Man pages for rSHAPE
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... |
