runReplicate: This is the function that runs the main body, or meaningful...
In rSHAPE: Simulated Haploid Asexual Population Evolution

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.

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"))

`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

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.

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

rSHAPE documentation built on July 19, 2019, 5:05 p.m.