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R package for analysis of social defeat data
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README.md

socialdefeat

R package for analysis of social defeat data

INSTALLATION

Install dependencies

First, grab the dependencies:

install.packages(c("cluster", "mclust"), dependencies = TRUE)

If this fails, try setting a CRAN mirror

chooseCRANmirror()

and then running the installation again.

Get the source

You can get the source from git or from a zip file.

Get the source from git

Clone the repository containing the source

git clone https://github.com/cookpa/socialdefeat.git

Get the source from a ZIP file

You can grab a ZIP file by going to the project's page and clicking the "Download ZIP" button.

Note that the ZIP file will be called "socialdefeat-master" and will unzip to a folder of that name. Rename this folder "socialdefeat".

Install the package

You need to know the path to the directory where you put the source. For example

sdPath <- "~/code/R/socialdefeat" 

On Windows, you can get the path by holding down shift and right-clicking on the "socialdefeat" folder, then selecting "Copy as path".

On a Mac, you can drag the folder from Finder into the R console or a Terminal to see the path.

To check you've got the right path, do

list.files(sdPath)

You should see

> list.files(sdPath)
[1] "DESCRIPTION" "man" "NAMESPACE" "R" "README.md"

Now you are ready to install:

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

Loading the package for use

library(socialdefeat)

View the documentation

help(package = socialdefeat)

Read the function man pages for EM classification (recommended) or clustering-based classification.

The bootstrap methods return an initial classification as well as the bootstrap results.

For production purposes, use at least 1000 iterations and preferably 10000.

Uninstall

First unload the package:

detach("package:socialdefeat", unload=TRUE)

Then remove it

remove.packages("socialdefeat")
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