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sidb

Soil Incubation Database sidb

https://github.com/SoilBGC-Datashare/sidb

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    10 of 19 committers (52.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.4%) to scientific vocabulary

Keywords

database open-data science scientific soil
Last synced: 6 months ago · JSON representation

Repository

Soil Incubation Database sidb

Basic Info
Statistics
  • Stars: 19
  • Watchers: 14
  • Forks: 11
  • Open Issues: 6
  • Releases: 2
Topics
database open-data science scientific soil
Created over 9 years ago · Last pushed 7 months ago
Metadata Files
Readme License

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:

R 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.

Owner

  • Name: SoilBGC-Datashare
  • Login: SoilBGC-Datashare
  • Kind: organization

GitHub Events

Total
  • Issues event: 3
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 15
  • Fork event: 1
Last Year
  • Issues event: 3
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 15
  • Fork event: 1

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 590
  • Total Committers: 19
  • Avg Commits per committer: 31.053
  • Development Distribution Score (DDS): 0.81
Past Year
  • Commits: 19
  • Committers: 2
  • Avg Commits per committer: 9.5
  • Development Distribution Score (DDS): 0.158
Top Committers
Name Email Commits
JeffBM j****l@g****m 112
Carlos A. Sierra c****a@b****e 83
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
Committer Domains (Top 20 + Academic)
bgc-jena.mpg.de: 5 sas.upenn.edu: 2 mit.edu: 1 minas-mbp.fritz.box: 1 hawaii.edu: 1 agro.uba.ar: 1 dartmouth.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • 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: 3.33
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 8 hours
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jb388 (10)
  • CaitlinPries (2)
  • mazizirad (1)
  • brandonnodnarb (1)
  • flamholz (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 4
proxy.golang.org: github.com/SoilBGC-Datashare/sidb
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 6 months ago
proxy.golang.org: github.com/soilbgc-datashare/sidb
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 6 months ago

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