cosore

R package: continuous soil respiration database

Principles and general information

Only free use data accepted.

The package, and the process of contributing data, should be as focused and simple as possible (but no simpler).

All contributors will be included on a database definition paper.

The database is completely open for reuse. 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.

This database is not designed for, and should not be treated as, a permanent data repository. COSORE is a community database, but not an institutionally-backed repository like Figshare, DataONE, ESS-DIVE, etc. We recommend depositing your data in one of these first, and providing its DOI in metadata.

Database design

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.

As much as possible, metadata are kept to a minimum. There are five metadata files, but only two of them absolutely need to be filled out:

DESCRIPTION.txt

• Site name
• Longitude
• Latitude
• Elevation [optional]
• UTC_offset
• Timezone
• IGBP cover type
• Instrument name
• File format
• Timestamp format
• Primary publication DOI or URL [optional]
• Other publications DOI or URL [optional]
• Data DOI or URL [optional]
• Acknowledgment text [optional]

CONTRIBUTORS.txt

Information on arbitrary number (>=1) of contributors. The first contributor listed is assumed to be the point of contact for the dataset.

• First name, family name, email
• ORCID (https://orcid.org) [optional]
• Role (https://www.casrai.org/credit.html) [optional]

PORTS.txt

For each multiplexer port, can define:

• Treatment ("None" by default)
• Species [optional]
• Chamber area [optional]

COLUMNS.txt

This maps between dataset fields and standardized database fields. It include an optional compute-on-columns capability (e.g. to change units or combine columns).

ANCILLARY.txt

This file contains ancillary data: stand structure, carbon cycle, disturbance, etc. [all optional]

Operation

When asked (via csr_build() to build the synthesis dataset, the cosore R package

• Scans its inst/extdata folder for metadata on all installed datasets
• Parses the metadata, and then based on Instrument_name and File_format calls the appropriate function to parse the raw data (which for size reasons are not located in the repository)
• This is done via a drake pipeline, so we only rebuild datasets when needed
• Currently a list of lists is returned, where each entry is a list of the relevant dataset objects (description, contributors, etc);
• User-side convenience functions generate data frames ready (or readier) for analysis
• Reports are generated for the overall database and each individual dataset.

Data access

• Following the example of BAAD, there is a lightweight cosore.data package intended to provide data access to users. It does not work yet.

Priorities

• Structured/standardized continuous IRGA data
• Raw LI-8100A data
• Other data, e.g. long term survey measurements