Simulated Haploid Asexual Population Evolution

addDrift | This is a simple little function used to represent drift by... |

addQuotes | This is a function to add quotation marks around each element... |

adjustBirths | This function ensures that a vector of values will sum to a... |

birthFunction | This function calculates the number of births for the vector... |

buildPedigree | This is a convenience script to build an named list of empty... |

calc_relativeFitness | This is a function to calculate the relative fitness for a... |

compute_distGrowth | This function is used to calculate the effect size and timing... |

create_genotypeFrame | This is a convenience function to ensure that we have a... |

createGenotypes | This function searches the nearby mutational space of a focal... |

deathFunction | This allows SHAPE to simulate the death process as a... |

defineNeighbours | The function will identify the binary string of all possible... |

defineSHAPE | These are some global reference options that SHAPE will use... |

expGrowth | This function uses the exponential growth model and can... |

extractInfo_focalID | This is a function to extract genotype/lineage specific... |

extract_popDemographics | This is a function that steps forward through time steps of a... |

find_neededNeighbours | This function querries if a suite of genotypes exist within... |

findParent | This function will look through a pedigree data.frame and... |

fitnessDist | This is the function that will call for draws from... |

fitnessLandscape | This function will calculate the fitness values for genotypes... |

growthFunction | This is a wrapper function where the birth and death related... |

logisticGrowth | This function is simply an implementation of the logistic... |

logisticMap | This is the discrete time logistic growth function known as... |

lossSampling | This function actually calculates the stochastic loss to... |

mutationFunction | This allows SHAPE to simulate the mutation process as a... |

name_batchString | This function is used to build or split character string to... |

name_batchSubmit | This is a function to programatically create R batch... |

name_bodyScript | This is a function to programatically create R script names |

nameEnviron | This quick little function is a means for me to create the... |

nameObject | This quick little function is a means for me to create the... |

name_parameterScript | This is a function to programatically create R script names |

name_subScript | This is a function to programatically create R batch... |

nameTable | This is a standardising function which allows SHAPE to... |

nameTable_neighbourhood | This is a standardising function which allows SHAPE to... |

nameTable_step | This is a standardising function which allows SHAPE to... |

querryEstablished | This function is used to find which elements of a population... |

reportPopulations | This is a convenience function to ensure that our population... |

reset_shapeDB | This is a convenience function to refresh connections to... |

retrieve_binaryString | This is a function to search our mutational database and then... |

runProcessing | This is a wrapper function to process a SHAPE run and extract... |

runReplicate | This is the function that runs the main body, or meaningful... |

runSHAPE | This is the actual running of shape, it will initialise... |

set_const_NK_interactionsMat | This is a function to just return a matrix that defines the... |

set_const_RMF_globalOptima | This function samples the space of all possible genotypes and... |

set_DepbySite_ancestFitness | This is a convenience function for setting the dependent... |

set_RMF_indWeight | In a RMF fitness landscape model, there is a weighting value... |

set_siteByState_fitnessMat | This function is designed to establish an initial object... |

shapeCombinations | This is a function to take the input parameters and build the... |

shapeExperiment | This is a function used to read the SHAPE_experimentalDesign... |

stopError | This is a convenience wrapper for sending an error and ending... |

summarise_evolRepeatability | This function will use output from summarise_experimentFiles... |

summariseExperiment | This function is a wrapper for getting a summary of the... |

summarise_experimentFiles | This function will find all initially processed output files... |

summarise_experimentParameters | This function will use output from summarise_experimentFiles... |

summarise_popDemographics | This function will use output from summarise_experimentFiles... |

trimQuotes | This is a function to trim a string by removing the first and... |

updateLines | This is a function which is used to update lines that are... |

writeParameters | This is a file for updating the post analysis plotting script... |

write_subScript | This function is used to programatically take vectors of... |

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