R-Project for reproducible research on archaeological ceramics compositional data

License Script: GPL http://www.gnu.org/licenses/gpl-3.0.html

Description

• A series of routines for exploratory analysis of ceramic compositions

• Designed for fully reproducible research

• It is applied on a well-known Roman-British Pottery data published by Tubb et al (1980)

• Statistics based on M.J. Baxter and Jaume Buxeda i Garrigós observations on compositional data

• Includes data visualization tools and robust statistical treatments

• The routines are contained in three folders:

     * 01_Exploration
  
     * 02_Group_creation
  
     * 03_Output
  

Running the Arch Flow project

Debian Linux

All commands should be executed with root privileges, unless contrary specified:

Add dirmngr for adding public keys and add CRAN public key:

apt-get update
apt-get install dirmngr
apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'

If Using Debian 8, install Debian Jessie CRAN repository:

echo "" >> /etc/apt/sources.list
echo "# CRAN R source" >> /etc/apt/sources.list
echo "deb http://cran.cnr.berkeley.edu//bin/linux/debian jessie-cran34/" >> /etc/apt/sources.list

If Using Debian 9, install Debian Stretch CRAN repository:

echo "" >> /etc/apt/sources.list
echo "# CRAN R source" >> /etc/apt/sources.list
echo "deb http://cran.cnr.berkeley.edu//bin/linux/debian stretch-cran34/" >> /etc/apt/sources.list

Install Packages:

apt-get update
apt-get install git
apt-get install r-base r-base-dev
apt-get install libcurl4-openssl-dev
apt-get install libssl-dev

Then download the appropriate package for your architecture and version from https://www.rstudio.com/products/rstudio/download/ and open a terminal with root privileges in the directory of the downloaded file and execute the dkpg command (rstudio-1.1.423-amd64.deb used as example, use your downloaded file version):

dpkg --install rstudio-1.1.423-amd64.deb

The following commands can be executed as normal user (non root).

Clone the Arch Flow project to your computer. Open the terminal where you want to clone it and type:

git clone https://github.com/esteful/arch_flow.git

Launch RStudio and open the project, using the desktop interface (open RStudio and go to "File"-> "Open Project..." and selecting the "arch_flow.Rproj" file) or opening the terminal in the cloned project directory and typing:

rstudio arch_flow.Rproj

Open the "install.r" file and hit the "Run" button or press Ctrl+Enter keys. This may take a while, it takes more than 40 minutes in a i5 with 4 GB RAM and SSD.

##Updates The scripts have been tested in R 3.3.0 and 3.3.5 Version of R. For the latter, when RStudio renders html, requires some packages to be updated.

Credits

Following packages have been used for the current project.

ArchData: David L. Carlson and Georg Roth (2016). archdata: Example Datasets from Archaeological Research. R package version 1.1. https://CRAN.R-project.org/package=archdata

Compositions: K. Gerald van den Boogaart, Raimon Tolosana and Matevz Bren (2014). compositions: Compositional Data Analysis. R package version 1.40-1. https://CRAN.R-project.org/package=compositions

Dendextend: Tal Galili (2015). dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering. Bioinformatics. DOI: 10.1093/bioinformatics/btv428

Dplyr: Hadley Wickham, Romain Francois, Lionel Henry and Kirill Müller (2017). dplyr: A Grammar of Data Manipulation. R package version 0.7.3. https://CRAN.R-project.org/package=dplyr

Plotrix: Lemon, J. (2006) Plotrix: a package in the red light district of R. R-News, 6(4): 8-12.

Ggbiplot: Vincent Q. Vu (2011). ggbiplot: A ggplot2 based biplot. R package version 0.55. http://github.com/vqv/ggbiplot