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