Description Usage Arguments Value Note
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.
1 2 3 4 5 | 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.
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