rglobi vignette - an R interface to the aggregated biotic interaction data of GloBI (https://www.globalbioticinteractions.org) ====== ### About the package `rglobi` allows easy access to the GLoBI database by wrapping the existing API. ******************** ### Quick start #### First, install `rglobi` ```r install.packages("devtools") ``` ``` ## ## The downloaded binary packages are in ## /var/folders/v4/0_y78_xj1x7b72l89cwc2kq80000gp/T//RtmpF6qc1T/downloaded_packages ``` ```r devtools::install_github("ropensci/rglobi") ``` ``` ## Downloading github repo ropensci/rglobi@master ## Installing rglobi ## '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL \ ## '/private/var/folders/v4/0_y78_xj1x7b72l89cwc2kq80000gp/T/RtmpF6qc1T/devtools15b730380a08/ropensci-rglobi-0b49250' \ ## --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library' \ ## --install-tests ## ## Reloading installed rglobi ``` ```r library("rglobi") ``` Note that since rglobi is still pretty new, only the dev version of the library is available at this time. We hope to publish a version to CRAN once the library matures. For more information see [GitHub](https://github.com/ropensci/rglobi). #### Find interactions involving a certain species Determining which species interact with each other (and how and where) is a major focus of ecology. The Global Biotic Interactions Database offers data on multiple interaction types, and the `rglobi` library offers several ways to specify and access these interactions. `get_interactions()` is the primary function used if data on a specific interaction type is required. A focus taxon is entered (may be specified as "Genus species" or higher level (e.g., Genus, Family, Class)). ```r hsapiens <- get_interactions(taxon = "Homo sapiens", interaction.type = "preysOn") head(hsapiens) ``` ``` ## source_taxon_external_id source_taxon_name ## 1 EOL:327955 Homo sapiens ## 2 EOL:327955 Homo sapiens ## 3 EOL:327955 Homo sapiens ## 4 EOL:327955 Homo sapiens ## 5 EOL:327955 Homo sapiens ## 6 EOL:327955 Homo sapiens ## source_taxon_path ## 1 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 2 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 3 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 4 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 5 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 6 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## source_specimen_life_stage interaction_type target_taxon_external_id ## 1 NA preysOn EOL:328048 ## 2 NA preysOn EOL:328716 ## 3 NA preysOn EOL:1666 ## 4 NA preysOn EOL:326518 ## 5 NA preysOn EOL:4453589 ## 6 NA preysOn EOL:2815988 ## target_taxon_name ## 1 Nandinia binotata ## 2 Cephalophus monticola ## 3 Manidae ## 4 Atherurus africanus ## 5 Cercopithecus nictitans nictitans ## 6 Serpentes ## target_taxon_path ## 1 Animalia | Chordata | Mammalia | Carnivora | Nandiniidae | Nandinia | Nandinia binotata ## 2 Animalia | Chordata | Mammalia | Artiodactyla | Bovidae | Cephalophus | Cephalophus monticola ## 3 Animalia | Chordata | Mammalia | Pholidota | Manidae ## 4 Animalia | Chordata | Mammalia | Rodentia | Hystricidae | Atherurus | Atherurus africanus ## 5 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Cercopithecoidea | Cercopithecidae | Cercopithecinae | Cercopithecini | Cercopithecus | Cercopithecus nictitans | Cercopithecus nictitans nictitans ## 6 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Reptilia | Squamata | Serpentes ## target_specimen_life_stage latitude longitude study_title ## 1 NA NA NA NA ## 2 NA NA NA NA ## 3 NA NA NA NA ## 4 NA NA NA NA ## 5 NA NA NA NA ## 6 NA NA NA NA ``` `get_predators_of()` and `get_prey_of()` are wrappers for `get_interactions()` that remove the need to specify interaction type ```r hsapiens <- get_prey_of("Homo sapiens") head(hsapiens) ``` ``` ## source_taxon_external_id source_taxon_name ## 1 EOL:327955 Homo sapiens ## 2 EOL:327955 Homo sapiens ## 3 EOL:327955 Homo sapiens ## 4 EOL:327955 Homo sapiens ## 5 EOL:327955 Homo sapiens ## 6 EOL:327955 Homo sapiens ## source_taxon_path ## 1 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 2 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 3 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 4 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 5 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## 6 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Hominoidea | Hominidae | Homininae | Homo | Homo sapiens ## source_specimen_life_stage interaction_type target_taxon_external_id ## 1 NA preysOn EOL:328048 ## 2 NA preysOn EOL:328716 ## 3 NA preysOn EOL:1666 ## 4 NA preysOn EOL:326518 ## 5 NA preysOn EOL:4453589 ## 6 NA preysOn EOL:2815988 ## target_taxon_name ## 1 Nandinia binotata ## 2 Cephalophus monticola ## 3 Manidae ## 4 Atherurus africanus ## 5 Cercopithecus nictitans nictitans ## 6 Serpentes ## target_taxon_path ## 1 Animalia | Chordata | Mammalia | Carnivora | Nandiniidae | Nandinia | Nandinia binotata ## 2 Animalia | Chordata | Mammalia | Artiodactyla | Bovidae | Cephalophus | Cephalophus monticola ## 3 Animalia | Chordata | Mammalia | Pholidota | Manidae ## 4 Animalia | Chordata | Mammalia | Rodentia | Hystricidae | Atherurus | Atherurus africanus ## 5 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Primates | Haplorrhini | Simiiformes | Cercopithecoidea | Cercopithecidae | Cercopithecinae | Cercopithecini | Cercopithecus | Cercopithecus nictitans | Cercopithecus nictitans nictitans ## 6 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Reptilia | Squamata | Serpentes ## target_specimen_life_stage latitude longitude study_title ## 1 NA NA NA NA ## 2 NA NA NA NA ## 3 NA NA NA NA ## 4 NA NA NA NA ## 5 NA NA NA NA ## 6 NA NA NA NA ``` For a complete list of supported interaction types, ```r get_interaction_types() ``` ``` ## interaction source target ## 1 preysOn predator prey ## 2 preyedUponBy prey predator ## 3 parasiteOf parasite host ## 4 hasParasite host parasite ## 5 pollinates pollinator plant ## 6 pollinatedBy plant pollinator ## 7 pathogenOf pathogen host ## 8 hasPathogen plant pollinator ## 9 symbiontOf source target ## 10 interactsWith source target ``` For data sources in which type of interactions was not specified, the interaction is labeled "interacts_with". If you wish to view all interactions instead of specific types (e.g., parasitism and predation instead of just one of the two), the `get_interactions_by_taxa()` function allows this. In addition, the function provides options to search for interactions between two groups (source and target taxa, see above table) and only find interactions in a certain region. ```r rattus <- get_interactions_by_taxa(sourcetaxon = "Rattus") head(rattus) ``` ``` ## source_taxon_external_id source_taxon_name ## 1 EOL:328447 Rattus rattus ## 2 EOL:328447 Rattus rattus ## 3 EOL:328447 Rattus rattus ## 4 EOL:328447 Rattus rattus ## 5 EOL:328447 Rattus rattus ## 6 EOL:328447 Rattus rattus ## source_taxon_path ## 1 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Rodentia | Myomorpha | Muridae | Murinae | Rattus | Rattus rattus ## 2 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Rodentia | Myomorpha | Muridae | Murinae | Rattus | Rattus rattus ## 3 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Rodentia | Myomorpha | Muridae | Murinae | Rattus | Rattus rattus ## 4 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Rodentia | Myomorpha | Muridae | Murinae | Rattus | Rattus rattus ## 5 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Rodentia | Myomorpha | Muridae | Murinae | Rattus | Rattus rattus ## 6 Animalia | Bilateria | Deuterostomia | Chordata | Vertebrata | Gnathostomata | Tetrapoda | Mammalia | Theria | Eutheria | Rodentia | Myomorpha | Muridae | Murinae | Rattus | Rattus rattus ## source_specimen_life_stage interaction_type target_taxon_external_id ## 1 NA interactsWith EOL:13340393 ## 2 NA interactsWith EOL:10702710 ## 3 NA interactsWith EOL:5004474 ## 4 NA interactsWith EOL:4968671 ## 5 NA interactsWith EOL:4965412 ## 6 NA interactsWith EOL:4963889 ## target_taxon_name ## 1 Mastophorus muris ## 2 Trypanosoma lewisi ## 3 Calodium hepaticum ## 4 Raillietina ## 5 Nippostrongylus brasiliensis ## 6 Syphacia ## target_taxon_path ## 1 Animalia | Nematoda | Secernentea | Spirurida | Spiruridae | Mastophorus | Mastophorus muris ## 2 Cellular organisms | Eukaryota | Euglenozoa | Kinetoplastida | Trypanosomatidae | Trypanosoma | Herpetosoma | Trypanosoma lewisi ## 3 Calodium hepaticum ## 4 Animalia | Platyhelminthes | Cestoda | Cyclophyllidea | Davaineidae | Raillietina ## 5 Animalia | Nematoda | Secernentea | Strongylida | Heligosomidae | Nippostrongylus | Nippostrongylus brasiliensis ## 6 Animalia | Nematoda | Secernentea | Ascaridida | Oxyuridae | Syphacia ## target_specimen_life_stage latitude longitude study_title ## 1 NA NA NA NA ## 2 NA NA NA NA ## 3 NA NA NA NA ## 4 NA NA NA NA ## 5 NA NA NA NA ## 6 NA NA NA NA ``` Only a source taxa need be identified, but you can also specify a target taxon and/or geographic boundary (Coordinates must be in decimal degrees ([EPSG:4326](https://spatialreference.org/ref/epsg/wgs-84/)) and correspond to the west, south, east, and northern boundaries (i.e., min x, min y, max x, max y). ```r aves_crustacea_northern_hemisphere <- get_interactions_by_taxa( sourcetaxon = "Aves", targettaxon = "Crustacea", bbox=c(-180, 0, 180, 90 )) head(aves_crustacea_northern_hemisphere) ``` ``` ## source_taxon_external_id source_taxon_name ## 1 EOL:18884 Cepphus ## 2 EOL:1047918 Anas platyrhynchos ## 3 EOL:1049560 Recurvirostra americana ## 4 EOL:1049376 Arenaria melanocephala ## 5 EOL:1048977 Bucephala albeola ## 6 EOL:1048977 Bucephala albeola ## source_taxon_path ## 1 Animalia | Chordata | Aves | Charadriiformes | Alcidae | Cepphus ## 2 Animalia | Chordata | Aves | Anseriformes | Anatidae | Anas | Anas platyrhynchos ## 3 Animalia | Chordata | Aves | Charadriiformes | Recurvirostridae | Recurvirostra | Recurvirostra americana ## 4 Animalia | Chordata | Aves | Charadriiformes | Scolopacidae | Arenaria | Arenaria melanocephala ## 5 Animalia | Chordata | Aves | Anseriformes | Anatidae | Bucephala | Bucephala albeola ## 6 Animalia | Chordata | Aves | Anseriformes | Anatidae | Bucephala | Bucephala albeola ## source_specimen_life_stage interaction_type target_taxon_external_id ## 1 NA preysOn EOL:2625033 ## 2 NA preysOn EOL:2620777 ## 3 NA interactsWith EOL:2625033 ## 4 NA preysOn EOL:2620777 ## 5 NA interactsWith EOL:2625033 ## 6 NA preysOn EOL:2620777 ## target_taxon_name ## 1 Copepoda ## 2 Gammaridea ## 3 Copepoda ## 4 Gammaridea ## 5 Copepoda ## 6 Gammaridea ## target_taxon_path ## 1 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea | Maxillopoda | Copepoda ## 2 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea | Malacostraca | Eumalacostraca | Peracarida | Amphipoda | Gammaridea ## 3 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea | Maxillopoda | Copepoda ## 4 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea | Malacostraca | Eumalacostraca | Peracarida | Amphipoda | Gammaridea ## 5 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea | Maxillopoda | Copepoda ## 6 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea | Malacostraca | Eumalacostraca | Peracarida | Amphipoda | Gammaridea ## target_specimen_life_stage latitude longitude study_title ## 1 NA NA NA NA ## 2 NA NA NA NA ## 3 NA NA NA NA ## 4 NA NA NA NA ## 5 NA NA NA NA ## 6 NA NA NA NA ``` #### Find interactions in a geographic areas Instead of a taxon-specific approach, users may also wish to gather information on all interactions occuring in a specific area. For example, a group developing ecoystem models for the Gulf of Mexico may want to consider all the data from that region. `rglobi` enables this type of search by allowing users to specify a rectangular bounding box. Coordinates must be in decimal degrees ([EPSG:4326](https://spatialreference.org/ref/epsg/wgs-84/)) and correspond to the west, south, east, and northern boundaries (i.e., min x, min y, max x, max y). ```r gulfinteractions <- get_interactions_in_area( bbox=c(-97.0, 17.5, -81, 31)) head(gulfinteractions) ``` ``` ## source_taxon_external_id source_taxon_name ## 1 EOL:1 Animalia ## 2 EOL:1905 Actinopterygii ## 3 EOL:2598871 Crustacea ## 4 EOL:208553 Chloroscombrus chrysurus ## 5 EOL:208553 Chloroscombrus chrysurus ## 6 EOL:208553 Chloroscombrus chrysurus ## source_taxon_path ## 1 Animalia ## 2 Biota | Animalia | Chordata | Vertebrata | Gnathostomata | Pisces | Actinopterygii ## 3 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea ## 4 Animalia | Chordata | Actinopterygii | Perciformes | Carangidae | Chloroscombrus | Chloroscombrus chrysurus ## 5 Animalia | Chordata | Actinopterygii | Perciformes | Carangidae | Chloroscombrus | Chloroscombrus chrysurus ## 6 Animalia | Chordata | Actinopterygii | Perciformes | Carangidae | Chloroscombrus | Chloroscombrus chrysurus ## source_specimen_life_stage interaction_type target_taxon_external_id ## 1 NA preyedUponBy EOL:208553 ## 2 NA preyedUponBy EOL:208553 ## 3 NA preyedUponBy EOL:208553 ## 4 NA preysOn EOL:1 ## 5 NA preysOn EOL:1905 ## 6 NA preysOn EOL:2598871 ## target_taxon_name ## 1 Chloroscombrus chrysurus ## 2 Chloroscombrus chrysurus ## 3 Chloroscombrus chrysurus ## 4 Animalia ## 5 Actinopterygii ## 6 Crustacea ## target_taxon_path ## 1 Animalia | Chordata | Actinopterygii | Perciformes | Carangidae | Chloroscombrus | Chloroscombrus chrysurus ## 2 Animalia | Chordata | Actinopterygii | Perciformes | Carangidae | Chloroscombrus | Chloroscombrus chrysurus ## 3 Animalia | Chordata | Actinopterygii | Perciformes | Carangidae | Chloroscombrus | Chloroscombrus chrysurus ## 4 Animalia ## 5 Biota | Animalia | Chordata | Vertebrata | Gnathostomata | Pisces | Actinopterygii ## 6 Animalia | Bilateria | Protostomia | Ecdysozoa | Arthropoda | Crustacea ## target_specimen_life_stage latitude longitude study_title ## 1 NA NA NA NA ## 2 NA NA NA NA ## 3 NA NA NA NA ## 4 NA NA NA NA ## 5 NA NA NA NA ## 6 NA NA NA NA ``` To see all locations for which interactions have entered in GloBi, ```r areas <- get_interaction_areas() head(areas) ``` ``` ## Latitude Longitude ## 1 29.34695 -92.98061 ## 2 29.03260 -92.28701 ## 3 28.03673 -96.11108 ## 4 27.62409 -95.77403 ## 5 26.33146 -96.03294 ## 6 30.25024 -86.13114 ``` You can also restrict this search to a certain area: ```r areas <- get_interaction_areas (bbox=c(-67.87,12.79,-57.08,23.32)) head(areas) ``` ``` ## Latitude Longitude ## 1251 18.24829 -66.49989 ## 1255 18.33884 -65.82572 ## 1268 18.06667 -63.06667 ## 1339 13.16667 -59.53333 ```