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Open Sustainable Technology

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sidb

Contains information on laboratory soil incubation experiments, with emphasis on time series of CO2 release.
https://github.com/SoilBGC-Datashare/sidb

Category: Natural Resources
Sub Category: Soil and Land

Keywords

database open-data science scientific soil

Last synced: about 12 hours ago
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Repository metadata

Soil Incubation Database sidb

Readme.md

DOI
Build Status

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 (Currently out of date).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.

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Last synced: 7 days ago

Total Commits: 589
Total Committers: 19
Avg Commits per committer: 31.0
Development Distribution Score (DDS): 0.81

Commits in past year: 18
Committers in past year: 2
Avg Commits per committer in past year: 9.0
Development Distribution Score (DDS) in past year: 0.111

Name Email Commits
JeffBM j****l@g****m 112
Carlos A. Sierra c****a@b****e 82
hvoelkel v****i@w****e 73
Carlos A. Sierra c****s@b****e 63
Shane Stoner s****r@b****e 47
mazizirad m****i@b****e 41
Caitlin Hicks Pries c****s@d****u 41
wilarXPS15 w****n@g****m 28
Heidi Voelkel h****l@b****e 21
mazizirad m****a@M****l 20
christinaschaedel 4****l 16
Agustín Sarquis a****s@a****r 16
susanecrow c****s@h****u 7
Caitlin Pries c****n@B****l 6
Alain Plante a****e@s****u 5
mtilyou m****u@g****m 5
mazizirad m****a@M****x 4
Alison Hoyt a****t@m****u 1
mtilyou m****u@s****u 1

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Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 15
Total pull requests: 0
Average time to close issues: 7 days
Average time to close pull requests: N/A
Total issue authors: 5
Total pull request authors: 0
Average comments per issue: 3.4
Average comments per pull request: 0
Merged pull request: 0
Bot issues: 0
Bot pull requests: 0

Past year issues: 2
Past year pull requests: 0
Past year average time to close issues: about 8 hours
Past year average time to close pull requests: N/A
Past year issue authors: 2
Past year pull request authors: 0
Past year average comments per issue: 1.0
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/SoilBGC-Datashare/sidb

Top Issue Authors

  • jb388 (10)
  • CaitlinPries (2)
  • mazizirad (1)
  • brandonnodnarb (1)
  • flamholz (1)

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Package metadata

proxy.golang.org: github.com/soilbgc-datashare/sidb

proxy.golang.org: github.com/SoilBGC-Datashare/sidb

Dependencies

Rpkg/DESCRIPTION cran
  • R >= 3.6.0 depends
  • FME * imports
  • SoilR * imports
  • dplyr * imports
  • rlang * imports
  • stringr * imports
  • yaml * imports
  • ggplot2 * suggests
  • knitr * suggests
  • plyr * suggests
  • rmarkdown * suggests
  • testthat * suggests

Score: -Infinity