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Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (https://obis.org).
Version: 2.11.3
Date: 2022-09-24
URL: https://github.com/iobis/robis
BugReports: https://github.com/iobis/robis/issues
Depends: R (≥ 3.1.3)
Imports: httr, dplyr, jsonlite, leaflet, ggplot2, tidyr, httpcache, tibble, mapedit, sf, rlang, purrr, stringr, curl, data.table, tidyselect, xml2, glue, memoise, stats, methods
Collate: robis.R util.R area.R checklist.R dataset.R dna.R map.R mof.R node.R occurrence.R taxon.R
License: MIT + file LICENSE
Suggests: testthat, knitr, rmarkdown, spelling
RoxygenNote: 7.2.1
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2022-09-24 17:15:18 UTC; pieter
Author: Pieter Provoost [cre, aut], Samuel Bosch [aut], Ward Appeltans [ctb], OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-24 17:30:02 UTC

Fetch a list of areas

Description

Fetch a list of areas

Usage

area(verbose = FALSE)

Arguments

verbose

logical. Optional parameter to enable verbose logging (default = FALSE).

Value

The areas.

Examples

areas <- area(verbose = FALSE)

Create a checklist.

Description

Create a checklist.

Usage

checklist(scientificname = NULL, taxonid = NULL, datasetid = NULL,
  nodeid = NULL, instituteid = NULL, areaid = NULL, startdate = NULL, enddate = NULL,
  startdepth = NULL, enddepth = NULL, geometry = NULL, redlist = NULL,
  hab = NULL, wrims = NULL, dropped = NULL, flags = NULL, exclude = NULL,
  verbose = FALSE)

Arguments

scientificname

the scientific name.

taxonid

the taxon identifier (WoRMS AphiaID).

datasetid

the dataset identifier.

nodeid

the OBIS node identifier.

instituteid

the OBIS institute identifier.

areaid

the OBIS area identifier.

startdate

the earliest date on which occurrence took place.

enddate

the latest date on which the occurrence took place.

startdepth

the minimum depth below the sea surface.

enddepth

the maximum depth below the sea surface.

geometry

a WKT geometry string.

redlist

include only IUCN Red List species.

hab

include only IOC-UNESCO HAB species.

wrims

include only WRiMS species.

dropped

only include dropped records (TRUE), exclude dropped records (NULL) or include dropped records (include).

flags

quality flags which need to be set.

exclude

quality flags to be excluded from the results.

verbose

logical. Optional parameter to enable verbose logging (default = FALSE).

Value

The checklist.

Examples

taxa <- checklist(scientificname = "Tellinidae")
taxa <- checklist(geometry = "POLYGON ((2.3 51.8, 2.3 51.6, 2.6 51.6, 2.6 51.8, 2.3 51.8))")
taxa <- checklist(areaid = 10181)

Create a list of datasets.

Description

Create a list of datasets.

Usage

dataset(scientificname = NULL, taxonid = NULL, datasetid = NULL,
  nodeid = NULL, instituteid = NULL, areaid = NULL, startdate = NULL,
  enddate = NULL, startdepth = NULL, enddepth = NULL, geometry = NULL,
  redlist = NULL, hab = NULL, wrims = NULL, hasextensions = NULL,
  exclude = NULL, verbose = FALSE)

Arguments

scientificname

the scientific name.

taxonid

the taxon identifier (WoRMS AphiaID).

datasetid

the dataset identifier.

nodeid

the OBIS node identifier.

instituteid

the OBIS institute identifier.

areaid

the OBIS area identifier.

startdate

the earliest date on which occurrence took place.

enddate

the latest date on which the occurrence took place.

startdepth

the minimum depth below the sea surface.

enddepth

the maximum depth below the sea surface.

geometry

a WKT geometry string.

redlist

include only IUCN Red List species.

hab

include only IOC-UNESCO HAB species.

wrims

include only WRiMS species.

hasextensions

which extensions need to be present (e.g. MeasurementOrFact, DNADerivedData, default = NULL).

exclude

quality flags to be excluded from the results.

verbose

logical. Optional parameter to enable verbose logging (default = FALSE).

Value

The datasets.

Examples

datasets <- dataset(scientificname = "Tellinidae")
datasets <- dataset(geometry = "POLYGON ((2.3 51.8, 2.3 51.6, 2.6 51.6, 2.6 51.8, 2.3 51.8))")
datasets <- dataset(areaid = 10181)

Extract DNA records from occurrence data with a dna column.

Description

Extract DNA records from occurrence data with a dna column.

Usage

dna_records(df, fields = "id")

Arguments

df

the occurrence dataframe.

fields

columns from the occurrence dataframe to include.

Value

The DNA records.

Generate a citation from metadata elements.

Description

Generate a citation from metadata elements.

Usage

generate_citation(title, published, url, contacts)

Arguments

title

the dataset title.

published

the dataset published date.

url

the dataset url.

contacts

the dataset contacts as a dataframe.

Value

A citation string.

Get a WKT geometry by drawing on a map.

Description

Get a WKT geometry by drawing on a map.

Usage

get_geometry(provider_tiles = "Esri.WorldGrayCanvas")

Arguments

provider_tiles

the base map provider.

Value

A WKT representation of a geometry.

Create a ggplot2 map.

Description

Create a ggplot2 map.

Usage

map_ggplot(data, color = "#ff3399")

Arguments

data

the occurrences from occurrence().

color

color to be used for the dots.

Value

A ggplot object.

Create a leaflet map.

Description

Create a leaflet map.

Usage

map_leaflet(data, color = "#ff3399",
  provider_tiles = "Esri.WorldGrayCanvas", popup = function(x) { x["id"] },
  antarctic = FALSE)

Arguments

data

the occurrences from occurrence().

color

color to be used for the dots.

provider_tiles

the base map provider.

popup

function generating the popup content.

antarctic

use antarctic polar stereographic projection.

Value

A leaflet object.

Extract measurements or facts from occurrence data with a mof column.

Description

Extract measurements or facts from occurrence data with a mof column.

Usage

measurements(df, fields = "id")

Arguments

df

the occurrence dataframe.

fields

columns from the occurrence dataframe to include.

Value

The measurements.

Fetch a list of nodes

Description

Fetch a list of nodes

Usage

node(verbose = FALSE)

Arguments

verbose

logical. Optional parameter to enable verbose logging (default = FALSE).

Value

The nodes

Examples

nodes <- node()

Find occurrences.

Description

Find occurrences.

Usage

occurrence(scientificname = NULL, taxonid = NULL, datasetid = NULL,
  nodeid = NULL, instituteid = NULL, areaid = NULL, startdate = NULL, enddate = NULL,
  startdepth = NULL, enddepth = NULL, geometry = NULL,
  measurementtype = NULL, measurementtypeid = NULL, measurementvalue = NULL,
  measurementvalueid = NULL, measurementunit = NULL, measurementunitid = NULL,
  redlist = NULL, hab = NULL, wrims = NULL, extensions = NULL, hasextensions = NULL,
  mof = NULL, dna = NULL, absence = NULL, event = NULL, dropped = NULL,
  flags = NULL, exclude = NULL, fields = NULL, qcfields = NULL, verbose = FALSE)

Arguments

scientificname

the scientific name.

taxonid

the taxon identifier (WoRMS AphiaID).

datasetid

the dataset identifier.

nodeid

the OBIS node identifier.

instituteid

the OBIS institute identifier.

areaid

the OBIS area identifier.

startdate

the earliest date on which occurrence took place.

enddate

the latest date on which the occurrence took place.

startdepth

the minimum depth below the sea surface.

enddepth

the maximum depth below the sea surface.

geometry

a WKT geometry string.

measurementtype

the measurement type to be included in the measurements data.

measurementtypeid

the measurement type ID to be included in the measurements data.

measurementvalue

the measurement value to be included in the measurements data.

measurementvalueid

the measurement value ID to be included in the measurements data.

measurementunit

the measurement unit to be included in the measurements data.

measurementunitid

the measurement unit ID to be included in the measurements data.

redlist

include only IUCN Red List species.

hab

include only IOC-UNESCO HAB species.

wrims

include only WRiMS species.

extensions

which extensions to include (e.g. MeasurementOrFact, DNADerivedData, default = NULL).

hasextensions

which extensions need to be present (e.g. MeasurementOrFact, DNADerivedData, default = NULL).

mof

include measurements data (default = NULL).

dna

include DNA data (default = NULL).

absence

only include absence records (TRUE), exclude absence records (NULL) or include absence records (include).

event

only include pure event records (TRUE), exclude pure event records (NULL) or include event records (include).

dropped

only include dropped records (TRUE), exclude dropped records (NULL) or include dropped records (include).

flags

quality flags which need to be set.

exclude

quality flags to be excluded from the results.

fields

fields to be included in the results.

qcfields

include lists of missing and invalid fields (default = NULL).

verbose

logical. Optional parameter to enable verbose logging (default = FALSE).

Value

The occurrence records.

Examples

records <- occurrence(scientificname = "Abra sibogai")
records <- occurrence(taxonid = 141438, startdate = as.Date("2007-10-10"))

R client for the OBIS API

Description

This is an R client for the Ocean Biodiversity Information System (OBIS) API which is documented at https://api.obis.org.

Code and issues for this package are managed at https://github.com/iobis/robis.

Author(s)

Pieter Provoost, p.provoost@unesco.org

Samuel Bosch

Get taxon by taxon ID.

Description

Get taxon by taxon ID.

Usage

taxon(taxonid, verbose = FALSE)

Arguments

taxonid

the taxon identifier (WoRMS AphiaID).

verbose

logical. Optional parameter to enable verbose logging (default = FALSE).

Value

Tibble containing taxon records.

Examples

taxon(c(141433, 141434))

Extract extension records from occurrence data with nested extension column.

Description

Extract extension records from occurrence data with nested extension column.

Usage

unnest_extension(df, extension, fields = "id")

Arguments

df

the occurrence dataframe.

extension

the extension type (e.g. 'MeasurementOrFact', 'DNADerivedData').

fields

columns from the occurrence dataframe to include.

Value

The extension records.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.