runProcessing {rSHAPE}

This is a wrapper function to process a SHAPE run and extract meaningful summary information.

Description

This is a wrapper function to process a SHAPE run and extract meaningful summary information.

Usage

runProcessing(func_saveFile, func_subNaming, func_stepsCon,
  func_landscapeCon, func_hoodCon, func_estProp, func_size_timeStep,
  func_processObjects = getOption("shape_processedObjects"),
  func_hoodPriority = getOption("shape_const_hoodDepth"))

Arguments

func_saveFile

This is the filepath where the SHAPE run processed objects are to be saved.

func_subNaming

This is a logical which controls if the tables which report on all genotypes with X mutations should be forced into a single table or it SHAPE is allowed to split them into multiple tables.

func_stepsCon

This is the filepath to an SQLite database storing information for the stepwise changes of a SHAPE run.

func_landscapeCon

This is the filepath to an SQLite database storing information for the complete explored and neighbouring fitness landscape of a SHAPE run.

func_hoodCon

This is the filepath to an SQLite database storing information for high priority mutational neighbourhood information

func_estProp

This value is used to define the threshold size required for a population before it is considered established.

func_size_timeStep

This is the proportion of a standard biological generation being considered to be within a single time step.

func_processObjects

This is a vector of character strings which define the names of what objects will be produced and creates a global objects. DO NOT CHANGE THESE VALUES.

func_hoodPriority

This is an object to control which strains we get deep neighbourhood information for It should be one of "none","limited","priority","full" setting this higher will cost more and more in post analysis runtime.

Value

This returns a string vector stating the result of trying to process for the specified filepath.

Note

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