extractInfo_focalID {rSHAPE}

This is a function to extract genotype/lineage specific information. This info will be mostly through time style of information but will also include information about it's line of descent, growth pressures pre-establishment, and population size.

Description

This is a function to extract genotype/lineage specific information. This info will be mostly through time style of information but will also include information about it's line of descent, growth pressures pre-establishment, and population size.

Usage

extractInfo_focalID(func_focalID, func_estValue, func_stepsCon,
  func_landscapeCon, func_hoodCon, func_refMatrix, func_subNaming,
  func_genomeLength = getOption("shape_genomeLength"),
  func_max_numMutations = getOption("shape_max_numMutations"),
  func_allow_backMutations = getOption("shape_allow_backMutations"),
  func_descentSep = getOption("shape_string_lineDescent"),
  func_hoodExplore = getOption("shape_const_hoodDepth"),
  func_stringSep = getOption("shape_sepString"))

Arguments

func_focalID

This is the vector of genotype ID(s) of the focal lineage(s) for which information is to be extracted.

func_estValue

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

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_refMatrix

Is a matrix of a SHAPE run's population demographics at a step in time. I will be querried for information regarding a genotype's number of mutations and fitness value. of genotypes, but is not required but is also required

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_genomeLength

The number of positions simulated within the individual's genomes.

func_max_numMutations

The maximum number of mutations that could occur in a single mutation event – CAUTION: This should never be anything other than 1 as per how SHAPE is currently implemented.

func_allow_backMutations

This is a logical toggle controlling if reversions are allowed – meaning loss of mutations.

func_descentSep

This is the standard string used to collapse line of descent information.

func_hoodExplore

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. NOTE: That use of limited requires that you pass a func_refMatrix of expected shape (has a "genotypeID" column)!

func_stringSep

A common string separator used to merge information.

Value

This returns a list object with several pieces of summary information for the focal genotype ID.

Note

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