| Encoding: | UTF-8 |
| Language: | en-US |
| Type: | Package |
| Title: | Interface to Global Biotic Interactions |
| Description: | A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI) (https://www.globalbioticinteractions.org/). GloBI provides access to spatial-temporal species interaction records from sources all over the world. rglobi provides methods to search species interactions by location, interaction type, and taxonomic name. |
| Version: | 0.3.4 |
| Date: | 2023-10-06 |
| URL: | https://docs.ropensci.org/rglobi/, https://github.com/ropensci/rglobi |
| BugReports: | https://github.com/ropensci/rglobi/issues |
| VignetteBuilder: | knitr |
| Depends: | R (≥ 3.0.1) |
| License: | MIT + file LICENSE |
| Imports: | readr (≥ 1.3.1), RCurl (≥ 0.3.4), curl (≥ 0.3.3) |
| Suggests: | testthat(≥ 0.7), openssl, httr, markdown, knitr |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Packaged: | 2023-10-06 13:56:19 UTC; jorrit |
| Author: | Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey Slyusarev [aut], Helen Waters [aut] |
| Maintainer: | Jorrit Poelen <jhpoelen@jhpoelen.nl> |
| Repository: | CRAN |
| Date/Publication: | 2023-10-06 15:40:08 UTC |
List data fields identified in GloBI database
Description
Returns data frame with supported data fields
Usage
get_data_fields(opts = list(), read_csv = read_csv_online)
Arguments
opts |
list of named options to configure GloBI API |
read_csv |
function used to find csv associated to query url, defaulting to online query method |
Value
Returns data frame of supported data fields
Examples
get_data_fields()
Find locations at which interactions were observed
Description
Returns all locations (latitude,longitude) of interactions in data base or area specified in arguments
Usage
get_interaction_areas(bbox = NULL, read_csv = read_csv_online, ...)
Arguments
bbox |
Coordinates in EPSG:4326 decimal degrees defining "left, bottom, right, top" of bounding box |
read_csv |
function used to find csv associated to query url, defaulting to online query method |
... |
list of named options to configure GloBI API |
Value
Returns data frame of coordinates
See Also
Other areas:
get_interactions_in_area()
Examples
get_interaction_areas ()
get_interaction_areas (bbox=c(-67.87,12.79,-57.08,23.32))
Get Interaction Matrix. Constructs an interaction matrix indicating whether source taxa (rows) or target taxa (columns) are known to interact with given type.
Description
Get Interaction Matrix. Constructs an interaction matrix indicating whether source taxa (rows) or target taxa (columns) are known to interact with given type.
Usage
get_interaction_matrix(
source.taxon.names = list("Homo sapiens"),
target.taxon.names = list("Mammalia"),
interaction.type = "eats",
opts = list(),
read_csv = read_csv_online
)
Arguments
source.taxon.names |
list of source taxon names (e.g. list('Mammalia', 'Aves', 'Ariopsis felis')) |
target.taxon.names |
list of target taxon names |
interaction.type |
the preferred interaction type (e.g. preysOn) |
opts |
list of options to configure GloBI API |
read_csv |
function used to find csv associated to query url, defaulting to online query method |
Value
matrix representing species interactions between source and target taxa
See Also
Other interactions:
get_interaction_types(),
get_interactions_by_taxa(),
get_interactions_by_type(),
get_interactions(),
get_predators_of(),
get_prey_of()
Examples
get_interaction_matrix("Homo sapiens", "Mammalia", "interactsWith")
List interactions identified in GloBI database
Description
Returns data frame with supported interaction types
Usage
get_interaction_types(opts = list(), read_csv = read_csv_online)
Arguments
opts |
list of named options to configure GloBI API |
read_csv |
function used to find csv associated to query url, defaulting to online query method |
Value
Returns data frame of supported interaction types
See Also
Other interactions:
get_interaction_matrix(),
get_interactions_by_taxa(),
get_interactions_by_type(),
get_interactions(),
get_predators_of(),
get_prey_of()
Examples
get_interaction_types()
Get Species Interaction from GloBI
Description
Get Species Interaction from GloBI
Usage
get_interactions(taxon = "Homo sapiens", interaction.type = "preysOn", ...)
Arguments
taxon |
canonical scientific name of source taxon (e.g. Homo sapiens) |
interaction.type |
the preferred interaction type (e.g. preysOn) |
... |
list of options to configure GloBI API |
Value
species interactions between source and target taxa
See Also
Other interactions:
get_interaction_matrix(),
get_interaction_types(),
get_interactions_by_taxa(),
get_interactions_by_type(),
get_predators_of(),
get_prey_of()
Examples
get_interactions("Homo sapiens", "preysOn")
get_interactions("Insecta", "parasiteOf")
Return interactions involving specific taxa
Description
Returns interactions involving specific taxa. Secondary (target) taxa and spatial boundaries may also be set
Usage
get_interactions_by_taxa(
sourcetaxon,
targettaxon = NULL,
interactiontype = NULL,
accordingto = NULL,
showfield = c("source_taxon_external_id", "source_taxon_name", "source_taxon_path",
"source_specimen_life_stage", "interaction_type", "target_taxon_external_id",
"target_taxon_name", "target_taxon_path", "target_specimen_life_stage", "latitude",
"longitude", "study_citation", "study_external_id", "study_source_citation"),
otherkeys = NULL,
bbox = NULL,
returnobservations = FALSE,
opts = list(),
read_csv = read_csv_online
)
Arguments
sourcetaxon |
Taxa of interest (consumer, predator, parasite); may be specified as "Genus species" or higher level (e.g., Genus, Family, Class). |
targettaxon |
Taxa of interest (prey, host); may be specified as "Genus species" or higher level (e.g., Genus, Family, Class) |
interactiontype |
Interaction types of interest (prey, host); may be specified as listed by get_interaction_types() |
accordingto |
Data source of interest |
showfield |
Data fields of interest (e. g. source_taxon_external_id, source_taxon_name); may be specified as listed by get_data_fields() |
otherkeys |
list of key-value pairs to query any field not covered by other parameters; keys may be specified as listed by get_data_fields() |
bbox |
Coordinates in EPSG:4326 decimal degrees defining "left, bottom, right, top" of bounding box |
returnobservations |
if true, all individual observations are returned, else only distinct relationships |
opts |
list of named options to configure GloBI API |
read_csv |
function used to find csv associated to query url, defaulting to online query method |
Value
Returns data frame of interactions
Note
For data sources in which type of interactions were not specified, the interaction is labeled "interacts_with"
See Also
Other interactions:
get_interaction_matrix(),
get_interaction_types(),
get_interactions_by_type(),
get_interactions(),
get_predators_of(),
get_prey_of()
Examples
get_interactions_by_taxa(sourcetaxon = "Rattus")
get_interactions_by_taxa(sourcetaxon = "Aves", targettaxon = "Rattus")
get_interactions_by_taxa(sourcetaxon = "Rattus rattus",
bbox = c(-67.87,12.79,-57.08,23.32))
Get Species Interactions by Interaction Type from GloBI
Description
Get Species Interactions by Interaction Type from GloBI
Usage
get_interactions_by_type(interactiontype = c("interactsWith"), ...)
Arguments
interactiontype |
the requested interaction type (e.g. preysOn) |
... |
list of options to configure GloBI API |
Value
species interactions given provided interaction type(s)
See Also
Other interactions:
get_interaction_matrix(),
get_interaction_types(),
get_interactions_by_taxa(),
get_interactions(),
get_predators_of(),
get_prey_of()
Examples
get_interactions_by_type(interactiontype = c("eats", "eatenBy"))
get_interactions_by_type(interactiontype = "parasiteOf")
Return all interactions in specified area
Description
Returns all interactions in data base in area specified in arguments
Usage
get_interactions_in_area(bbox, ...)
Arguments
bbox |
Coordinates in EPSG:4326 decimal degrees defining "left, bottom, right, top" of bounding box |
... |
list of named options to configure GloBI API |
Value
Returns data frame of interactions
See Also
Other areas:
get_interaction_areas()
Examples
get_interactions_in_area(bbox = c(-67.87, 12.79, -57.08, 23.32))
Get a List of Predators of a Given Prey Taxon
Description
Get a List of Predators of a Given Prey Taxon
Usage
get_predators_of(taxon = "Rattus rattus", ...)
Arguments
taxon |
scientific name of prey taxon. Can be any taxonomic rank (e.g. Rattus rattus, Decapoda) |
... |
list of named options to configure the GloBI API |
Value
list of recorded prey-predator interactions that involve the desired prey taxon.
See Also
Other interactions:
get_interaction_matrix(),
get_interaction_types(),
get_interactions_by_taxa(),
get_interactions_by_type(),
get_interactions(),
get_prey_of()
Examples
get_predators_of("Rattus rattus")
get_predators_of("Primates")
Get a List of Prey for given Predator Taxon
Description
Get a List of Prey for given Predator Taxon
Usage
get_prey_of(taxon = "Homo sapiens", ...)
Arguments
taxon |
scientific name of predator taxon. Can be any taxonomic rank (e.g. Homo sapiens, Animalia) |
... |
list of named options to configure GloBI API |
Value
list of recorded predator-prey interactions that involve the desired predator taxon
See Also
Other interactions:
get_interaction_matrix(),
get_interaction_types(),
get_interactions_by_taxa(),
get_interactions_by_type(),
get_interactions(),
get_predators_of()
Examples
get_prey_of("Homo sapiens")
get_prey_of("Primates")