extract_popDemographics {rSHAPE}

This is a function that steps forward through time steps of a SHAPE run and extracts population demographic information. This includes Fitness, Number of Lineages, and Transitions between dominant genotypes. Most important it will also return the information related to which lineages will eventually establish in the population, a piece of information that will be critical for downstream lineage specific information extraction.

Description

This is a function that steps forward through time steps of a SHAPE run and extracts population demographic information. This includes Fitness, Number of Lineages, and Transitions between dominant genotypes. Most important it will also return the information related to which lineages will eventually establish in the population, a piece of information that will be critical for downstream lineage specific information extraction.

Usage

extract_popDemographics(func_stepsCon, func_estValue, func_landscapeCon,
  func_hoodCon, func_size_timeStep)

Arguments

func_stepsCon

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

func_estValue

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

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 (which is simply a subset of the full mutational landscape).

func_size_timeStep

This is the proportion of a standard biological generation which is to be simulated in a single time step.

Value

This return a list object that contains various pieces of usefull summary demographic information.

Note

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