflow should be dispatched, i.e. run. They are not intended to be able to directly change any results of a tool just how they are executed.

Warning

In practice results might still change when changing dispatching options due to unforeseen details of the underlying system.

Option

Description

broadcaster

The broadcaster to use for broadcasting log messages during the run. The options are terminal and null. terminal is the default and outputs messages to the terminal. null will turn off broadcasting.

dispatcher

The dispatcher use for executing the workflow. The options are local_dask and local_serial. Default is local_dask. For more information see Dispatching

name

The name of the tool run. For more information see Context

ncores

Maximum number of CPU cores to use. Default is to use all available cores on the computer.

ref

The path to the tool run. For more information see Context