Evaluating the Efficacy of Collagen Isolation Using Stable Isotope Analysis and Infrared Spectroscopy

This repository contains the data, code, and manuscript editing history for Trayler, R. B., Valencia Landa, P., Kim, S. L., (2023) Evaluating the Efficacy of Collagen Isolation Using Stable Isotope Analysis and Infrared Spectroscopy, Journal of Archaeological Science

File Structure

.
├── data
    └── deer_ATR          # raw deer data 
    └── goat_ATR          # raw goat data
    └── shark_ART         # raw shark data
    └── isotope_data      # stable isotope data
    └── processed_spectra # post processed FTIR spectra 
├── R                     # R scripts to be run in numerical order 0 - 4
    └── functions         # data processing functions 
├── figures               # output directory for pdf figures
├── manuscript.md         # pandoc markdown formatted manuscript
├── reviewer_comments.md  # pandoc markdown formatted responce to reviwers
└── README.md

Manuscript

This manuscript is written in Pandoc flavored markdown. Follow the instructions here to install pandoc. The manuscript also relies on the pandoc-crossref filter to handle figure, table, and section numbering.

The manuscript file, manuscript.md can be compiled into a nicely formatted PDF by running the following pandoc command.

pandoc -s manuscript.md -o manuscript.pdf --pdf-engine=xelatex --filter pandoc-crossref --citeproc --number-sections