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rglobi_vignette.Rmd
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rglobi_vignette.Rmd
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<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Introduction to the rglobi package}
-->
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
```