Context | The Mangal project | Data structure | Authentication | How to use rmangal | Overall approach | Search functions | Search and list available datasets | Finding a specific network | Search for a specific taxon | Get networks associated with a search_* object | Integrated workflow with rmangal | Batch analysis | Geolocate Mangal networks with sf | Taxonomic analysis | Network analysis with igraph | Network manipulation and visualization with tidygraph and ggraph | Creating a list references for a set of networks | References
Package: rmangal 2.2.2
Kevin Cazelles
rmangal: 'Mangal' Client
An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal-interactions.github.io/mangal-api/>).
Authors:
rmangal_2.2.2.tar.gz
rmangal_2.2.2.zip(r-4.7)rmangal_2.2.2.zip(r-4.6)rmangal_2.2.2.zip(r-4.5)
rmangal_2.2.2.tgz(r-4.6-any)rmangal_2.2.2.tgz(r-4.5-any)
rmangal_2.2.2.tar.gz(r-4.7-any)rmangal_2.2.2.tar.gz(r-4.6-any)
rmangal_2.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rmangal/json (API)
| # Install 'rmangal' in R: |
| install.packages('rmangal', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #332
Bug tracker:https://github.com/ropensci/rmangal/issues
Pkgdown/docs site:https://docs.ropensci.org
Datasets:
- rmangal_endpoints - Mangal API's endpoints
ecologynetworksfood websinteractionsdata publicationsopen access
Last updated from:9c566bad99 (on main). Checks:10 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 185 | ||
| pkgdown docs | OK | 302 | ||
| source / vignettes | OK | 218 | ||
| linux-release-x86_64 | OK | 184 | ||
| macos-release-arm64 | OK | 107 | ||
| macos-oldrel-arm64 | OK | 95 | ||
| windows-devel | OK | 170 | ||
| windows-release | OK | 133 | ||
| windows-oldrel | OK | 121 | ||
| wasm-release | OK | 144 |
Exports:as.igraphcombine_mgNetworksget_citationget_collectionget_network_by_idget_network_by_id_indivrmangal_requestrmangal_request_singletonsearch_datasetssearch_interactionssearch_networkssearch_networks_sfsearch_nodessearch_referencessearch_taxonomy
Dependencies:askpassclicpp11curlgluehttr2igraphjsonlitelatticelifecyclemagrittrMatrixopensslpkgconfigR6rappdirsrlangsysvctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Coerce 'mgNetworksCollection' or 'mgNetwork' objects to 'igraph' objects. | as.igraph.mgNetwork as.igraph.mgNetworksCollection |
| List interactions type contained in mangal-db | avail_type |
| Combine Mangal networks | combine_mgNetworks |
| Retrieve all references pertaining to the networks collection or individual network | get_citation get_citation.mgNetwork get_citation.mgNetworksCollection |
| Get a collection of networks | get_collection get_collection.default get_collection.mgSearchDatasets get_collection.mgSearchInteractions get_collection.mgSearchNetworks get_collection.mgSearchNodes get_collection.mgSearchReferences get_collection.mgSearchTaxonomy |
| Retrieve network information, nodes, edges and references for a given set of Mangal network IDs | get_network_by_id get_network_by_id_indiv print.mgNetwork print.mgNetworksCollection summary.mgNetwork summary.mgNetworksCollection |
| Mangal API's endpoints | rmangal_endpoints |
| Low-level request function for the Mangal API | rmangal_request rmangal_request_singleton |
| Query datasets | search_datasets |
| Query interactions | search_interactions |
| Query networks | search_networks search_networks_sf |
| Query nodes | search_nodes |
| Query references | search_references |
| Query taxonomy | search_taxonomy |
