README.md

In KamilSJaron/ConjunctionStats: The parser of simulations of hybrid zones performed by simulator Conjunction (http://github.com/KamilSJaron/Conjunction)

ConjunctionStats: an R package for parsing the output of Conjunction, the simulator of secondary contact.

Developed by: Kamil S Jaron, Amina Echchiki

ConjunctionStats is a package for parsing the output of Conjunction into R, to allow statistical analysis.

Installation

ConjunctionStats requires two packages to be installed "hzar" and "RColorBrewer".

Install via classical install

In terminal:

git clone https://github.com/KamilSJaron/ConjunctionStats.git
cd ./ConjunctionStats/

In R:

# install.packages('hzar')
# install.packages('RColorBrewer')

install.packages("./ConjunctionStats", repos = NULL, type="source")

Install via GitHub

In R:

# install.packages("devtools")

library(devtools)
install_github("KamilSJaron/ConjunctionStats", build_vignettes=FALSE)

Usage

Load the package

library(ConjunctionStats)

Access functions and documentation

# display function source code: FunctionName
# display function documentation: ?FunctionName
# example
ReadSetting
?ReadSetting

List of useful functions

Here we only list all the functions, detailed descritions you can find in the manual pages of functions and plenty of examples you can find at repository ConjunctionExamples

ConjunctionStats nomenclature

• All non-internal functions are in CamelStyle
• Read... functions are reading files.
• Fill... functions are outputing an input object with some newly computed statictics
• Trim... functions are outputing an input object trimmed # if(get == trim){I should merge them}
• Get... finctions are outputing a summary, statistics or reduced input object
• Plot... functions are plotting usually using paletes from package Rcolorbrewer

The core and the main purpose of the package is to provide an easy way how to import Conjunction output to R and compute some statistics.

0D

to fill

1D or 2D

setting <- ReadSetting(setting_file) # reads setting file, returns a dataframe of performed simulations
sims <- ReadSummary(out_file) # reads output file, returns a list of dataframes of demes of simulations
setting <- FillSetting(sims, setting, method='hzar') # add estimates of widths to setting frame using non-linear fitting of logistic function, depreciated for multilocus clines

The second part of the package is used for plotting common hybrid zone graphics. See man pages of funcitons to see details.

# high level plotting functions
PlotSim(...) # plot mean hybrid index, mean LD and average fitness across demes of one simulation
PlotStat(...) # make a dot plot with coloring of points according one of variables

# purely low level function
PlotAverages(...) # add averages to a plot, usually combined with PlotStat

KamilSJaron/ConjunctionStats documentation built on May 7, 2019, 12:06 p.m.