franticspider/rstringmol

This is the R package "Rstringmol", a tool for automating the analysis of runs of the stringmol automata chemistry.

Installing Rstringmol

The Rstringmol package was built using devtools, and is hosted on github. To install the package in R, you'll need to have devtools installed first:

install.packages("devtools")

Then install Rstringmol itself:

devtools::install_github("Rstringmol",build_vignettes = T,force = T,subdir = "Rstringmol")

Vignettes

Long-form help documentation is available via R vignettes for this package. Each vignette describes how to perform the analysis described in the academic papers listed below.

To access the vignettes from within R, enter:

browseVignettes(package="Rstringmol")

..this should open a browser window with links to the following vignettes:

• stringmol-analysis which describes the analysis for paper [1]
• stringmol-analysis-II which describes the analysis for paper [2]

Linux-Ubuntu notes

If the devtools install fails in linux, you may need to install curl, which has to be done outside of R in a Terminal. Type the following:

sudo apt-get install libcurl4-openssl-dev

Python code and documentation

This package now has some python code which was used to generate the graphics in paper [2]. Documentation for this can be found in the docs/ sub-directory.

Papers using Rstringmol

• [1] Hickinbotham, S., Stepney, S. and Hogeweg, P., "Nothing in evolution makes sense except in the light of parasitism: evolution of complex replication strategies", Royal Society Open Science 8 (8) 210441
• [2] Stepney, S. and Hickinbotham, S. "On the Open-Endendness of Detecting Open-Endedness", Artificial Life Journal, In press