Title: | 'NatureServe' Interface |
---|---|
Description: | Interface to 'NatureServe' (<https://www.natureserve.org/>). Includes methods to get data, image metadata, search taxonomic names, and make maps. |
Authors: | Scott Chamberlain [aut] |
Maintainer: | Christopher Tracey <[email protected]> |
License: | MIT + file LICENSE |
Version: | 1.0.0.91 |
Built: | 2024-08-29 23:10:23 UTC |
Source: | https://github.com/ropensci/natserv |
Interface to NatureServe https://www.natureserve.org/
Scott Chamberlain [email protected]
state (character) state 2 letter abbreviation
state_name (character) state full name
Get taxon by uid, id, or elCode
ns_altid(uid = NULL, id = NULL, el_code = NULL, ...)
ns_altid(uid = NULL, id = NULL, el_code = NULL, ...)
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 |
see https://explorer.natureserve.org/api-docs/#_taxon_data_model for details on the response data
A list with lots of elements
https://explorer.natureserve.org/api-docs/
## Not run: ns_altid(uid = "ELEMENT_GLOBAL.2.154701") ns_altid(id = "154701") ns_altid(el_code = "PDRAN0F010") ## End(Not run)
## 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
ns_ecohier(uid, ...)
ns_ecohier(uid, ...)
uid |
(character) A NatureServe taxon id (The taxon’s Element Global UID) |
... |
Curl options passed on to |
see https://explorer.natureserve.org/api-docs/#_taxon_data_model for details on the response data
A list with lots of elements
https://explorer.natureserve.org/api-docs/
## Not run: ns_ecohier("ELEMENT_GLOBAL.2.683060") ## End(Not run)
## Not run: ns_ecohier("ELEMENT_GLOBAL.2.683060") ## End(Not run)
Search exports
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, ...)
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, ...)
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 |
ns_export()
returns a single character string (a job id)
ns_export_status()
returns a list of metadata concerning the
status of the export
https://explorer.natureserve.org/api-docs/
## 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$url)) ## End(Not run)
## Not run: x <- ns_export(text = "robin") res <- ns_export_status(x) str(res) res$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
ns_id(uid, ...)
ns_id(uid, ...)
uid |
(character) A NatureServe taxon id (The taxon’s Element Global UID). required. |
... |
Curl options passed on to |
see https://explorer.natureserve.org/api-docs/#_taxon_data_model for details on the response data
A list with lots of elements
https://explorer.natureserve.org/api-docs/
## Not run: ns_id("ELEMENT_GLOBAL.2.154701") ## End(Not run)
## Not run: ns_id("ELEMENT_GLOBAL.2.154701") ## End(Not run)
Combined search
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, ... )
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, ... )
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 |
https://explorer.natureserve.org/api-docs/
Other search:
ns_search_eco()
,
ns_search_spp()
## 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)
## 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
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, ... )
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, ... )
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 |
https://explorer.natureserve.org/api-docs/
Other search:
ns_search_comb()
,
ns_search_spp()
## 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)
## 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
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, ... )
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, ... )
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 |
https://explorer.natureserve.org/api-docs/
Other search:
ns_search_comb()
,
ns_search_eco()
## 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)
## 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)