skeleSim v0.9.8

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Genetic Simulation Engine

A shiny interface and supporting tools to guide users in choosing appropriate simulations, setting parameters, calculating summary genetic statistics, and organizing data output, all within the R environment. In addition to supporting existing forward and reverse-time simulators, new simulators can be integrated into the environment relatively easily.

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skeleSim

Description

skeleSim is a tool to guide users in choosing appropriate simulations, setting parameters, calculating summary genetic statistics, and organizing data output, all within the R environment. skeleSim is designed to be an extensible environment that can 'wrap' around any simulation software to increase its accessibility and use.

Installation

To install the latest version from GitHub:

# make sure you have Rtools installed
if (!require('devtools')) install.packages('devtools')
# install from GitHub
devtools::install_github('christianparobek/skeleSim', build_vignettes = TRUE)

Execution

To run the shiny app:

# Load the skeleSim package
library(skeleSim)

# Run the app
skeleSimGUI()

Contact

version 0.9.6

  • fixed bug in haplotype summary producing error:
    Error in summary(loc.g)$strata.smry : 
    $ operator is invalid for atomic vectors
    

version 0.9.5

  • First CRAN release.

Functions in skeleSim

Name Description
rmetasim.params-class rmetasim Parameters Class
rms.init.landscape.func Initialize a landscape object
analysis.funcs Analysis functions for skeleSim parameter objects
rms.run Run rmetasim
fastsimcoal.params-class fastsimcoal Parameters Class
fsc.scenarioCheck Check parameters for fastsimcoal
skeleSim.internals SkeleSim internal functions
fsc.write Write fastsimcoal files
skeleSimGUI GUI for skeleSim system
rms.convert Extract genetic data from landscape object
rms.scenarioCheck Check parameters for rmetasim
rms.init.landscape Initialize a landscape object
rms.write Write metasim file
fsc.loadScenario Load skeleSim scenario parameters for fastsimcoal
runSim Run simulation
fsc.run Run fastsimcoal
skeleSim-package Genetic simulation engine
skeleSim.checks Check all simulation parameters
skeleSim.classes skeleSim Parameters Class
getGammaMutRates Get a Vector of Randomly Chosen Mutation Rates
No Results!

Vignettes of skeleSim

Name
ForecastImages/RmetasimLocus.png
ForecastImages/screen1_Actions.png
ForecastImages/screen2_Gen_Conf.png
ForecastImages/screen3_Pop_Samp_Sizes.png
ForecastImages/screen4_Migr_rate.png
ForecastImages/screen5_Loc_Mut_rate.png
ForecastImages/screen6_Metasim_pop_matrices.png
ForecastImages/screen7_Metasim_allele_freq.png
ForecastImages/screen8_ssClass.png
ForecastImages/screen9_Scen2_diff_migr.png
SampleSizeImages/screen2_GenConf.JPG
SampleSizeImages/screen3_ScenConf.JPG
SampleSizeImages/screen5_migr_rates.JPG
SampleSizeImages/screen6_loci.JPG
SampleSizeImages/screen7_simcoal_history.JPG
Choosemetasim.png
Choosermetasim2.png
Forecasting.Rmd
Installing.Rmd
SampleSize.Rmd
ScenarioConf_LocChar.png
ScenarioConf_PopChar.png
Simulating.Rmd
obsvdheterozygosity.png
No Results!

Last month downloads

Details

Type Package
URL https://github.com/christianparobek/skeleSim
BugReports https://github.com/christianparobek/skeleSim/issues
License GPL-2
LazyLoad Yes
LazyData true
Collate skeleSim-package.R skeleSim.classes.R fsc.classes.R rms.classes.R skeleSim.internals.R skeleSimGUI.R analysis.funcs.R fsc.loadScenario.R fsc.run.R fsc.scenarioCheck.R rms.convert.R rms.init.land.function.R rms.init.landscape.R rms.internals.R rms.run.R rms.scenarioCheck.R runSim.R skeleSim.checks.R getGammaMutRates.R
VignetteBuilder knitr
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-11-27 16:30:29 UTC; astrand
Repository CRAN
Date/Publication 2017-11-27 22:37:36 UTC

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