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Data Access and Management","monthly_downloads":255,"total_dependent_repos":1,"total_dependent_packages":0,"readme":"# rmangal :package: - an R Client for the Mangal database \u003cimg src=\"man/figures/logo.png\" width=\"130\" align=\"right\" alt=\"rmangal logo\"/\u003e\n\n[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/332_status.svg)](https://github.com/ropensci/software-review/issues/332)\n[![R CMD Check](https://github.com/ropensci/rmangal/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/rmangal/actions/workflows/R-CMD-check.yaml)\n[![codecov](https://app.codecov.io/gh/ropensci/rmangal/graph/badge.svg?token=lGqUVLM2o3)](https://app.codecov.io/gh/ropensci/rmangal)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![rmangal status badge](https://ropensci.r-universe.dev/rmangal/badges/version)](https://ropensci.r-universe.dev/rmangal)\n[![CRAN status](https://www.r-pkg.org:443/badges/version/rmangal)](https://CRAN.R-project.org/package=rmangal)\n\n\n## Context\n\n[Mangal](https://mangal.io/#/) -- a global ecological interactions database --\nserializes ecological interaction matrices into nodes (e.g. taxon, individuals\nor population) and interactions (i.e. edges). For each network, Mangal offers\nthe opportunity to store study context such as the location, sampling\nenvironment, inventory date and information pertaining to the original\npublication. For all nodes involved in the ecological networks, Mangal\nreferences unique taxonomic identifiers such as Encyclopedia of Life (EOL),\nCatalogue of Life (COL), Global Biodiversity Information Facility (GBIF) etc.\nand can extend nodes information to individual traits.\n\n**rmangal** is an R client to the Mangal database and provides various functions\nto explore its content through search functions. It offers methods to retrieve\nnetworks structured as `mgNetwork` or `mgNetworksCollection` S3 objects and\nmethods to convert `mgNetwork` to other class objects in order to analyze and\nvisualize networks properties: [`igraph`](https://igraph.org/r/),\n[`tidygraph`](https://github.com/thomasp85/tidygraph), and\n[`ggraph`](https://github.com/thomasp85/ggraph).\n\n\n## Installation\n\nSo far, only the development version is available and can be installed via the [remotes](https://CRAN.R-project.org/package=remotes) :package:\n\n```r\nR\u003e remotes::install_github(\"ropensci/rmangal\")\nR\u003e library(\"rmangal\")\n```\n\n\n## How to use `rmangal`\n\nThere are [seven `search_*()` functions](https://docs.ropensci.org/rmangal/reference/index.html#section-explore-database) to explore the content of Mangal, for instance `search_datasets()`:\n\n```r\nR\u003e mgs \u003c- search_datasets(\"lagoon\")\nFound 2 datasets.\n```\n\nOnce this first step is achieved, networks found can be retrieved with the `get_collection()` function.\n\n```r\nR\u003e mgn \u003c- get_collection(mgs)\n```\n\n`get_collection()` returns an object `mgNetwork` if there is one network\nreturned, otherwise an object `mgNetworkCollection`, which is a list of\n`mgNetwork` objects.\n\n\n```r\nR\u003e class(mgn)\n[1] \"mgNetworksCollection\"\nR\u003e mgn\n── Network Collection ──\n\n6 networks in collection\n\n── Network #86 \n• Dataset: #22\n• Description: Dietary matrix of the Huizache–Caimanero lagoon\n• Size: 189 edges, 26 nodes\n• Taxonomic IDs coverage for nodes:\nITIS: 81%, BOLD: 81%, EOL: 85%, COL: 81%, GBIF: 0%, NCBI: 85%\n• Published in reference # DOI: 10.1016/s0272-7714(02)00410-9\n\n── Network #1104 \n• Dataset: #53\n• Description: Food web of the shallow sublittoral at Cape Ann\n• Size: 107 edges, 35 nodes\n• Taxonomic IDs coverage for nodes:\nITIS: 77%, BOLD: 71%, EOL: 77%, COL: 74%, GBIF: 3%, NCBI: 71%\n• Published in reference # DOI: 10.2307/1948658\n\n── Network #1108 \n• Dataset: #53\n• Description: Food web of the high salt marsh at Cape Ann\n• Size: 44 edges, 19 nodes\n• Taxonomic IDs coverage for nodes:\nITIS: 58%, BOLD: 53%, EOL: 58%, COL: 53%, GBIF: 11%, NCBI: 53%\n• Published in reference # DOI: 10.2307/1948658\n\n── Network #1105 \n• Dataset: #53\n• Description: Food web of the rocky shore at Cape Ann\n• Size: 124 edges, 29 nodes\n• Taxonomic IDs coverage for nodes:\nITIS: 90%, BOLD: 86%, EOL: 90%, COL: 86%, GBIF: 10%, NCBI: 86%\n• Published in reference # DOI: 10.2307/1948658\n\n── Network #1107 \n• Dataset: #53\n• Description: Food web of the low salt marsh at Cape Ann\n• Size: 60 edges, 25 nodes\n• Taxonomic IDs coverage for nodes:\nITIS: 80%, BOLD: 68%, EOL: 76%, COL: 68%, GBIF: 12%, NCBI: 72%\n• Published in reference # DOI: 10.2307/1948658\n\n── Network #1106 \n• Dataset: #53\n• Description: Food web of the mudflat at Cape Ann\n• Size: 175 edges, 37 nodes\n• Taxonomic IDs coverage for nodes:\nITIS: 86%, BOLD: 84%, EOL: 86%, COL: 84%, GBIF: 3%, NCBI: 84%\n• Published in reference # DOI: 10.2307/1948658\n\n```\n\n[`igraph`](https://igraph.org/r/) and\n[`tidygraph`](https://github.com/thomasp85/tidygraph) offer powerful features to\nanalyze networks and **rmangal** provides functions to convert `mgNetwork` to\n`igraph` and `tbl_graph` so that the user can easily benefit from those\npackages.\n\n\n\n```r\nR\u003e ig \u003c- as.igraph(mgn[[1]])\nR\u003e class(ig)\n[1] \"igraph\"\nR\u003e library(tidygraph)\nR\u003e tg \u003c- as_tbl_graph(mgn[[1]])\nR\u003e class(tg)\n[1] \"tbl_graph\" \"igraph\"\n```\n\n:book: Note that the vignette [\"Get started with\nrmangal\"](https://docs.ropensci.org/rmangal/articles/rmangal.html) will guide\nthe reader through several examples and provide further details about **rmangal** features.\n\n\n## Verbosity \n\nSince `rmangal` version 2.2, the function verbosity is controlled by the option\n`rmangal.verbose`. To quiet all rmangal functions, use: \n\n```R\noptions(rmangal.verbose = \"quiet\")\n```\n\nand to switch on the verbosity do:\n\n```R\noptions(rmangal.verbose = \"verbose\")\n```\n\n\n\n## How to publish ecological networks\n\nWe are working on that part. The networks publication process will be\nfacilitated with structured objects and tests suite to maintain data integrity\nand quality. Comments and suggestions are welcome, feel free to open issues.\n\n## `rmangal` vs `rglobi`\n\nThose interested only in pairwise interactions among taxa may consider using\n`rglobi`, an R package that provides an interface to the [GloBi\ninfrastructure](https://www.globalbioticinteractions.org/about.html). GloBi\nprovides open access to aggregated interactions from heterogeneous sources. In\ncontrast, Mangal gives access to the original networks and open the gate to\nstudy ecological networks properties (i.e. connectance, degree etc.) along large\nenvironmental gradients, which wasn't possible using the GloBi infrastructure.\n\n\n## Older versions \n\n* See https://github.com/mangal-interactions/rmangal-v1 for the first version of the client.\n* Note that due to changes in the RESTful API, there is no backward compatibility.\n\n\n## Acknowledgment\n\nWe are grateful to [Noam Ross](https://github.com/noamross) for acting as an editor during the review process. We also thank [Anna Willoughby](https://github.com/arw36) and [Thomas Lin Petersen](https://github.com/thomasp85) for reviewing the package. Their comments strongly contributed to improving the quality of `rmangal`.\n\n\n## Code of conduct\n\nPlease note that the `rmangal` project is released with a [Contributor Code of Conduct](https://mangal.io/doc/r/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n## Meta\n\n* Get citation information for `rmangal` in R doing `citation(package = 'rmangal')`\n* Please [report any issues or bugs](https://github.com/ropensci/rmangal/issues).\n\n[![rofooter](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["rmarkdown","blog","computational-ecology","ecology","weather-data","biodiversity","cites","endangered-species","trade"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/117782","html_url":"https://ost.ecosyste.ms/projects/117782"}