querryEstablished

This is a matrix which must contain at least one column named as func_sizeCol which contains
the number of individuals in the communities' populations. But it may also be required to include a column
func_fitCol if func_estProp is "Desai".

func_inMatrix

DO NOT MODIFY - this is the column name that is querried to find population sizes

func_sizeCol

DO NOT MODIFY - this is the column name that is querried to find population fitness -
only important if func_estProp is set to "Desai"

func_fitCol

If this value is less than 1 - This is the proportion of the current community size which
is used to define a population as established it returns the rows of. If this value is greater than 1, it is
the minimum number of individuals required before a population is considered as established.
Lastly, it can be the character string "Desai", at which point - as per Desai 2007 - a lineage is established
once it has 1/s individuals.

func_estProp

This function is used to find which elements of a population matrix are deemed as established. Established is determined
by having a number of individuals greater than or equal to a definable proportion of the summed community size.

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.

Jonathan Dench

rSHAPE

Simulated Haploid Asexual Population Evolution

querryEstablished function

This function is used to find which elements of a population matrix are deemed as established.  Established is determined
by having a number of individuals greater than or equal to a definable proportion of the summed community size. — querryEstablished

This function is used to find which elements of a population matrix are deemed as established.  Established is determined
by having a number of individuals greater than or equal to a definable proportion of the summed community size.

querryEstablished: This function is used to find which elements of a population matrix are deemed as established. Established is determined by having a number of individuals greater than or equal to a definable proportion of the summed community size.

Description

Usage

Arguments

Value