remove all hyperlinked urls from fxn documentation

R/apg.R

@@ -4,7 +4,7 @@
 #' Group III system of flowering plant classification.
 #'
 #' @param ... Curl args passed on to [crul::verb-GET]
-#' @references <http://www.mobot.org/MOBOT/research/APweb/>
+#' @references http://www.mobot.org/MOBOT/research/APweb/
 #' @name apg
 #' @examples \dontrun{
 #' head(apgOrders())

R/apg_lookup.R

@@ -10,7 +10,7 @@
 #' @details Internally in this function, we use the datasets [apg_families]
 #' and [apg_orders] - see their descriptions for the data in them.
 #' The functions [apgOrders()] [apgFamilies()] are for scraping
-#' current content from the <http://www.mobot.org/MOBOT/research/APweb/>
+#' current content from the http://www.mobot.org/MOBOT/research/APweb/
 #' website
 #'
 #' The datasets used in this function are from the most recent version of

R/bold_search.R

@@ -38,7 +38,7 @@
 #' * thirdparty Returns information from third parties. Includes wikipedia
 #' summary, wikipedia URL, GBIF map.
 #'
-#' @references <http://www.boldsystems.org/index.php/resources/api>
+#' @references http://www.boldsystems.org/index.php/resources/api
 #' @return A list of data.frame's.
 #' @examples \dontrun{
 #' # A basic example

R/eubon.R

@@ -45,7 +45,7 @@
 #' affects the search mode `scientificNameLike` and `vernacularNameLike`; other
 #' search modes are expected to return only one record per check list
 #' @param ... Curl options passed on to [crul::verb-GET]
-#' @references <https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html>
+#' @references https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
 #' @family eubon-methods
 #' @examples \dontrun{
 #' eubon_search("Prionus")

R/eubon_capabilities.R

@@ -2,7 +2,7 @@
 #'
 #' @export
 #' @param ... Curl options passed on to [crul::verb-GET]
-#' @references <https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html>
+#' @references https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
 #' @family eubon-methods
 #' @examples \dontrun{
 #' eubon_capabilities()

R/eubon_children.R

@@ -16,7 +16,7 @@
 #' return the responses that have been received so far. The default timeout is
 #' 0 ms (wait for ever)
 #' @param ... Curl options passed on to [crul::verb-GET]
-#' @references <https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html>
+#' @references https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
 #' @return a data.frame or an empty list if no results found
 #' @note There is no pagination in this method, so you may or may not be
 #' getting all the results for a search. Sorry, out of our control

R/eubon_hierarchy.R

@@ -16,7 +16,7 @@
 #' return the responses that have been received so far. The default timeout is
 #' 0 ms (wait for ever)
 #' @param ... Curl options passed on to [crul::verb-GET]
-#' @references <https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html>
+#' @references https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
 #' @note There is no pagination in this method, so you may or may not be
 #' getting all the results for a search. Sorry, out of our control
 #' @family eubon-methods

R/gbif_name_usage.R

@@ -25,7 +25,7 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @param limit Number of records to return
 #' @param start Record number to start at
-#' @references <https://www.gbif.org/developer/summary>
+#' @references https://www.gbif.org/developer/summary
 #' @return A list of length two. The first element is metadata. The second is
 #' either a data.frame (verbose=FALSE, default) or a list (verbose=TRUE)
 

R/genbank2uid.R

@@ -5,7 +5,7 @@
 #' @param batch_size The number of queries to submit at a time.
 #' @param key (character) NCBI Entrez API key. optional. See Details.
 #' @param ... Curl args passed on to [crul::HttpClient]
-#' @details See <https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html> for
+#' @details See https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html for
 #' help on why there are two identifiers, and the difference between them.
 #' 
 #' @section Authentication:

R/get_nbnid.R

@@ -25,7 +25,7 @@
 #' used in [as.nbnid()]
 #' @template getreturn
 #'
-#' @references <https://api.nbnatlas.org/>
+#' @references https://api.nbnatlas.org/
 #' @return an object of class nbnid, a light wrapper around a character
 #' string that is the taxonomic ID - includes attributes with relavant
 #' metadata

R/gn_parse.R

@@ -6,7 +6,7 @@
 #' @return A data.frame with results, the submitted names, and the
 #' parsed names with additional information.
 #' @seealso [gbif_parse()], [gni_parse()]
-#' @references <http://gni.globalnames.org/>
+#' @references http://gni.globalnames.org/
 #' @examples \dontrun{
 #' gn_parse("Cyanistes caeruleus")
 #' gn_parse("Plantago minor")

R/gni_parse.R

@@ -6,7 +6,7 @@
 #' @return A data.frame with results, the submitted names, and the
 #' parsed names with additional information.
 #' @seealso [gbif_parse()], [gn_parse()]
-#' @references <http://gni.globalnames.org/>
+#' @references http://gni.globalnames.org/
 #' @examples \dontrun{
 #' gni_parse("Cyanistes caeruleus")
 #' gni_parse("Plantago minor")

R/gni_search.R

@@ -34,8 +34,8 @@
 #' @return data.frame of results.
 #' @seealso [gnr_datasources()], [gni_search()]
 #' @keywords globalnamesindex names taxonomy
-#' @references <http://gni.globalnames.org/>,
-#' <https://github.com/dimus/gni/wiki/api>
+#' @references http://gni.globalnames.org/
+#' https://github.com/dimus/gni/wiki/api
 #' @details Note that you can use fuzzy searching, e.g., by attaching an
 #' asterisk to the end of a search term. See the first two examples below
 #' @examples \dontrun{

R/gnr_datasources.R

@@ -8,7 +8,7 @@
 #' @return data.frame/tibble
 #' @seealso [gnr_resolve()], [gni_search()]
 #' @keywords resolve names taxonomy
-#' @references <https://resolver.globalnames.org/data_sources>
+#' @references https://resolver.globalnames.org/data_sources
 #' @examples \dontrun{
 #' # all data sources
 #' gnr_datasources()

R/gnr_resolve.R

@@ -90,8 +90,8 @@
 #'
 #' @seealso [gnr_datasources()] [tnrs]
 #' @keywords resolve names taxonomy
-#' @references <http://gnrd.globalnames.org/api>
-#' <http://gnrd.globalnames.org/>
+#' @references http://gnrd.globalnames.org/api
+#' http://gnrd.globalnames.org/
 #' @examples \dontrun{
 #' gnr_resolve(sci = c("Helianthus annuus", "Homo sapiens"))
 #' gnr_resolve(sci = c("Asteraceae", "Plantae"))

R/ion.R

@@ -3,7 +3,7 @@
 #' @export
 #' @param x An LSID number. Required.
 #' @param ... Curl options passed on to [crul::verb-GET]
-#' @references <http://www.organismnames.com>
+#' @references http://www.organismnames.com
 #' @return A data.frame
 #' @examples \dontrun{
 #' ion(155166)

R/iucn_summary.R

@@ -49,7 +49,7 @@
 #' @section Redlist Authentication:
 #' `iucn_summary` uses the new Redlist API for searching for a IUCN ID, so we
 #' use the [rl_search()] function internally. This function
-#' requires an API key. Get the key at <https://apiv3.iucnredlist.org/api/v3/token>,
+#' requires an API key. Get the key at https://apiv3.iucnredlist.org/api/v3/token,
 #' and pass it to the `key` parameter, or store in your `.Renviron` file like
 #' `IUCN_REDLIST_KEY=yourkey` or in your `.Rprofile` file like
 #' `options(iucn_redlist_key="yourkey")`. We strongly encourage you to not pass

R/nbn_classification.R

@@ -7,7 +7,7 @@
 #' @return A data.frame
 #' @family nbn
 #' @author Scott Chamberlain, \email{myrmecocystus@@gmail.com}
-#' @references <https://api.nbnatlas.org/>
+#' @references https://api.nbnatlas.org/
 #' @examples \dontrun{
 #' nbn_classification(id="NHMSYS0000376773")
 #'

R/nbn_search.R

@@ -4,7 +4,7 @@
 #' @param sci_com (character) The query terms(s), a scientific or common name
 #' @param fq (character) Filters to be applied to the original query. These
 #' are additional params of the form fq=INDEXEDFIELD:VALUE e.g.
-#' fq=rank:kingdom. See <https://species-ws.nbnatlas.org/indexFields> for all
+#' fq=rank:kingdom. See https://species-ws.nbnatlas.org/indexFields for all
 #' the fields that are queryable.
 #' @param rows (integer) Number of records to return
 #' @param start (integer) Record offset, to enable paging
@@ -18,7 +18,7 @@
 #' @return a list with slots for metadata (`meta`) with list of response
 #' attributes, and data (`data`) with a data.frame of results
 #' @author Scott Chamberlain, \email{myrmecocystus@@gmail.com}
-#' @references <https://api.nbnatlas.org/>
+#' @references https://api.nbnatlas.org/
 #'
 #' @examples \dontrun{
 #' x <- nbn_search(sci_com = "Vulpes")

R/nbn_synonyms.R

@@ -5,7 +5,7 @@
 #' @param ... Further args passed on to [crul::verb-GET]
 #' @return A data.frame
 #' @family nbn
-#' @references <https://api.nbnatlas.org/>
+#' @references https://api.nbnatlas.org/
 #' @examples \dontrun{
 #' nbn_synonyms(id = 'NHMSYS0001501147')
 #' nbn_synonyms(id = 'NHMSYS0000456036')

R/pow_search.R

@@ -11,7 +11,7 @@
 #' @return a list with slots for metadata (`meta`) with list of response
 #' attributes, and data (`data`) with a data.frame of results
 #' @author Scott Chamberlain, \email{myrmecocystus@@gmail.com}
-#' @references <http://powo.science.kew.org/>
+#' @references http://powo.science.kew.org/
 #' @family pow
 #' @examples \dontrun{
 #' x <- pow_search(sci_com = "Quercus")

R/scrapenames.r

@@ -1,7 +1,7 @@
 #' @title Resolve names using Global Names Recognition and Discovery.
 #'
 #' @description Uses the Global Names Recognition and Discovery service, see
-#' <http://gnrd.globalnames.org/>.
+#' http://gnrd.globalnames.org/
 #'
 #' Note: this function sometimes gives data back and sometimes not. The API
 #' that this function is extremely buggy.
@@ -26,7 +26,7 @@
 #' against all available Data Sources.
 #' @param data_source_ids (optional) Type: string. Pipe separated list of
 #' data source ids to resolve found names against. See list of Data Sources
-#' <http://resolver.globalnames.org/data_sources>.
+#' http://resolver.globalnames.org/data_sources
 #' @param return_content (logical) return OCR'ed text. returns text
 #' string in `x$meta$content` slot. Default: `FALSE`
 #' @param ... Further args passed to [crul::verb-GET]

R/taxize-authentication.R

@@ -48,7 +48,7 @@
 #' or environment variables.
 #'
 #' We strongly recommend using environment variables
-#' (<https://en.wikipedia.org/wiki/Environment_variable>) over R options
+#' (https://en.wikipedia.org/wiki/Environment_variable) over R options
 #' because environment variables are widely used across programming
 #' languages, operating systems, and computing environments; whereas
 #' R options are specific to R.

R/taxize-package.R

@@ -50,7 +50,7 @@
 #'
 #' If the source above has a `TRUE` in the `SOAP?` column, it is not available
 #' in this package. They are available from a different package called **taxizesoap**.
-#' See the GitHub repo for how to install <https://github.com/ropensci/taxizesoap>
+#' See the GitHub repo for how to install https://github.com/ropensci/taxizesoap
 #' 
 #' @section Catalogue of Life (COL):
 #' COL introduced rate limiting recently in 2019 - which has made the API
@@ -136,7 +136,7 @@ NULL
 #'   * `genus` genus name
 #'   * `species` specific epithet name
 #' 
-#' @source <http://www.theplantlist.org>
+#' @source http://www.theplantlist.org
 #' @name theplantlist
 #' @docType data
 #' @keywords data
@@ -165,7 +165,7 @@ NULL
 #' are accepted from `family` column, with the new name from `synonym`
 #' if applicable
 #' 
-#' @source <http://www.mobot.org/MOBOT/research/APweb/>
+#' @source http://www.mobot.org/MOBOT/research/APweb/
 #' @name apg_families
 #' @docType data
 #' @keywords data
@@ -193,7 +193,7 @@ NULL
 #' are accepted from `order` column, with the new name from `synonym`
 #' if applicable
 #' 
-#' @source <http://www.mobot.org/MOBOT/research/APweb/>
+#' @source http://www.mobot.org/MOBOT/research/APweb/
 #' @name apg_orders
 #' @docType data
 #' @keywords data

R/tol_resolve.R

@@ -27,7 +27,7 @@
 #' Scott Chamberlain \email{myrmecocystus@@gmail.com}
 #' @seealso [gnr_resolve()], [tnrs()]
 #' @references
-#' <https://github.com/OpenTreeOfLife/germinator/wiki/TNRS-API-v3#match_names>
+#' https://github.com/OpenTreeOfLife/germinator/wiki/TNRS-API-v3#match_names
 #' @keywords resolve names taxonomy
 #' @examples \dontrun{
 #' tol_resolve(names=c("echinodermata", "xenacoelomorpha",

R/tp_dist.R

@@ -6,7 +6,7 @@
 #' for help on authentication
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @return List of two data.frame's, one named "location", and one "reference".
-#' @references <http://services.tropicos.org/help?method=GetNameDistributionsXml>
+#' @references http://services.tropicos.org/help?method=GetNameDistributionsXml
 #'
 #' @examples \dontrun{
 #' # Query using a taxon name Id

R/tp_search.R

@@ -16,7 +16,7 @@
 #' @param commonname Deprecated, see `com`
 #' @param ... Further args passed on to [crul::HttpClient]
 #' @return List or dataframe.
-#' @references <http://services.tropicos.org/help?method=SearchNameXml>
+#' @references http://services.tropicos.org/help?method=SearchNameXml
 #' @details More details on the `name` parameter: Tropicos will fail
 #' if you include a period (`.`) in your name string, e.g., `var.`,
 #' so we replace periods before the request is made to the Tropicos web service.

R/tpl_get.r

@@ -12,7 +12,7 @@
 #' Writes csv files to x.
 #' @author John Baumgartner \email{johnbb@@student.unimelb.edu.au}
 #' @seealso [tpl_families()]
-#' @references The Plant List <http://www.theplantlist.org>
+#' @references The Plant List http://www.theplantlist.org
 #' @examples \dontrun{
 #' # Get a few families
 #' dir <- file.path(tempdir(), "abc")

R/vascan_search.r

@@ -9,7 +9,7 @@
 #' @param ... (list) Further args passed on to [crul::verb-GET]
 #' @author Scott Chamberlain {myrmecocystus@@gmail.com}
 #' @return json, xml or a list.
-#' @references API docs <https://data.canadensys.net/vascan/api>
+#' @references API docs https://data.canadensys.net/vascan/api
 #' @keywords names taxonomy
 #' @details Note that we lowercase all outputs in data.frame's, but when a
 #' list is given back, we don't touch the list names.