A first data analysis using COSORE is published!
The Global Change Biology paper is published!
The cosore
package consists of data, metadata, and software tools for COSORE, a reproducibility-oriented
community database for continuous soil respiration data.
To use the database from within R, install this cosore
package by for example devtools::install_github("bpbond/cosore")
.
To download the COSORE database in a flat-file format, i.e. accessible by any data analysis tool, click on the Releases tab above.
A step-by-step guide to using COSORE is available here.
To contribute to the database, fill out the metadata form.
Only free use data (CC BY 4) accepted. We request that users cite the database definition paper, and strongly encourage them to (i) cite all dataset primary publications, and (ii) involve data contributors as co-authors when possible.
The package, and the process of contributing and accessing data, should be as focused and simple as possible (but no simpler).
All data contributors will be included on an introductory database paper planned for spring 2020.
COSORE is not designed to be, and should not be treated as, a permanent data repository. It is a community database, but not an institutionally-backed repository like Figshare, DataONE, ESS-DIVE, etc. We recommend (but not require) depositing your data in one of these first, and providing its DOI in your COSORE dataset metadata.
This database is comprised of a collection of datasets, each converted to a standard format and units. A dataset is one or more files of continuous (automated) soil respiration data, with accompanying metadata, with all measurements taken at a single site and with constant treatment assignments (i.e. they may vary between chambers but not over time).
COSORE is designed to be a relatively lightweight database, and metadata are kept to a minimum. Each dataset has seven tables:
description
- includes data on the
site name; location; timezone name
and IGBP cover type; measurement instrument;
publication and data links; and acknowledgments and notes.contributors
- contributor information, including name, email, ORCID, and
CRediT role.ports
- continuous systems typically, but not always, are comprised of a single
analyzer plumbed to multiple chambers through a multiplexer. This table lists,
for each multiplexer port, measurement variable (typically Rs, Rh, or NEE);
treatment; species, and chamber/collar details.columns
- describes the mapping between the raw dataset fields and
standardized COSORE fields; used during the import of raw (contributed) data.ancillary
- arbitrary ancillary data: stand structure, carbon cycle, disturbance, etc. [All optional.]data
- the actual chamber respiration data, with many possible fields including the required ones:
beginning and end timestamps, flux rate, and port number. May also include meteorological
and soil data, flux fit diagnostics, error codes, etc.diagnostics
- this is generated by the data import process, and summarizes
records that were dropped, problems found, etc.Four primary functions are available for R users:
csr_database()
returns a summary data frame about the entire database (all constituent datasets)
csr_dataset()
returns a single dataset, as a list of data frames
csr_table()
returns a single table, across one or many datasets
csr_metadata()
returns a metadata table describing all fields in dataset tables
Reports can be generated for the overall database (csr_report_database()
)
and each individual dataset (csr_report_dataset()
).
There are a number of developer functions as well, i.e. not intended for the average
COSORE user. Perhaps most importantly this includes csr_build()
, which scans for
and parses metadata on all installed datasets, then loads the data,
parsing raw data as necessary and available.
R users will find it easiest to install this package and then use the functions above. Anyone can also download flat (csv) files from the Releases page.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.