Simulated Haploid Asexual Population Evolution
This is a simple little function used to represent drift by introducin...
This is a function to add quotation marks around each element of a cha...
This function ensures that a vector of values will sum to a given numb...
This function calculates the number of births for the vector of popula...
This is a convenience script to build an named list of empty lists, wh...
This is a function to calculate the relative fitness for a vector of f...
This function is used to calculate the effect size and timing of the n...
This is a convenience function to ensure that we have a standard shape...
This function searches the nearby mutational space of a focal genotype...
This allows SHAPE to simulate the death process as a deterministic val...
The function will identify the binary string of all possible neighbour...
These are some global reference options that SHAPE will use and I cons...
This function uses the exponential growth model and can either calcula...
This is a function that steps forward through time steps of a SHAPE ru...
This is a function to extract genotype/lineage specific information. T...
This function querries if a suite of genotypes exist within the fitnes...
This function will look through a pedigree data.frame and recursively ...
This is the function that will call for draws from distributions.
This function will calculate the fitness values for genotypes being ne...
This is a wrapper function where the birth and death related parameter...
This function is simply an implementation of the logistic growth equat...
This is the discrete time logistic growth function known as the logist...
This function actually calculates the stochastic loss to populations.
This allows SHAPE to simulate the mutation process as a deterministic ...
This function is used to build or split character string to be used fo...
This is a function to programatically create R batch submission script...
This is a function to programatically create R script names
This is a function to programatically create R script names
This is a function to programatically create R batch submission script...
This quick little function is a means for me to create the strings of ...
This quick little function is a means for me to create the strings of ...
This is a standardising function which allows SHAPE to programatiicall...
This is a standardising function which allows SHAPE to programatiicall...
This is a standardising function which allows SHAPE to programatiicall...
This function is used to find which elements of a population matrix ar...
This is a convenience function to ensure that our population demograph...
This is a convenience function to refresh connections to database file...
This is a function to search our mutational database and then find the...
This is a wrapper function to process a SHAPE run and extract meaningf...
This is the function that runs the main body, or meaningful execution,...
This is the actual running of shape, it will initialise objects and va...
This is a function to just return a matrix that defines the sitewise d...
This function samples the space of all possible genotypes and then def...
This is a convenience function for setting the dependent fitness value...
In a RMF fitness landscape model, there is a weighting value applied t...
This function is designed to establish an initial object which maps th...
This is a function to take the input parameters and build the paramete...
This is a function used to read the SHAPE_experimentalDesign type inpu...
This is a convenience wrapper for sending an error and ending the SHAP...
This function will use output from summarise_experimentFiles and summa...
This function will find all initially processed output files from indi...
This function will use output from summarise_experimentFiles to locate...
This function will use output from summarise_experimentFiles and summa...
This function is a wrapper for getting a summary of the results of an ...
This is a function to trim a string by removing the first and last cha...
This is a function which is used to update lines that are searched and...
This function is used to programatically take vectors of paramters and...
This is a file for updating the post analysis plotting script and crea...
In silico experimental evolution offers a cost-and-time effective means to test evolutionary hypotheses. Existing evolutionary simulation tools focus on simulations in a limited experimental framework, and tend to report on only the results presumed of interest by the tools designer. The R-package for Simulated Haploid Asexual Population Evolution ('rSHAPE') addresses these concerns by implementing a robust simulation framework that outputs complete population demographic and genomic information for in silico evolving communities. Allowing more than 60 parameters to be specified, 'rSHAPE' simulates evolution across discrete time-steps for an evolving community of haploid asexual populations with binary state genomes. These settings are for the current state of 'rSHAPE' and future steps will be to increase the breadth of evolutionary conditions permitted. At present, most effort was placed into permitting varied growth models to be simulated (such as constant size, exponential growth, and logistic growth) as well as various fitness landscape models to reflect the evolutionary landscape (e.g.: Additive, House of Cards - Stuart Kauffman and Simon Levin (1987) <doi:10.1016/S0022-5193(87)80029-2>, NK - Stuart A. Kauffman and Edward D. Weinberger (1989) <doi:10.1016/S0022-5193(89)80019-0>, Rough Mount Fuji - Neidhart, Johannes and Szendro, Ivan G and Krug, Joachim (2014) <doi:10.1534/genetics.114.167668>). This package includes numerous functions though users will only need defineSHAPE(), runSHAPE(), shapeExperiment() and summariseExperiment(). All other functions are called by these main functions and are likely only to be on interest for someone wishing to develop 'rSHAPE'. Simulation results will be stored in files which are exported to the directory referenced by the shape_workDir option (defaults to tempdir() but do change this by passing a folderpath argument for workDir when calling defineSHAPE() if you plan to make use of your results beyond your current session). 'rSHAPE' will generate numerous replicate simulations for your defined range of experimental parameters. The experiment will be built under the experimental working directory (i.e.: referenced by the option shape_workDir set using defineSHAPE() ) where individual replicate simulation results will be stored as well as processed results which I have made in an effort to facilitate analyses by automating collection and processing of the potentially thousands of files which will be created. On that note, 'rSHAPE' implements a robust and flexible framework with highly detailed output at the cost of computational efficiency and potentially requiring significant disk space (generally gigabytes but up to tera-bytes for very large simulation efforts). So, while 'rSHAPE' offers a single framework in which we can simulate evolution and directly compare the impacts of a wide range of parameters, it is not as quick to run as other in silico simulation tools which focus on a single scenario with limited output. There you have it, 'rSHAPE' offers you a less restrictive in silico evolutionary playground than other tools and I hope you enjoy testing your hypotheses.