runReplicate {rSHAPE}

This is the function that runs the main body, or meaningful execution, of SHAPE experiments. In other words this is the main work-horse function that calls all the other parts and will execute you simulation run. It has the main parts of: 1. Stochastic Events; 2. Deaths; 3. Births; 4. Mutations; and during mutations this is where the mutational landscape is queried and updated as required. NOTE: Many of its internal operations are controlled by options with the suffix "shape_" and are not explicitly passed as arguments at call to this function.

Description

This is the function that runs the main body, or meaningful execution, of SHAPE experiments. In other words this is the main work-horse function that calls all the other parts and will execute you simulation run. It has the main parts of: 1. Stochastic Events; 2. Deaths; 3. Births; 4. Mutations; and during mutations this is where the mutational landscape is queried and updated as required. NOTE: Many of its internal operations are controlled by options with the suffix "shape_" and are not explicitly passed as arguments at call to this function.

Usage

runReplicate(func_inputFrames, func_currStep, func_stepCounter,
  func_growthModel = getOption("shape_const_growthForm"),
  func_growthRate = getOption("shape_const_growthRate"),
  func_landscapeModel = getOption("shape_simModel"),
  func_fileName_dataBase = getOption("shape_fileName_dataBase"))

Arguments

func_inputFrames

This is a list of data.frames, either 1 or 2 elements, reporting on the last one or two steps in the simulation.

func_currStep

This is an integer value counting the absolute step in the simulation, its value is never reset.

func_stepCounter

This is an integer value which is a counter in the most tradititional sense. It's job is to track if it's time for a Stochastic event to trigger and its value is reset at that point.

func_growthModel

This is the growth model of the SHAPE run, it is passed here as a computational convenience since it is used numerous times in the function

func_growthRate

This is the growth rate of the SHAPE run, it is passed here as a computational convenience since it is used numerous times in the function

func_landscapeModel

This is the fitness landscape model of the SHAPE run, it is passed here as a computational convenience since it is used numerous times in the function

func_fileName_dataBase

This is the filepaths of DBs of the SHAPE run, it is passed here as a computational convenience since it is used numerous times in the function

Value

Returns a new list of 2 data.frames reporting on the state of SHAPE community for the last 2 time steps - ie: the one just run, and the most prior step.

Note

There is no example as this cannot work outisde of a runSHAPE call, it requires data produced by the simulation experiment.