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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