Title: | 'NatureServe' Interface |
Description: | Interface to 'NatureServe' (https://www.natureserve.org/). Includes methods to get data, image metadata, search taxonomic names, and make maps. |
Version: | 1.0.0 |
License: | MIT + file LICENSE |
URL: | https://docs.ropensci.org/natserv, https://github.com/ropensci/natserv |
BugReports: | https://github.com/ropensci/natserv/issues |
LazyData: | true |
VignetteBuilder: | knitr |
Language: | en-US |
Encoding: | UTF-8 |
Depends: | R(≥ 3.2.1) |
Imports: | crul (≥ 0.7.0), jsonlite, tibble |
Suggests: | testthat, knitr, vcr |
RoxygenNote: | 7.1.0 |
X-schema.org-applicationCategory: | Taxonomy |
X-schema.org-keywords: | taxonomy, species, API, web-services, NatureServe, metadata, maps |
X-schema.org-isPartOf: | https://ropensci.org |
NeedsCompilation: | no |
Packaged: | 2020-05-15 21:02:58 UTC; sckott |
Author: | Scott Chamberlain |
Maintainer: | Scott Chamberlain <myrmecocystus@gmail.com> |
Repository: | CRAN |
Date/Publication: | 2020-05-16 22:30:07 UTC |
natserv
Description
Interface to NatureServe https://www.natureserve.org/
Author(s)
Scott Chamberlain myrmecocystus@gmail.com
A data.frame with 49 rows and 2 columns
Description
state (character) state 2 letter abbreviation
state_name (character) state full name
Get taxon by uid, id, or elCode
Description
Get taxon by uid, id, or elCode
Usage
ns_altid(uid = NULL, id = NULL, el_code = NULL, ...)
Arguments
uid |
(character) A NatureServe taxon id (The taxon’s Element Global UID) |
id |
The primary key value (ELEMENT_GLOBAL_ID) of the record within Central Biotics |
el_code |
The Biotics Element Code (ELCODE_BCD) of the record |
... |
Curl options passed on to |
Details
see https://explorer.natureserve.org/api-docs/#_taxon_data_model for details on the response data
Value
A list with lots of elements
References
https://explorer.natureserve.org/api-docs/
Examples
## Not run:
ns_altid(uid = "ELEMENT_GLOBAL.2.154701")
ns_altid(id = "154701")
ns_altid(el_code = "PDRAN0F010")
## End(Not run)
Get a summary of the upper level hierarchy for an Ecosystem record
Description
Get a summary of the upper level hierarchy for an Ecosystem record
Usage
ns_ecohier(uid, ...)
Arguments
uid |
(character) A NatureServe taxon id (The taxon’s Element Global UID) |
... |
Curl options passed on to |
Details
see https://explorer.natureserve.org/api-docs/#_taxon_data_model for details on the response data
Value
A list with lots of elements
References
https://explorer.natureserve.org/api-docs/
Examples
## Not run:
ns_ecohier("ELEMENT_GLOBAL.2.683060")
## End(Not run)
Search exports
Description
Search exports
Usage
ns_export(
text = NULL,
text_adv = NULL,
status = NULL,
location = NULL,
record_type = NULL,
record_subtype = NULL,
modified_since = NULL,
format = "json",
lang = "en",
...
)
ns_export_status(id, ...)
Arguments
text |
(character) basic text search, equiavalent to |
text_adv |
(list) advanced search, must specify the following three
elements: |
status |
(character) conservation status, one of G1, G2, G3, G4, G5, GH, GX, GNR, GNA, GU. case insensitive |
location |
(list) location, country and sub-country. specify either
|
record_type |
(character) limit results by record type, one of "species" or "ecosystem" |
record_subtype |
(character) limit results by record sub-type, one of: "class", "subclass", "formation", "division", "macrogroup", "group", "alliance", "association", "terrestrial_ecological_system" |
modified_since |
(character) search for records modified since a given time. value must be a date and time with a UTC offset in ISO 8601 format. optional |
format |
(character) output format, one of "json" or "xlsx" |
lang |
(character) language, one of "en", "es", or "fr" |
... |
Curl options passed on to |
id |
(character) a job id, from output of |
Value
ns_export()
returns a single character string (a job id)
ns_export_status()
returns a list of metadata concerning the
status of the export
References
https://explorer.natureserve.org/api-docs/
Examples
## Not run:
x <- ns_export(text = "robin")
res <- ns_export_status(x)
str(res)
res$state
res$data$errorMessage
res$data$url
w <- ns_export(text_adv = list(searchToken = "western",
matchAgainst="allScientificNames", operator="startsWith"))
m <- ns_export_status(w)
head(jsonlite::fromJSON(m$data$url))
## End(Not run)
Get taxon by uid
Description
Get taxon by uid
Usage
ns_id(uid, ...)
Arguments
uid |
(character) A NatureServe taxon id (The taxon’s Element Global UID). required. |
... |
Curl options passed on to |
Details
see https://explorer.natureserve.org/api-docs/#_taxon_data_model for details on the response data
Value
A list with lots of elements
References
https://explorer.natureserve.org/api-docs/
Examples
## Not run:
ns_id("ELEMENT_GLOBAL.2.154701")
## End(Not run)
Combined search
Description
Combined search
Usage
ns_search_comb(
text = NULL,
text_adv = NULL,
status = NULL,
location = NULL,
record_type = NULL,
record_subtype = NULL,
modified_since = NULL,
page = NULL,
per_page = NULL,
...
)
Arguments
text |
(character) basic text search, equiavalent to |
text_adv |
(list) advanced search, must specify the following three
elements: |
status |
(character) conservation status, one of G1, G2, G3, G4, G5, GH, GX, GNR, GNA, GU. case insensitive |
location |
(list) location, country and sub-country. specify either
|
record_type |
(character) limit results by record type, one of "species" or "ecosystem" |
record_subtype |
(character) limit results by record sub-type, one of: "class", "subclass", "formation", "division", "macrogroup", "group", "alliance", "association", "terrestrial_ecological_system" |
modified_since |
(character) search for records modified since a given time. value must be a date and time with a UTC offset in ISO 8601 format. optional |
page |
(integer) Zero-indexed page number; default: 0. optional |
per_page |
(integer) Records per page; default: 20. optional |
... |
Curl options passed on to |
References
https://explorer.natureserve.org/api-docs/
See Also
Other search:
ns_search_eco()
,
ns_search_spp()
Examples
## Not run:
ns_search_comb(text = "robin")
ns_search_comb(text_adv = list(searchToken = "western",
matchAgainst="allScientificNames", operator="startsWith"))
ns_search_comb(status = "G1")
ns_search_comb(location = list(nation = "US"))
ns_search_comb(location = list(nation = "US", subnation = "VA"))
ns_search_comb(record_type = "species")
ns_search_comb(record_subtype = "macrogroup")
ns_search_comb(modified_since = "2020-04-30T00:00:00+0000")
ns_search_comb(page = 0, per_page = 2)
## End(Not run)
Ecosystem search
Description
Ecosystem search
Usage
ns_search_eco(
text = NULL,
text_adv = NULL,
status = NULL,
location = NULL,
ecosystem_taxonomy = NULL,
record_subtype = NULL,
modified_since = NULL,
page = NULL,
per_page = NULL,
...
)
Arguments
text |
(character) basic text search, equiavalent to |
text_adv |
(list) advanced search, must specify the following three
elements: |
status |
(character) conservation status, one of G1, G2, G3, G4, G5, GH, GX, GNR, GNA, GU. case insensitive |
location |
(list) location, country and sub-country. specify either
|
ecosystem_taxonomy |
(character) the classification code of the higher level (ancestor) ecosystem. E.g.'s: "1" (Class code), "1.B" (Subclass code), "1.B.2" (Formation code), "1.B.2.Nd" (Division code), "M886" (Macrogroup key), "G206" (Group key), "A3328" (Alliance Key) |
record_subtype |
(character) limit results by record sub-type, one of: "class", "subclass", "formation", "division", "macrogroup", "group", "alliance", "association", "terrestrial_ecological_system" |
modified_since |
(character) search for records modified since a given time. value must be a date and time with a UTC offset in ISO 8601 format. optional |
page |
(integer) Zero-indexed page number; default: 0. optional |
per_page |
(integer) Records per page; default: 20. optional |
... |
Curl options passed on to |
References
https://explorer.natureserve.org/api-docs/
See Also
Other search:
ns_search_comb()
,
ns_search_spp()
Examples
## Not run:
ns_search_eco(text = "robin")
ns_search_eco(text_adv = list(searchToken = "bird",
matchAgainst = "allNames", operator="similarTo"))
ns_search_eco(status = "G1")
ns_search_eco(location = list(nation = "US"))
ns_search_eco(location = list(nation = "US", subnation = "VA"))
ns_search_eco(ecosystem_taxonomy = "M067")
ns_search_eco(record_subtype = "macrogroup")
ns_search_eco(modified_since = "2020-04-30T00:00:00+0000")
ns_search_eco(page = 0, per_page = 2)
## End(Not run)
Species search
Description
Species search
Usage
ns_search_spp(
text = NULL,
text_adv = NULL,
status = NULL,
location = NULL,
species_taxonomy = NULL,
record_subtype = NULL,
modified_since = NULL,
page = NULL,
per_page = NULL,
...
)
Arguments
text |
(character) basic text search, equiavalent to |
text_adv |
(list) advanced search, must specify the following three
elements: |
status |
(character) conservation status, one of G1, G2, G3, G4, G5, GH, GX, GNR, GNA, GU. case insensitive |
location |
(list) location, country and sub-country. specify either
|
species_taxonomy |
(list) species taxonomy. either a list with
|
record_subtype |
(character) limit results by record sub-type, one of: "class", "subclass", "formation", "division", "macrogroup", "group", "alliance", "association", "terrestrial_ecological_system" |
modified_since |
(character) search for records modified since a given time. value must be a date and time with a UTC offset in ISO 8601 format. optional |
page |
(integer) Zero-indexed page number; default: 0. optional |
per_page |
(integer) Records per page; default: 20. optional |
... |
Curl options passed on to |
References
https://explorer.natureserve.org/api-docs/
See Also
Other search:
ns_search_comb()
,
ns_search_eco()
Examples
## Not run:
ns_search_spp(text = "robin")
ns_search_spp(text_adv = list(searchToken = "bird",
matchAgainst = "allNames", operator="similarTo"))
ns_search_spp(status = "G1")
ns_search_spp(location = list(nation = "US"))
ns_search_spp(location = list(nation = "US", subnation = "VA"))
ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Animalia", level = "kingdom"))
ns_search_spp(species_taxonomy = list(informalTaxonomy = "birds"))
ns_search_spp(record_subtype = "macrogroup")
ns_search_spp(modified_since = "2020-04-30T00:00:00+0000")
ns_search_spp(page = 0, per_page = 2)
## End(Not run)