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PhyDyn Utilities

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Igor Siveroni edited this page May 29, 2020 · 8 revisions

pdutils: PhyDyn Utilities

pdutils is a set of utility programs designed to help users with the creation of PhyDyn population models and analyses. pdutils is provided as a jar file available from the /jars directory in the PhyDyn repository.

PhyDyn utilities can be accessed by running the jar file with suitable arguments:

> java -jar <pdutils-jar> <pdu-command> <pdu-arguments>

pdutils is work in progress. Available functionality is listed below.

Code Generation Tools

Translation of PhyDyn population models to R models.

phydynutils can be used to extract a PopModelODE object from a PhyDyn analysis file and generate the corresponding phydynR or Odin R model file. The following commands are available:

  • <command> ::= generate-phydynr
    Generates a phydynR popmodel file from a xml containing the PhyDyn analysis.
> java -jar generate-phydynr <xml-file> <phydynr-file>
  • <command> ::= generate-odin
    Generates a odin R file from a xml containing the PhyDyn analysis.
> java -jar generate-phydynr <xml-file> <odin-file>

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phydynutils: PhyDyn Utilities

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