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Soil Incubation Database (SIDb)

Introduction

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...

Structure

Data

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 (Readme.md), 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.

Rpkg

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:

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

Scripts

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

docs

Files for generating the SIDb website.

Out

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

Demo

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 (Currently out of date).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.

Tests

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.

Contribute

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. E., 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, 12, 1511–1524, https://doi.org/10.5194/essd-12-1511-2020, 2020.