Skip to content


Switch branches/tags

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time

DOI Build Status

Soil Incubation Database (SIDb)


This repository contains all the SIDb data files and source code. The database contains information on laboratory soil incubation experiments, with emphasis on time series of CO2 release.

Scroll down to learn how to work with SIDb data, contribute new data, properly cite the database, and get to know the inner workings of SIDb...



This folder contains all the data currently in SIDb. For each incubation study there is a yaml file with metada and a time series data file in .csv format. A list of the studies currently in SIDb (studies_list.csv), as well as a guide for entering new data (, an annotated blank template file (template_metadata.yaml), and a blank initConditions.csv file are also located in this folder.

The data are stored in software agnostic formats (.yaml, .csv) to facilitate data access via your preferred workflow. A pre-compiled version of the database (v1) can be obtained by installing the R package. See the next section (Rpkg) for more information.


This folder contains an R package for loading entries from the database as well as tools for data manipulation, querying the database, and generating reports. To install, open R and run:

devtools::install_github('SoilBGC-Datashare/sidb/Rpkg', build_vignettes = TRUE)


This folder contains R code and other scripts useful for visualizing and analyzing the data.


Files for generating the SIDb website.


This folder contains specific reports of the database generated from scripts in the Scripts folder


This folder contains R markdown files with reproducible code to demonstrate specific data analyses. (Currently out of date). For current examples and tutorials showing how to load SIDb data in R and work with it see: vignettes.


This folder contains tests to guarantee the integrity of the database. Make sure that you can run all tests without errors before contributing to the database.


This database is public and everybody is welcome to use it for scientific research. Users are also encouraged to contribute their own data and scripts to the dataset. To contribute please send a pull request. Pull requests will only be accepted if submitted code/data pass our code and data validation tests. Information on how to run these tests yourself can be found here: QA/QC Readme.

How to cite

Schädel, C., Beem-Miller, J., Aziz Rad, M., Crow, S. E., Hicks Pries, C., Ernakovich, J., Hoyt, A. M., Plante, A., Stoner, S., Treat, C. C., and Sierra, C. A.: Decomposability of soil organic matter over time: The Soil Incubation Database (SIDb, version 1.0) and guidance for incubation procedures, Earth Syst. Sci. Data Discuss.,, in review, 2019.