This repository contains a PDF written protocol with figures describing a method for measuring root respiration using an infrared gas analyzer (LI-850) and the R script necessary for processing the text files to derive CO2 flux. Just download the ZIP file, unzip locally, open either the PDF or the .R file. root_respiration_protocol.pdf - The illustrated protocol includes instruments and parts needed. root_respiration_script.R - A script for processing the included 15 .txt files as examples from a LI-850 Gas Analyzer and extract absolute CO2 flux with example code for how to incorporate root mass or length to derive specific root respiration. It is intended to run directly in RStudio and will automatically set the working directory in that case. Please cite this repository if the protocol or R script is used in your work. Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2020). Protocol and data analysis scripts for high-throughput phenotyping of specific root respiration [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4247873 The first manuscript using and describing this method is available: Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2021). Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture. New Phytologist. DOI: 10.1111/nph.17329