rglobi vignette - an R interface to the aggregated biotic interaction data of GloBI (<a href="https://www.globalbioticinteractions.org">https://www.globalbioticinteractions.org</a>)

# rglobi vignette - an R interface to the aggregated biotic interaction data of GloBI (https://www.globalbioticinteractions.org)

##

###

# 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`

    install.packages("devtools")

    ##
    ## The downloaded binary packages are in
    ## 	/var/folders/v4/0_y78_xj1x7b72l89cwc2kq80000gp/T//RtmpF6qc1T/downloaded_packages

    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

    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.

#### 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)).

    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

    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,

    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.

    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) and correspond to the west, south, east, and northern boundaries (i.e., min x, min y, max x, max y).

    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) and correspond to the west, south, east, and northern boundaries (i.e., min x, min y, max x, max y).

    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,

    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:

    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