R package citation, R package reverse dependencies, R package scholars, install an r package from GitHub hy is package acceptance pending why is package undeliverable amazon why is package on hold dhl tour packages why in r package r and r package full form why is r free why r is bad which r package to install which r package has which r package which r package version which r package readxl which r package ggplot which r package fread which r package license where is package.json where is package-lock.json where is package.swift where is package explorer in eclipse where is package where is package manager unity where is package installer android where is package manager console in visual studio who r package which r package to install which r package version who is package who is package deal who is package design r and r package full form r and r package meaning what r package has what package r what is package in java what is package what is package-lock.json what is package in python what is package.json what is package installer do r package can't install r packages r can't find package r can't load package can't load xlsx package r can't install psych package r can't install sf package r Write if else in NONMEM pk pd
rSHAPE
View on CRAN: Click
here
Download and install rSHAPE package within the R console
Install from CRAN:
install.packages("rSHAPE")
Install from Github:
library("remotes")
install_github("cran/rSHAPE")
Install by package version:
library("remotes")
install_version("rSHAPE", "0.3.2")
Attach the package and use:
library("rSHAPE")
Maintained by
Jonathan Dench
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-07-19
Latest Update: 2019-07-19
Description:
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) , NK - Stuart A. Kauffman and Edward D. Weinberger (1989) , Rough Mount Fuji - Neidhart, Johannes and Szendro, Ivan G and Krug, Joachim (2014) ). 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.
How to cite:
Jonathan Dench (2019). rSHAPE: Simulated Haploid Asexual Population Evolution. R package version 0.3.2, https://cran.r-project.org/web/packages/rSHAPE. Accessed 21 Nov. 2024.
Previous versions and publish date:
No previous versions
Other packages that cited rSHAPE R package
View rSHAPE citation profile
Other R packages that rSHAPE depends,
imports, suggests or enhances
Complete documentation for rSHAPE
Functions, R codes and Examples using
the rSHAPE R package
Some associated functions: addDrift . addQuotes . adjustBirths . birthFunction . buildPedigree . calc_relativeFitness . compute_distGrowth . createGenotypes . create_genotypeFrame . deathFunction . defineNeighbours . defineSHAPE . expGrowth . extractInfo_focalID . extract_popDemographics . findParent . find_neededNeighbours . fitnessDist . fitnessLandscape . growthFunction . logisticGrowth . logisticMap . lossSampling . mutationFunction . nameEnviron . nameObject . nameTable . nameTable_neighbourhood . nameTable_step . name_batchString . name_batchSubmit . name_bodyScript . name_parameterScript . name_subScript . querryEstablished . reportPopulations . reset_shapeDB . retrieve_binaryString . runProcessing . runReplicate . runSHAPE . set_DepbySite_ancestFitness . set_RMF_indWeight . set_const_NK_interactionsMat . set_const_RMF_globalOptima . set_siteByState_fitnessMat . shapeCombinations . shapeExperiment . stopError . summariseExperiment . summarise_evolRepeatability . summarise_experimentFiles . summarise_experimentParameters . summarise_popDemographics . trimQuotes . updateLines . writeParameters . write_subScript .
Some associated R codes: sourceSHAPE.R . Full rSHAPE package functions and examples
Downloads during the last 30 days
Get rewarded with contribution points by
helping add
Reviews / comments / questions /suggestions ↴↴↴
Today's Hot Picks in Authors and Packages
pkgdepends
Find recursive dependencies of 'R' packages from various
sources. Solve the dependencies to obtain ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Gábor Csárdi (view profile)
r2resize
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Obinna Obianom (view profile)
SCBiclust
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Erika S. Helgeson (view profile)
RcppHNSW
'Hnswlib' is a C++ library for Approximate Nearest Neighbors.
This package provides a minimal R int ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: James Melville (view profile)
deductive
Attempt to repair inconsistencies and missing values in
data records by using information from vali ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Mark van der Loo (view profile)
crossrun
Joint distribution of number of crossings and the
longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Tore Wentzel-Larsen (view profile)