This git repository is designed to guide to user through the analysis of X-Ray microscopy data from foraminifera incubated under different ocean acidification conditions. This analysis has two steps:
- setup of the git repository with appropriate data downloads
- Run the analysis using the provided rmarkdown document
The data for this analysis is hosted on figshare. Download the data with the desired method (e.g. direct download, curl, figshare api, etc), move them into the current working directory at the top of the git repository, and decompress the data using the following command
tar -vzf waterAnalysis.tar.gz -c waterAnalysis
tar -xvzf thicknessData.tar.gz
mkdir thicknessAnalysis
mv OA*.csv thicknessAnalysis/
At this point, all of the data should be prepared for analysis.
There is an Rmarkdown file that is called Analysis_Markdown.rmd. It is recommended to open this file in Rstudio for analysis; however, running this analysis locally can consume large computational resources and may not be viable. Therefore, it is recommended to run this analysis on an HPC cluster and utilize Rstudio using a resource such as open on demand or by threading Rstudio from a cluster using singularity (A useful guide may be found here)