summarise_evolRepeatability {rSHAPE}

This function will use output from summarise_experimentFiles and summarise_experimentParameters to help with expectations concerning run output and handling. This will save an RData file which will contain one object: all_popSets, which is a list of relevant control information about I/O and then a series of other RData files which contain the demographics information as a matrix with the mean and standard deviation of demographics for all replicates.

Description

This function will use output from summarise_experimentFiles and summarise_experimentParameters to help with expectations concerning run output and handling. This will save an RData file which will contain one object: all_popSets, which is a list of relevant control information about I/O and then a series of other RData files which contain the demographics information as a matrix with the mean and standard deviation of demographics for all replicates.

Usage

summarise_evolRepeatability(funcSave_jobExpression,
  func_saveFile = getOption("shape_procExp_filenames")["repeatability"],
  func_experimentDir = getOption("shape_workDir"),
  func_saveDir = getOption("shape_postDir"),
  func_refFile = getOption("shape_procExp_filenames")[c("fileList",
  "parameters")], func_workEnvir = new.env(),
  func_objPrefix = "Repeat_",
  func_sepString = getOption("shape_sepString"),
  func_string_line_ofDescent = getOption("shape_string_lineDescent"),
  func_processedPattern = getOption("shape_processedData_filePattern"),
  func_sepLines = getOption("shape_sepLines"))

Arguments

funcSave_jobExpression

This is a string expression that can be used to find elements of the experiment being analysed. It should be some robust unique string or regular expression.

func_saveFile

This is the filepath and filename (ending in .RData please) to which the results of this step will be saved.

func_experimentDir

This is the filepath to the root directoy under which all your experimental files can be found.

func_saveDir

This is the directory to which output will be saved.

func_refFile

This is the filepath to the reference file that contains information regarding all the processed files for the rSHAPE experiment.

func_workEnvir

This is an environment used to load files with the load function. It's used to encapsulate the loaded information to a controlled space.

func_objPrefix

This is a character string for programatic naming of objects of this type.

func_sepString

This is rSHAPE's sepString option but here to be passed into foreach

func_string_line_ofDescent

This is rSHAPE's option of similar name to be passed into foreach

func_processedPattern

This is rSHAPE's option of the similar name to be passed into foreach

func_sepLines

This is rSHAPE's option of the similar name passed into foreach

Note

There is no example as this cannot work without a complete rSHAPE experiment to be analysed.