rredlist/0000755000175100001440000000000013000457275012123 5ustar hornikusersrredlist/tests/0000755000175100001440000000000012576160216013270 5ustar hornikusersrredlist/tests/testthat/0000755000175100001440000000000012651736665015143 5ustar hornikusersrredlist/tests/testthat/test-rl_common_names.R0000644000175100001440000000200112651614665021377 0ustar hornikuserscontext("rl_common_names functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_common_names('Loxodonta africana') expect_is(aa, "list") expect_is(aa$name, "character") expect_is(aa$result, "data.frame") expect_true(any(grepl("elephant", aa$result$taxonname, ignore.case = TRUE))) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_common_names('Loxodonta africana', parse = FALSE) expect_is(aa, "list") expect_is(aa$name, "character") expect_is(aa$result, "list") expect_true(any(grepl("elephant", vapply(aa$result, "[[", "", "taxonname"), ignore.case = TRUE))) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_common_names_('Loxodonta africana') expect_is(aa, "character") expect_is(jsonlite::fromJSON(aa), "list") }) test_that("no results", { skip_on_cran() aa <- rl_common_names('Loxodonta asdfadf') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/testthat/test-rl_narrative.R0000644000175100001440000000216112651735044020721 0ustar hornikuserscontext("rl_narrative functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_narrative('Fratercula arctica') expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "data.frame") expect_named(aa$result[,1:3], c("species_id", "taxonomicnotes", "rationale")) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_narrative('Fratercula arctica', parse = FALSE) expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "list") expect_named(aa$result[[1]][1:3], c("species_id", "taxonomicnotes", "rationale")) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_narrative_('Fratercula arctica') aajson <- jsonlite::fromJSON(aa) expect_is(aa, "character") expect_is(aajson, "list") expect_named(aajson, c("name", "result")) }) test_that("no results", { skip_on_cran() aa <- rl_narrative('Loxodonta asdfadf') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/testthat/test-rl_threats.R0000644000175100001440000000210312651736356020403 0ustar hornikuserscontext("rl_threats functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_threats('Fratercula arctica') expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "data.frame") expect_named(aa$result[,1:3], c("code", "title", "timing")) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_threats('Fratercula arctica', parse = FALSE) expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "list") expect_named(aa$result[[1]][1:3], c("code", "title", "timing")) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_threats_('Fratercula arctica') aajson <- jsonlite::fromJSON(aa) expect_is(aa, "character") expect_is(aajson, "list") expect_named(aajson, c("name", "result")) }) test_that("no results", { skip_on_cran() aa <- rl_threats('Loxodonta asdfadf') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/testthat/test-rl_measures.R0000644000175100001440000000205112651734633020553 0ustar hornikuserscontext("rl_measures functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_measures('Fratercula arctica') expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "data.frame") expect_named(aa$result, c("code", "title")) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_measures('Fratercula arctica', parse = FALSE) expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "list") expect_named(aa$result[[1]], c("code", "title")) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_measures_('Fratercula arctica') aajson <- jsonlite::fromJSON(aa) expect_is(aa, "character") expect_is(aajson, "list") expect_named(aajson, c("name", "result")) }) test_that("no results", { skip_on_cran() aa <- rl_measures('Loxodonta asdfadf') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/testthat/test-rl_sp_category.R0000644000175100001440000000247012651750450021246 0ustar hornikuserscontext("rl_sp_category functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_sp_category('VU') expect_is(aa, "list") expect_named(aa, c("count", "category", "result")) expect_is(aa$count, "integer") expect_is(aa$category, "character") expect_equal(aa$category, "VU") expect_is(aa$result, "data.frame") expect_named(aa$result, c('taxonid', 'scientific_name', 'subspecies', 'rank', 'subpopulation')) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_sp_category('VU', parse = FALSE) expect_is(aa, "list") expect_named(aa, c("count", "category", "result")) expect_is(aa$count, "integer") expect_is(aa$category, "character") expect_equal(aa$category, "VU") expect_is(aa$result, "list") expect_named(aa$result[[1]], c('taxonid', 'scientific_name', 'subspecies', 'rank', 'subpopulation')) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_sp_category_('VU') aajson <- jsonlite::fromJSON(aa) expect_is(aa, "character") expect_is(aajson, "list") expect_named(aajson, c("count", "category", "result")) }) test_that("no results", { skip_on_cran() aa <- rl_sp_category('asdfad') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/testthat/test-fail-well.R0000644000175100001440000000221612654220430020075 0ustar hornikuserscontext("package fails well") test_that("fails well on bad key", { skip_on_cran() expect_error(rl_common_names('Loxodonta africana', key = "adfds"), "Token not valid") expect_error(rl_common_names_('Loxodonta africana', key = "adfds"), "Token not valid") }) test_that("fails well when correct parameters not given", { skip_on_cran() expect_error(rl_search(), "is not TRUE") expect_error(rl_search_(), "is not TRUE") }) test_that("fails well when an invalid region passed", { skip_on_cran() # results in an `error` slot, which we catch expect_error(rl_habitats(id = 22694927, region = 34234), "Region not found.") expect_error(rl_habitats_(id = 22694927, region = 34234), "Region not found.") expect_error(rl_search(id = 22694927, region = '3wer'), "Region not found.") expect_error(rl_search_(id = 22694927, region = '3wer'), "Region not found.") expect_error(rl_measures(id = 22694927, region = '3wer'), "Region not found.") expect_error(rl_measures_(id = 22694927, region = '3wer'), "Region not found.") }) rredlist/tests/testthat/test-rl_habitat.R0000644000175100001440000000216512651734464020353 0ustar hornikuserscontext("rl_habitats functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_habitats('Fratercula arctica') expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "data.frame") expect_true(any(grepl("breeding", aa$result$season, ignore.case = TRUE))) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_habitats('Fratercula arctica', parse = FALSE) expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "list") expect_true(any(grepl("breeding", vapply(aa$result, "[[", "", "season"), ignore.case = TRUE))) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_habitats_('Fratercula arctica') aajson <- jsonlite::fromJSON(aa) expect_is(aa, "character") expect_is(aajson, "list") expect_named(aajson, c("name", "result")) }) test_that("no results", { skip_on_cran() aa <- rl_habitats('Loxodonta asdfadf') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/testthat/test-rl_synonyms.R0000644000175100001440000000242412651736631020632 0ustar hornikuserscontext("rl_synonyms functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_synonyms('Loxodonta africana') expect_is(aa, "list") expect_named(aa, c("name", "count", "result")) expect_is(aa$name, "character") expect_is(aa$count, "integer") expect_is(aa$result, "data.frame") expect_named(aa$result, c('accepted_id', 'accepted_name', 'authority', 'synonym', 'syn_authority')) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_synonyms('Loxodonta africana', parse = FALSE) expect_is(aa, "list") expect_named(aa, c("name", "count", "result")) expect_is(aa$name, "character") expect_is(aa$count, "integer") expect_is(aa$result, "list") expect_named(aa$result[[1]], c('accepted_id', 'accepted_name', 'authority', 'synonym', 'syn_authority')) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_synonyms_('Loxodonta africana') aajson <- jsonlite::fromJSON(aa) expect_is(aa, "character") expect_is(aajson, "list") expect_named(aajson, c("name", "count", "result")) }) test_that("no results", { skip_on_cran() aa <- rl_synonyms('Loxodonta asdfadf') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/testthat/test-rl_search.R0000644000175100001440000000217312651733475020204 0ustar hornikuserscontext("rl_search functions") test_that("high level works - parsing", { skip_on_cran() aa <- rl_search('Fratercula arctica') expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "data.frame") expect_true(any(grepl("arctica", aa$result$scientific_name, ignore.case = TRUE))) }) test_that("high level works - not parsing", { skip_on_cran() aa <- rl_search('Fratercula arctica', parse = FALSE) expect_is(aa, "list") expect_named(aa, c("name", "result")) expect_is(aa$name, "character") expect_is(aa$result, "list") expect_true(any(grepl("arctica", vapply(aa$result, "[[", "", "scientific_name"), ignore.case = TRUE))) }) test_that("low level works", { skip_on_cran() library("jsonlite") aa <- rl_search_('Fratercula arctica') aajson <- jsonlite::fromJSON(aa) expect_is(aa, "character") expect_is(aajson, "list") expect_named(aajson, c("name", "result")) }) test_that("no results", { skip_on_cran() aa <- rl_search('Loxodonta asdfadf') expect_is(aa, "list") expect_is(aa$result, "list") expect_equal(length(aa$result), 0) }) rredlist/tests/test-all.R0000644000175100001440000000005112651601267015134 0ustar hornikuserslibrary(testthat) test_check("rredlist") rredlist/NAMESPACE0000644000175100001440000000145713000214755013343 0ustar hornikusers# Generated by roxygen2: do not edit by hand export(rl_citation) export(rl_common_names) export(rl_common_names_) export(rl_countries) export(rl_countries_) export(rl_habitats) export(rl_habitats_) export(rl_history) export(rl_history_) export(rl_measures) export(rl_measures_) export(rl_narrative) export(rl_narrative_) export(rl_regions) export(rl_regions_) export(rl_search) export(rl_search_) export(rl_sp) export(rl_sp_) export(rl_sp_category) export(rl_sp_category_) export(rl_sp_citation) export(rl_sp_citation_) export(rl_sp_count) export(rl_sp_count_) export(rl_sp_country) export(rl_sp_country_) export(rl_synonyms) export(rl_synonyms_) export(rl_threats) export(rl_threats_) export(rl_version) importFrom(httr,GET) importFrom(httr,content) importFrom(httr,stop_for_status) importFrom(jsonlite,fromJSON) rredlist/NEWS.md0000644000175100001440000000115513000221161013202 0ustar hornikusersrredlist 0.2.0 ============== ### NEW FEATURES * New methods added to get historical assessments: `rl_history()` and `rl_history_()` (#8) ### MINOR IMPROVEMENTS * Fixed description of what `rl_common_names` does. In addition, clarified descriptino of what other functions do as well, whenever it was unclear (#12) ### BUG FIXES * Some API tokens were being blocked, fixed now (#7) * On some operating systems (at least some versions of Windows), queries that included taxonomic names weren't being processed correctly. It is fixed now (#11) rredlist 0.1.0 ============== ### NEW FEATURES * Released to CRAN. rredlist/R/0000755000175100001440000000000013000224422012306 5ustar hornikusersrredlist/R/rl_search.R0000644000175100001440000000207513000213153014376 0ustar hornikusers#' Search by taxon name, IUCN id, and region #' #' @export #' @template commonargs #' @template all #' @template info #' @examples \dontrun{ #' rl_search('Fratercula arctica') #' rl_search('Fratercula arctica', region = 'europe') #' rl_search(id = 12392) #' rl_search(id = 22694927, region = 'europe') #' #' rl_search('Fratercula arctica', parse = FALSE) #' rl_search_('Fratercula arctica') #' rl_search_('Fratercula arctica', region = 'europe') #' } rl_search <- function(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_search_(name, id, region, key, ...), parse) } #' @export #' @rdname rl_search rl_search_ <- function(name = NULL, id = NULL, region = NULL, key = NULL, ...) { rr_GET(.search(name, id, region), key, ...) } .search <- function(name = NULL, id = NULL, region = NULL) { stopifnot(xor(!is.null(name), !is.null(id))) path <- if (!is.null(name)) { file.path("species", space(name)) } else { file.path("species/id", id) } if (!is.null(region)) { path <- file.path(path, "region", space(region)) } path } rredlist/R/rl_synonyms.R0000644000175100001440000000111013000213266015022 0ustar hornikusers#' Get species synonym information by taxonomic name #' #' @export #' @param name (character) Binomial taxonomic name #' @template all #' @template info #' @examples \dontrun{ #' rl_synonyms('Loxodonta africana') #' rl_synonyms('Loxodonta africana', parse = FALSE) #' rl_synonyms_('Loxodonta africana') #' } rl_synonyms <- function(name = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_synonyms_(name, key, ...), parse) } #' @export #' @rdname rl_synonyms rl_synonyms_ <- function(name = NULL, key = NULL, ...) { rr_GET(file.path("species/synonym", space(name)), key, ...) } rredlist/R/rl_threats.R0000644000175100001440000000177613000213167014617 0ustar hornikusers#' Get species threats by taxon name, IUCN id, and region #' #' @export #' @template commonargs #' @template all #' @template info #' @examples \dontrun{ #' rl_threats('Fratercula arctica') #' rl_threats('Fratercula arctica', region = 'europe') #' rl_threats(id = 12392) #' rl_threats(id = 22694927, region = 'europe') #' rl_threats_('Fratercula arctica') #' } rl_threats <- function(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_threats_(name, id, region, key, ...), parse) } #' @export #' @rdname rl_threats rl_threats_ <- function(name = NULL, id = NULL, region = NULL, key = NULL, ...) { rr_GET(.threats(name, id, region), key, ...) } .threats <- function(name = NULL, id = NULL, region = NULL) { stopifnot(xor(!is.null(name), !is.null(id))) path <- if (!is.null(name)) { file.path("threats/species/name", space(name)) } else { file.path("threats/species/id", id) } if (!is.null(region)) { path <- file.path(path, "region", space(region)) } path } rredlist/R/rl_version.R0000644000175100001440000000050312677562706014646 0ustar hornikusers#' Get the Red List API version #' #' @export #' @param key A IUCN API token #' @param ... Curl options passed to \code{\link[httr]{GET}} #' @return API version as character string #' @examples \dontrun{ #' rl_version() #' } rl_version <- function(key = NULL, ...) { rl_parse(rr_GET("version", key, ...), TRUE)$version } rredlist/R/rl_sp_count.R0000644000175100001440000000057413000213330014762 0ustar hornikusers#' Get total species count of taxa in the Red List #' #' @export #' @template all #' @template info #' @examples \dontrun{ #' rl_sp_count() #' rl_sp_count_() #' } rl_sp_count <- function(key = NULL, parse = TRUE, ...) { rl_parse(rl_sp_count_(key, ...), parse) } #' @export #' @rdname rl_sp_count rl_sp_count_ <- function(key = NULL, ...) { rr_GET("speciescount", key, ...) } rredlist/R/rl_countries.R0000644000175100001440000000054012651554273015165 0ustar hornikusers#' Get countries #' #' @export #' @template all #' @template info #' @examples \dontrun{ #' rl_countries() #' rl_countries_() #' } rl_countries <- function(key = NULL, parse = TRUE, ...) { rl_parse(rl_countries_(key, ...), parse) } #' @export #' @rdname rl_countries rl_countries_ <- function(key = NULL, ...) { rr_GET("country/list", key, ...) } rredlist/R/rl_sp_citation.R0000644000175100001440000000214713000213160015443 0ustar hornikusers#' Get citations by taxon name, IUCN id, and region #' #' @export #' @template commonargs #' @template all #' @template info #' @examples \dontrun{ #' rl_sp_citation('Balaena mysticetus') #' rl_sp_citation('Balaena mysticetus', region = 'europe') #' rl_sp_citation(id = 12392) #' #' rl_sp_citation(id = 2467, region = 'europe') #' rl_sp_citation(id = 2467, region = 'europe', parse = FALSE) #' rl_sp_citation_(id = 2467, region = 'europe') #' } rl_sp_citation <- function(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_sp_citation_(name, id, region, key, ...), parse) } #' @export #' @rdname rl_sp_citation rl_sp_citation_ <- function(name = NULL, id = NULL, region = NULL, key = NULL, ...) { rr_GET(.sp_citation(name, id, region), key, ...) } .sp_citation <- function(name = NULL, id = NULL, region = NULL) { stopifnot(xor(!is.null(name), !is.null(id))) path <- if (!is.null(name)) { file.path("species/citation", space(name)) } else { file.path("species/citation/id", id) } if (!is.null(region)) { path <- file.path(path, "region", space(region)) } path } rredlist/R/rredlist-package.R0000644000175100001440000000405113000214120015644 0ustar hornikusers#' rredlist - IUCN Red List Client #' #' @section Authentication: #' IUCN requires you to get your own API key, an alphanumeric string that you #' need to send in every request. Get it at #' \url{http://apiv3.iucnredlist.org/api/v3/token}. #' Keep this key private. You can pass the key in to each function via the #' \code{key} parameter, but it's better to store the key either as a #' environment variable (\code{IUCN_REDLIST_KEY}) or an R option #' (\code{iucn_redlist_key}) - we suggest using the former option. #' #' @section High vs. Low level package APIs: #' \strong{High level API} #' High level functions do the HTTP request and parse data to a data.frame for #' ease of downstream use. The high level functions have no underscore on #' the end of the function name, e.g., \code{\link{rl_search}} #' #' \strong{Low level API} #' The parsing to data.frame in the high level API does take extra time. #' The low level API only does the HTTP request, and gives back JSON without #' doing any more parsing. The low level functions DO have an underscore on #' the end of the function name, e.g., \code{\link{rl_search_}} #' #' @section No Spatial: #' This package does not include support for the spatial API, described at #' \url{http://apiv3.iucnredlist.org/spatial} #' #' @section Citing the Red List API: #' The citation is #' \code{IUCN 2015. IUCN Red List of Threatened Species. Version 2015-4 }. #' You can get this programatically via \code{\link{rl_citation}} #' #' @section Rate limiting: #' From the IUCN folks: Too many frequent calls, or too many calls per day #' might get your access blocked temporarily. If you're a heavy API user, the #' Red List Unit asked that you contact them, as there might be better options. #' They suggest a 2-second delay between your calls if you plan to make a #' lot of calls. #' #' @importFrom httr GET content stop_for_status #' @importFrom jsonlite fromJSON #' @name rredlist-package #' @aliases rredlist #' @docType package #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com} #' @keywords package NULL rredlist/R/rl_citation.R0000644000175100001440000000062712651747761015000 0ustar hornikusers#' Get the citation Red List API version #' #' @export #' @param key A IUCN API token #' @param ... Curl options passed to \code{\link[httr]{GET}} #' @return API citation as character string #' @examples \dontrun{ #' rl_citation() #' } rl_citation <- function(key = NULL, ...) { sprintf('IUCN 2015. IUCN Red List of Threatened Species. Version %s ', rl_version(key, ...)) } rredlist/R/rl_regions.R0000644000175100001440000000055612651554374014631 0ustar hornikusers#' Get regions #' #' @export #' @template all #' @template info #' @examples \dontrun{ #' rl_regions() #' rl_regions(parse = FALSE) #' rl_regions_() #' } rl_regions <- function(key = NULL, parse = TRUE, ...) { rl_parse(rl_regions_(key, ...), parse) } #' @export #' @rdname rl_regions rl_regions_ <- function(key = NULL, ...) { rr_GET("region/list", key, ...) } rredlist/R/rl_sp_country.R0000644000175100001440000000132412651554165015360 0ustar hornikusers#' Get species by country #' #' @export #' @param country (character) Country 2 letter character code #' @template all #' @template info #' @examples \dontrun{ #' rl_sp_country('AZ') #' rl_sp_country('NZ') #' #' # don't parse to data.frame, gives list #' rl_sp_country('NZ', parse = FALSE) #' # don't parse at all, get json back #' rl_sp_country_('NZ') #' #' # curl options #' library("httr") #' res <- rl_sp_country('NZ', config=verbose()) #' } rl_sp_country <- function(country, key = NULL, parse = TRUE, ...) { rl_parse(rl_sp_country_(country, key, ...), parse) } #' @export #' @rdname rl_sp_country rl_sp_country_ <- function(country, key = NULL, ...) { rr_GET(file.path("country/getspecies", country), key, ...) } rredlist/R/rl_habitats.R0000644000175100001440000000205313000213173014726 0ustar hornikusers#' Get species habitats by taxon name, IUCN id, and region #' #' @export #' @template commonargs #' @template all #' @template info #' @examples \dontrun{ #' rl_habitats('Fratercula arctica') #' rl_habitats('Fratercula arctica', region = 'europe') #' rl_habitats(id = 12392) #' rl_habitats(id = 22694927, region = 'europe') #' #' rl_habitats_('Fratercula arctica') #' rl_habitats_(id = 12392) #' } rl_habitats <- function(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_habitats_(name, id, region, key, ...), parse) } #' @export #' @rdname rl_habitats rl_habitats_ <- function(name = NULL, id = NULL, region = NULL, key = NULL, ...) { rr_GET(.habitats(name, id, region), key, ...) } .habitats <- function(name = NULL, id = NULL, region = NULL) { stopifnot(xor(!is.null(name), !is.null(id))) path <- if (!is.null(name)) { file.path("habitats/species/name", space(name)) } else { file.path("habitats/species/id", id) } if (!is.null(region)) { path <- file.path(path, "region", space(region)) } path } rredlist/R/rl_narrative.R0000644000175100001440000000213613000213204015117 0ustar hornikusers#' Get species narrative information by taxon name, IUCN id, and region #' #' @export #' @template commonargs #' @template all #' @template info #' @examples \dontrun{ #' rl_narrative('Fratercula arctica') #' rl_narrative('Fratercula arctica', region = 'europe') #' rl_narrative(id = 12392) #' rl_narrative(id = 22694927, region = 'europe') #' #' rl_narrative_('Fratercula arctica') #' rl_narrative_('Fratercula arctica', region = 'europe') #' } rl_narrative <- function(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_narrative_(name, id, region, key, ...), parse) } #' @export #' @rdname rl_narrative rl_narrative_ <- function(name = NULL, id = NULL, region = NULL, key = NULL, ...) { rr_GET(.narrative(name, id, region), key, ...) } .narrative <- function(name = NULL, id = NULL, region = NULL) { stopifnot(xor(!is.null(name), !is.null(id))) path <- if (!is.null(name)) { file.path("species/narrative", space(name)) } else { file.path("species/narrative/id", id) } if (!is.null(region)) { path <- file.path(path, "region", space(region)) } path } rredlist/R/rl_history.R0000644000175100001440000000203613000214712014631 0ustar hornikusers#' Get historical assessments by taxon name, IUCN id, and region #' #' @export #' @template commonargs #' @template all #' @template info #' @examples \dontrun{ #' rl_history('Loxodonta africana') #' rl_history('Ursus maritimus', region = 'europe') #' rl_history(id = 12392) #' rl_history(id = 22823, region = 'europe') #' #' rl_history_('Loxodonta africana') #' rl_history_(id = 12392) #' } rl_history <- function(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_history_(name, id, region, key, ...), parse) } #' @export #' @rdname rl_habitats rl_history_ <- function(name = NULL, id = NULL, region = NULL, key = NULL, ...) { rr_GET(.history(name, id, region), key, ...) } .history <- function(name = NULL, id = NULL, region = NULL) { stopifnot(xor(!is.null(name), !is.null(id))) path <- if (!is.null(name)) { file.path("species/history/name", space(name)) } else { file.path("species/history/id", id) } if (!is.null(region)) { path <- file.path(path, "region", space(region)) } path } rredlist/R/rl_common_names.R0000644000175100001440000000105313000213243015577 0ustar hornikusers#' Get common names for a given taxonomic name #' #' @export #' @param name (character) Binomial taxonomic name #' @template all #' @template info #' @examples \dontrun{ #' rl_common_names('Loxodonta africana') #' rl_common_names_('Loxodonta africana') #' } rl_common_names <- function(name = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_common_names_(name, key, ...), parse) } #' @export #' @rdname rl_common_names rl_common_names_ <- function(name = NULL, key = NULL, ...) { rr_GET(file.path("species/common_names", space(name)), key, ...) } rredlist/R/rl_measures.R0000644000175100001440000000211613000213200014742 0ustar hornikusers#' Get species conservation measures by taxon name, IUCN id, and region #' #' @export #' @template commonargs #' @template all #' @template info #' @examples \dontrun{ #' rl_measures('Fratercula arctica') #' rl_measures('Fratercula arctica', region = 'europe') #' rl_measures(id = 12392) #' rl_measures(id = 22694927, region = 'europe') #' #' rl_measures_('Fratercula arctica') #' rl_measures_(id = 22694927, region = 'europe') #' } rl_measures <- function(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) { rl_parse(rl_measures_(name, id, region, key, ...), parse) } #' @export #' @rdname rl_measures rl_measures_ <- function(name = NULL, id = NULL, region = NULL, key = NULL, ...) { rr_GET(.measures(name, id, region), key, ...) } .measures <- function(name = NULL, id = NULL, region = NULL) { stopifnot(xor(!is.null(name), !is.null(id))) path <- if (!is.null(name)) { file.path("measures/species/name", space(name)) } else { file.path("measures/species/id", id) } if (!is.null(region)) { path <- file.path(path, "region", space(region)) } path } rredlist/R/rl_sp_category.R0000644000175100001440000000107612651554073015474 0ustar hornikusers#' Get species by category #' #' @export #' @param category (character) 2 letter category code #' @template all #' @examples \dontrun{ #' rl_sp_category('VU') #' rl_sp_category('EN') #' rl_sp_category('EX') #' rl_sp_category('EX', parse = FALSE) #' rl_sp_category_('EX') #' } rl_sp_category <- function(category, key = NULL, parse = TRUE, ...) { rl_parse(rl_sp_category_(category, key, ...), parse) } #' @export #' @rdname rl_sp_category rl_sp_category_ <- function(category, key = NULL, parse = TRUE, ...) { rr_GET(file.path("species/category", category), key, ...) } rredlist/R/rl_sp.R0000644000175100001440000000056312651752622013577 0ustar hornikusers#' Get species #' #' @export #' @param page (interger) Page to get. Default: 1 #' @template all #' @examples \dontrun{ #' rl_sp(page = 3) #' } rl_sp <- function(page, key = NULL, parse = TRUE, ...) { rl_parse(rl_sp_(page, key, ...), parse) } #' @export #' @rdname rl_sp rl_sp_ <- function(page, key = NULL, ...) { rr_GET(file.path("species/page", page), key, ...) } rredlist/R/zzz.R0000644000175100001440000000171513000210716013273 0ustar hornikusersct <- function(l) Filter(Negate(is.null), l) rr_GET <- function(path, key, ...){ temp <- GET(file.path(rr_base(), path), query = ct(list(token = check_key(key))), ...) stop_for_status(temp) stopifnot(temp$headers$`content-type` == 'application/json; charset=utf-8') err_catcher(temp) content(temp, as = 'text', encoding = "UTF-8") } err_catcher <- function(x) { xx <- jsonlite::fromJSON(content(x, as = 'text', encoding = "UTF-8")) if (any(vapply(c("message", "error"), function(z) z %in% names(xx), logical(1)))) { stop(xx[[1]], call. = FALSE) } } rl_parse <- function(x, parse) { jsonlite::fromJSON(x, parse) } check_key <- function(x){ tmp <- if (is.null(x)) Sys.getenv("IUCN_REDLIST_KEY", "") else x if (tmp == "") { getOption("iucn_redlist_key", stop("need an API key for Red List data", call. = FALSE)) } else { tmp } } rr_base <- function() "http://apiv3.iucnredlist.org/api/v3" space <- function(x) gsub("\\s", "%20", x) rredlist/README.md0000644000175100001440000001321412735237517013414 0ustar hornikusersrredlist ======== [![Build Status](https://travis-ci.org/ropenscilabs/rredlist.svg?branch=master)](https://travis-ci.org/ropenscilabs/rredlist) [![codecov.io](https://codecov.io/github/ropenscilabs/rredlist/coverage.svg?branch=master)](https://codecov.io/github/ropenscilabs/rredlist?branch=master) [![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/rredlist)](https://github.com/metacran/cranlogs.app) [![cran version](http://www.r-pkg.org/badges/version/rredlist)](https://cran.r-project.org/package=rredlist) [IUCN Red List docs][docs] ## Authentication IUCN requires you to get your own API key, an alphanumeric string that you need to send in every request. Get it at [http://apiv3.iucnredlist.org/api/v3/token][token]. Keep this key private. You can pass the key in to each function via the `key` parameter, but it's better to store the key either as a environment variable (`IUCN_REDLIST_KEY`) or an R option (`iucn_redlist_key`) - we suggest using the former option. ## High vs. Low level package APIs __High level API__ High level functions do the HTTP request and parse data to a data.frame for ease of downstream use. The high level functions have no underscore on the end of the function name, e.g., `rl_search` __Low level API__ The parsing to data.frame in the high level API does take extra time. The low level API only does the HTTP request, and gives back JSON without doing any more parsing. The low level functions DO have an underscore on the end of the function name, e.g., `rl_search_` ## No Spatial This package does not include support for the spatial API, described at [http://apiv3.iucnredlist.org/spatial][spatial]. ## Citing IUCN API use the function `rl_citation()` ```r rl_citation() #> [1] "IUCN 2015. IUCN Red List of Threatened Species. Version 2015-4 " ``` ## Install CRAN ```r install.packages("rredlist") ``` Development version ```r devtools::install_github("ropenscilabs/rredlist") ``` ```r library("rredlist") ``` ## High level API High level functions do the HTTP request and parse to data to a data.frame for ease of downstream use. ```r rl_search('Fratercula arctica') #> $name #> [1] "Fratercula arctica" #> #> $result #> taxonid scientific_name kingdom phylum class order #> 1 22694927 Fratercula arctica ANIMALIA CHORDATA AVES CHARADRIIFORMES #> family genus main_common_name authority published_year #> 1 ALCIDAE Fratercula Atlantic Puffin (Linnaeus, 1758) 2015 #> category criteria marine_system freshwater_system terrestrial_system #> 1 VU A4abcde TRUE FALSE TRUE #> assessor reviewer #> 1 BirdLife International Symes, A. ``` Likely a bit faster is to parse to a list only, and not take the extra data.frame parsing time ```r rl_search('Fratercula arctica', parse = FALSE) #> $name #> [1] "Fratercula arctica" #> #> $result #> $result[[1]] #> $result[[1]]$taxonid #> [1] 22694927 #> #> $result[[1]]$scientific_name #> [1] "Fratercula arctica" ... ``` ## Low level API The parsing to data.frame in the high level API does take extra time. The low level API only does the HTTP request, and gives back JSON without doing any more parsing ```r rl_search_('Fratercula arctica') #> [1] "{\"name\":\"Fratercula arctica\",\"result\":[{\"taxonid\":22694927,\"scientific_name\":\"Fratercula arctica\",\"kingdom\":\"ANIMALIA\",\"phylum\":\"CHORDATA\",\"class\":\"AVES\",\"order\":\"CHARADRIIFORMES\",\"family\":\"ALCIDAE\",\"genus\":\"Fratercula\",\"main_common_name\":\"Atlantic Puffin\",\"authority\":\"(Linnaeus, 1758)\",\"published_year\":2015,\"category\":\"VU\",\"criteria\":\"A4abcde\",\"marine_system\":true,\"freshwater_system\":false,\"terrestrial_system\":true,\"assessor\":\"BirdLife International\",\"reviewer\":\"Symes, A.\"}]}" ``` To consume this JSON, you can use `jsonlite` ```r library("jsonlite") jsonlite::fromJSON(rl_search_('Fratercula arctica')) #> $name #> [1] "Fratercula arctica" #> #> $result #> taxonid scientific_name kingdom phylum class order #> 1 22694927 Fratercula arctica ANIMALIA CHORDATA AVES CHARADRIIFORMES #> family genus main_common_name authority published_year #> 1 ALCIDAE Fratercula Atlantic Puffin (Linnaeus, 1758) 2015 #> category criteria marine_system freshwater_system terrestrial_system #> 1 VU A4abcde TRUE FALSE TRUE #> assessor reviewer #> 1 BirdLife International Symes, A. ``` Or other tools, e.g., `jq` via the `jqr` R client ```r # devtools::install_github("ropensci/jqr") library("jqr") rl_search_('Fratercula arctica') %>% dot() #> { #> "name": "Fratercula arctica", #> "result": [ #> { #> "taxonid": 22694927, #> "scientific_name": "Fratercula arctica", #> "kingdom": "ANIMALIA", #> "phylum": "CHORDATA", #> "class": "AVES", #> "order": "CHARADRIIFORMES", #> "family": "ALCIDAE", #> "genus": "Fratercula", #> "main_common_name": "Atlantic Puffin", #> "authority": "(Linnaeus, 1758)", #> "published_year": 2015, #> "category": "VU", #> "criteria": "A4abcde", #> "marine_system": true, #> "freshwater_system": false, #> "terrestrial_system": true, ... ``` ## Meta * Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms. 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The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required. Version: 0.2.0 Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com")) License: MIT + file LICENSE URL: https://github.com/ropenscilabs/rredlist BugReports: https://github.com/ropenscilabs/rredlist/issues Imports: httr (>= 1.2.0), jsonlite (>= 1.1) Suggests: roxygen2 (>= 5.0.1), testthat, covr RoxygenNote: 5.0.1 NeedsCompilation: no Packaged: 2016-10-14 18:50:58 UTC; sacmac Author: Scott Chamberlain [aut, cre] Maintainer: Scott Chamberlain Repository: CRAN Date/Publication: 2016-10-15 18:52:13 rredlist/man/0000755000175100001440000000000013000224422012660 5ustar hornikusersrredlist/man/rl_sp_count.Rd0000644000175100001440000000154213000213455015504 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_sp_count.R \name{rl_sp_count} \alias{rl_sp_count} \alias{rl_sp_count_} \title{Get total species count of taxa in the Red List} \usage{ rl_sp_count(key = NULL, parse = TRUE, ...) rl_sp_count_(key = NULL, ...) } \arguments{ \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get total species count of taxa in the Red List } \examples{ \dontrun{ rl_sp_count() rl_sp_count_() } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_history.Rd0000644000175100001440000000224613000214755015361 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_history.R \name{rl_history} \alias{rl_history} \title{Get historical assessments by taxon name, IUCN id, and region} \usage{ rl_history(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{id}{(character) IUCN id} \item{region}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get historical assessments by taxon name, IUCN id, and region } \examples{ \dontrun{ rl_history('Loxodonta africana') rl_history('Ursus maritimus', region = 'europe') rl_history(id = 12392) rl_history(id = 22823, region = 'europe') rl_history_('Loxodonta africana') rl_history_(id = 12392) } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_sp_citation.Rd0000644000175100001440000000247713000213455016176 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_sp_citation.R \name{rl_sp_citation} \alias{rl_sp_citation} \alias{rl_sp_citation_} \title{Get citations by taxon name, IUCN id, and region} \usage{ rl_sp_citation(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) rl_sp_citation_(name = NULL, id = NULL, region = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{id}{(character) IUCN id} \item{region}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get citations by taxon name, IUCN id, and region } \examples{ \dontrun{ rl_sp_citation('Balaena mysticetus') rl_sp_citation('Balaena mysticetus', region = 'europe') rl_sp_citation(id = 12392) rl_sp_citation(id = 2467, region = 'europe') rl_sp_citation(id = 2467, region = 'europe', parse = FALSE) rl_sp_citation_(id = 2467, region = 'europe') } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_search.Rd0000644000175100001440000000243513000213455015121 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_search.R \name{rl_search} \alias{rl_search} \alias{rl_search_} \title{Search by taxon name, IUCN id, and region} \usage{ rl_search(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) rl_search_(name = NULL, id = NULL, region = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{id}{(character) IUCN id} \item{region}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Search by taxon name, IUCN id, and region } \examples{ \dontrun{ rl_search('Fratercula arctica') rl_search('Fratercula arctica', region = 'europe') rl_search(id = 12392) rl_search(id = 22694927, region = 'europe') rl_search('Fratercula arctica', parse = FALSE) rl_search_('Fratercula arctica') rl_search_('Fratercula arctica', region = 'europe') } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rredlist-package.Rd0000644000175100001440000000403613000214241016371 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rredlist-package.R \docType{package} \name{rredlist-package} \alias{rredlist} \alias{rredlist-package} \title{rredlist - IUCN Red List Client} \description{ rredlist - IUCN Red List Client } \section{Authentication}{ IUCN requires you to get your own API key, an alphanumeric string that you need to send in every request. Get it at \url{http://apiv3.iucnredlist.org/api/v3/token}. Keep this key private. You can pass the key in to each function via the \code{key} parameter, but it's better to store the key either as a environment variable (\code{IUCN_REDLIST_KEY}) or an R option (\code{iucn_redlist_key}) - we suggest using the former option. } \section{High vs. Low level package APIs}{ \strong{High level API} High level functions do the HTTP request and parse data to a data.frame for ease of downstream use. The high level functions have no underscore on the end of the function name, e.g., \code{\link{rl_search}} \strong{Low level API} The parsing to data.frame in the high level API does take extra time. The low level API only does the HTTP request, and gives back JSON without doing any more parsing. The low level functions DO have an underscore on the end of the function name, e.g., \code{\link{rl_search_}} } \section{No Spatial}{ This package does not include support for the spatial API, described at \url{http://apiv3.iucnredlist.org/spatial} } \section{Citing the Red List API}{ The citation is \code{IUCN 2015. IUCN Red List of Threatened Species. Version 2015-4 }. You can get this programatically via \code{\link{rl_citation}} } \section{Rate limiting}{ From the IUCN folks: Too many frequent calls, or too many calls per day might get your access blocked temporarily. If you're a heavy API user, the Red List Unit asked that you contact them, as there might be better options. They suggest a 2-second delay between your calls if you plan to make a lot of calls. } \author{ Scott Chamberlain \email{myrmecocystus@gmail.com} } \keyword{package} rredlist/man/rl_synonyms.Rd0000644000175100001440000000201313000213455015543 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_synonyms.R \name{rl_synonyms} \alias{rl_synonyms} \alias{rl_synonyms_} \title{Get species synonym information by taxonomic name} \usage{ rl_synonyms(name = NULL, key = NULL, parse = TRUE, ...) rl_synonyms_(name = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get species synonym information by taxonomic name } \examples{ \dontrun{ rl_synonyms('Loxodonta africana') rl_synonyms('Loxodonta africana', parse = FALSE) rl_synonyms_('Loxodonta africana') } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_sp.Rd0000644000175100001440000000107112651752632014311 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_sp.R \name{rl_sp} \alias{rl_sp} \alias{rl_sp_} \title{Get species} \usage{ rl_sp(page, key = NULL, parse = TRUE, ...) rl_sp_(page, key = NULL, ...) } \arguments{ \item{page}{(interger) Page to get. Default: 1} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \description{ Get species } \examples{ \dontrun{ rl_sp(page = 3) } } rredlist/man/rl_narrative.Rd0000644000175100001440000000251013000213455015641 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_narrative.R \name{rl_narrative} \alias{rl_narrative} \alias{rl_narrative_} \title{Get species narrative information by taxon name, IUCN id, and region} \usage{ rl_narrative(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) rl_narrative_(name = NULL, id = NULL, region = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{id}{(character) IUCN id} \item{region}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get species narrative information by taxon name, IUCN id, and region } \examples{ \dontrun{ rl_narrative('Fratercula arctica') rl_narrative('Fratercula arctica', region = 'europe') rl_narrative(id = 12392) rl_narrative(id = 22694927, region = 'europe') rl_narrative_('Fratercula arctica') rl_narrative_('Fratercula arctica', region = 'europe') } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_measures.Rd0000644000175100001440000000246513000213455015503 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_measures.R \name{rl_measures} \alias{rl_measures} \alias{rl_measures_} \title{Get species conservation measures by taxon name, IUCN id, and region} \usage{ rl_measures(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) rl_measures_(name = NULL, id = NULL, region = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{id}{(character) IUCN id} \item{region}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get species conservation measures by taxon name, IUCN id, and region } \examples{ \dontrun{ rl_measures('Fratercula arctica') rl_measures('Fratercula arctica', region = 'europe') rl_measures(id = 12392) rl_measures(id = 22694927, region = 'europe') rl_measures_('Fratercula arctica') rl_measures_(id = 22694927, region = 'europe') } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_common_names.Rd0000644000175100001440000000175613000213455016334 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_common_names.R \name{rl_common_names} \alias{rl_common_names} \alias{rl_common_names_} \title{Get common names for a given taxonomic name} \usage{ rl_common_names(name = NULL, key = NULL, parse = TRUE, ...) rl_common_names_(name = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get common names for a given taxonomic name } \examples{ \dontrun{ rl_common_names('Loxodonta africana') rl_common_names_('Loxodonta africana') } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_habitats.Rd0000644000175100001440000000255613000214755015463 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_habitats.R, R/rl_history.R \name{rl_habitats} \alias{rl_habitats} \alias{rl_habitats_} \alias{rl_history_} \title{Get species habitats by taxon name, IUCN id, and region} \usage{ rl_habitats(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) rl_habitats_(name = NULL, id = NULL, region = NULL, key = NULL, ...) rl_history_(name = NULL, id = NULL, region = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{id}{(character) IUCN id} \item{region}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get species habitats by taxon name, IUCN id, and region } \examples{ \dontrun{ rl_habitats('Fratercula arctica') rl_habitats('Fratercula arctica', region = 'europe') rl_habitats(id = 12392) rl_habitats(id = 22694927, region = 'europe') rl_habitats_('Fratercula arctica') rl_habitats_(id = 12392) } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_countries.Rd0000644000175100001440000000144612651554417015711 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_countries.R \name{rl_countries} \alias{rl_countries} \alias{rl_countries_} \title{Get countries} \usage{ rl_countries(key = NULL, parse = TRUE, ...) rl_countries_(key = NULL, ...) } \arguments{ \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get countries } \examples{ \dontrun{ rl_countries() rl_countries_() } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_threats.Rd0000644000175100001440000000233613000213455015326 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_threats.R \name{rl_threats} \alias{rl_threats} \alias{rl_threats_} \title{Get species threats by taxon name, IUCN id, and region} \usage{ rl_threats(name = NULL, id = NULL, region = NULL, key = NULL, parse = TRUE, ...) rl_threats_(name = NULL, id = NULL, region = NULL, key = NULL, ...) } \arguments{ \item{name}{(character) Binomial taxonomic name} \item{id}{(character) IUCN id} \item{region}{(character) Binomial taxonomic name} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get species threats by taxon name, IUCN id, and region } \examples{ \dontrun{ rl_threats('Fratercula arctica') rl_threats('Fratercula arctica', region = 'europe') rl_threats(id = 12392) rl_threats(id = 22694927, region = 'europe') rl_threats_('Fratercula arctica') } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_citation.Rd0000644000175100001440000000071012651747766015514 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_citation.R \name{rl_citation} \alias{rl_citation} \title{Get the citation Red List API version} \usage{ rl_citation(key = NULL, ...) } \arguments{ \item{key}{A IUCN API token} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ API citation as character string } \description{ Get the citation Red List API version } \examples{ \dontrun{ rl_citation() } } rredlist/man/rl_regions.Rd0000644000175100001440000000145412650531023015326 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_regions.R \name{rl_regions} \alias{rl_regions} \alias{rl_regions_} \title{Get regions} \usage{ rl_regions(key = NULL, parse = TRUE, ...) rl_regions_(key = NULL, ...) } \arguments{ \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get regions } \examples{ \dontrun{ rl_regions() rl_regions(parse = FALSE) rl_regions_() } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/man/rl_sp_category.Rd0000644000175100001440000000141212650531023016171 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_sp_category.R \name{rl_sp_category} \alias{rl_sp_category} \alias{rl_sp_category_} \title{Get species by category} \usage{ rl_sp_category(category, key = NULL, parse = TRUE, ...) rl_sp_category_(category, key = NULL, parse = TRUE, ...) } \arguments{ \item{category}{(character) 2 letter category code} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \description{ Get species by category } \examples{ \dontrun{ rl_sp_category('VU') rl_sp_category('EN') rl_sp_category('EX') rl_sp_category('EX', parse = FALSE) rl_sp_category_('EX') } } rredlist/man/rl_version.Rd0000644000175100001440000000066012651747766015373 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_version.R \name{rl_version} \alias{rl_version} \title{Get the Red List API version} \usage{ rl_version(key = NULL, ...) } \arguments{ \item{key}{A IUCN API token} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ API version as character string } \description{ Get the Red List API version } \examples{ \dontrun{ rl_version() } } rredlist/man/rl_sp_country.Rd0000644000175100001440000000215012650531023016057 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rl_sp_country.R \name{rl_sp_country} \alias{rl_sp_country} \alias{rl_sp_country_} \title{Get species by country} \usage{ rl_sp_country(country, key = NULL, parse = TRUE, ...) rl_sp_country_(country, key = NULL, ...) } \arguments{ \item{country}{(character) Country 2 letter character code} \item{key}{A IUCN API token} \item{parse}{(logical) Whether to parse to list (\code{FALSE}) or data.frame (\code{TRUE}). Default: \code{TRUE}} \item{...}{Curl options passed to \code{\link[httr]{GET}}} } \value{ A list, with the data in the \code{result} slot, unless using a function with a trailing underscore, in which case json as character string is returned. } \description{ Get species by country } \examples{ \dontrun{ rl_sp_country('AZ') rl_sp_country('NZ') # don't parse to data.frame, gives list rl_sp_country('NZ', parse = FALSE) # don't parse at all, get json back rl_sp_country_('NZ') # curl options library("httr") res <- rl_sp_country('NZ', config=verbose()) } } \references{ API docs at \url{http://apiv3.iucnredlist.org/api/v3/docs} } rredlist/LICENSE0000644000175100001440000000005712651752252013136 0ustar hornikusersYEAR: 2016 COPYRIGHT HOLDER: Scott Chamberlain