EML - Read and Write Ecological Metadata Language Files

Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.

Last updated 3 years ago

emleml-metadatametadata-standard

11.18 score 97 stars 7 dependents 374 scripts 938 downloads

dataone - R Interface to the DataONE REST API

Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.

Last updated 3 years ago

9.93 score 36 stars 3 dependents 472 scripts 572 downloads

codyn - Community Dynamics Metrics

Univariate and multivariate temporal and spatial diversity indices, rank abundance curves, and community stability measures. The functions implement measures that are either explicitly temporal and include the option to calculate them over multiple replicates, or spatial and include the option to calculate them over multiple time points. Functions fall into five categories: static diversity indices, temporal diversity indices, spatial diversity indices, rank abundance curves, and community stability measures. The diversity indices are temporal and spatial analogs to traditional diversity indices. Specifically, the package includes functions to calculate community richness, evenness and diversity at a given point in space and time. In addition, it contains functions to calculate species turnover, mean rank shifts, and lags in community similarity between two time points. Details of the methods are available in Hallett et al. (2016) <doi:10.1111/2041-210X.12569> and Avolio et al. (2019) <doi:10.1002/ecs2.2881>.

Last updated 4 years ago

9.10 score 34 stars 245 scripts 529 downloads

datapack - A Flexible Container to Transport and Manipulate Data and Associated Resources

Provides a flexible container to transport and manipulate complex sets of data. These data may consist of multiple data files and associated meta data and ancillary files. Individual data objects have associated system level meta data, and data files are linked together using the OAI-ORE standard resource map which describes the relationships between the files. The OAI- ORE standard is described at <https://www.openarchives.org/ore/>. Data packages can be serialized and transported as structured files that have been created following the BagIt specification. The BagIt specification is described at <https://tools.ietf.org/html/draft-kunze-bagit-08>.

Last updated 3 years ago

8.55 score 43 stars 4 dependents 195 scripts 540 downloads

metajam - Easily Download Data and Metadata from 'DataONE'

A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and metadata from 'DataONE' (<https://www.dataone.org>) and easily importing this information into R.

Last updated 7 months ago

datadata-analysismetadatarepositories

8.13 score 16 stars 75 scripts 155 downloads

redland - RDF Library Bindings in R

Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.

Last updated 1 years ago

redland

7.75 score 16 stars 13 dependents 98 scripts 1.3k downloads

emld - Ecological Metadata as Linked Data

This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.

Last updated 4 years ago

7.63 score 13 stars 8 dependents 69 scripts 634 downloads

arcticdatautils - Utilities for the Arctic Data Center

A set of utilities for working with the Arctic Data Center (https://arcticdata.io).

Last updated 9 months ago

5.63 score 10 stars 25 scripts

datamgmt - Data Management Utilities for Curating, Documenting, and Publishing Data

Data management utilities for curating, documenting, and publishing data.

Last updated 2 years ago

5.35 score 14 stars 6 scripts

recordr - R Provenance Tracking

Provide methods to record data provenance about R script executions. Provenance data includes files that were read and written by the script, along with information about the execution, such as start time end time, the R modules loaded during the execution, and other information describing the execution environment.

Last updated 6 years ago

provenancereproducible-research

4.98 score 19 stars 25 scripts 9 downloads

scythe - Harvest and register data package citations

Harvests data package citations from several API sources, including PLOS, Scopus, and Springer. This package uses modified functions from `rplos`, which is no longer maintained.

Last updated 6 months ago

3.87 score 7 stars 3 scripts