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Resources","sub_category":"Soil and Land","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"[![Build Status](https://travis-ci.org/bpbond/cosore.svg?branch=master)](https://travis-ci.org/bpbond/cosore) \n\n[![codecov](https://codecov.io/gh/bpbond/cosore/branch/master/graph/badge.svg)](https://codecov.io/gh/bpbond/cosore)\n\n\n# cosore\n\n**A first data analysis** using COSORE is [published](https://www.nature.com/articles/s41598-021-85764-8.epdf)!\n\n**The _Global Change Biology_** paper is [published](https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.15353)!\n\nThe `cosore` package consists of data, metadata, and software tools for COSORE, a reproducibility-oriented \ncommunity database for continuous soil respiration data.\n\n**To use the database from within R**, install this `cosore` package by for example `devtools::install_github(\"bpbond/cosore\")`.\n\n**To download the COSORE database in a flat-file format**, i.e. accessible by any\ndata analysis tool, click on the\n[Releases](https://github.com/bpbond/cosore/releases) tab above.\n\n**A step-by-step guide to using COSORE** is available [here](https://rpubs.com/bpbond/502069).\n\n**To contribute to the database**, fill out the [metadata form](https://forms.gle/xRSY7WwmWKTL6iCv5).\n\n## Principles and general information\n\nOnly free use data ([CC BY 4](https://creativecommons.org/licenses/by/4.0/)) accepted.\nWe request that users cite the \ndatabase definition paper, and strongly encourage them to (i) cite all dataset primary\npublications, and (ii) involve data contributors as co-authors when possible.\n\nThe package, and the process of contributing and accessing data, should be as focused and \nsimple as possible (but no simpler).\n\nAll data contributors will be included on an introductory database paper planned for spring 2020.\n\n**COSORE is not designed to be, and should not be treated as, a permanent\ndata repository.** It is a community database, but not an institutionally-backed repository \nlike [Figshare](https://figshare.com), [DataONE](https://www.dataone.org),\n[ESS-DIVE](https://ess-dive.lbl.gov), etc. We recommend (but not require)\ndepositing your data in one of these first,\nand providing its DOI in your COSORE dataset metadata.\n\n## Database design\n\nThis database is comprised of a collection of datasets, each converted to a standard format and units.\nA _dataset_ is one or more files of continuous (automated) soil respiration data,\nwith accompanying metadata, with all measurements taken at a single _site_ and with\nconstant _treatment_ assignments (i.e. they may vary between chambers but not over time).\n\nCOSORE is designed to be a relatively lightweight database, and metadata are kept to a minimum. \nEach dataset has seven _tables_:\n\n* `description` - includes data on the\nsite name; location; [timezone name](https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)\nand [IGBP cover type](http://www.eomf.ou.edu/static/IGBP.pdf); measurement instrument;\npublication and data links; and acknowledgments and notes.\n* `contributors` - contributor information, including name, email, [ORCID](https://orcid.org), and\n[CRediT role](https://www.casrai.org/credit.html).\n* `ports` - continuous systems typically, but not always, are comprised of a single \nanalyzer plumbed to multiple chambers through a multiplexer. This table lists,\nfor each multiplexer port, measurement variable (typically Rs, Rh, or NEE); \ntreatment; species, and chamber/collar details.\n* `columns` - describes the mapping between the raw _dataset_ fields and \nstandardized COSORE fields; used during the import of raw (contributed) data.\n* `ancillary` - arbitrary ancillary data: stand structure, carbon cycle, disturbance, etc. [All optional.]\n* `data` - the actual chamber respiration data, with many possible fields including the required ones: \nbeginning and end timestamps, flux rate, and port number. May also include meteorological\nand soil data, flux fit diagnostics, error codes, etc.\n* `diagnostics` - this is generated by the data import process, and summarizes\nrecords that were dropped, problems found, etc.\n\n## Operation\n\nFour primary functions are available for R users:\n* `csr_database()` returns a summary data frame about the entire database (all constituent datasets)\n* `csr_dataset()` returns a single _dataset_, as a list of data frames\n* `csr_table()` returns a single _table_, across one or many datasets\n* `csr_metadata()` returns a metadata table describing all fields in dataset tables \n\nReports can be generated for the overall database (`csr_report_database()`) \nand each individual dataset (`csr_report_dataset()`). \nThere are a number of developer functions as well, i.e. not intended for the average\nCOSORE user. 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