[med-svn] [r-cran-ritis] 02/06: New upstream version 0.6.0
Andreas Tille
tille at debian.org
Thu Nov 9 13:19:38 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-ritis.
commit 9ab15f8dad4b6b0b642933a631837cad94cd3cf9
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 2 12:40:45 2017 +0200
New upstream version 0.6.0
---
DESCRIPTION | 14 +--
LICENSE | 2 +-
MD5 | 200 ++++++++++++++++++-------------------
NEWS.md | 23 ++++-
R/accepted_names.R | 11 +-
R/any_match_count.R | 2 +-
R/comment_detail.R | 4 +-
R/common_names.R | 2 +-
R/core_metadata.R | 2 +-
R/coverage.R | 2 +-
R/credibility.R | 2 +-
R/currency.R | 2 +-
R/date_data.R | 2 +-
R/description.R | 4 +-
R/experts.R | 2 +-
R/full_record.R | 8 +-
R/geographic_divisions.R | 2 +-
R/geographic_values.R | 2 +-
R/global_species_completeness.R | 9 +-
R/hierarchy.R | 17 ++--
R/itis_facet.R | 2 +-
R/itis_group.R | 2 +-
R/itis_highlight.R | 2 +-
R/itis_search.R | 2 +-
R/jurisdiction.R | 5 +-
R/kingdoms.R | 2 +-
R/last_change_date.R | 2 +-
R/lsid2tsn.R | 2 +-
R/other_sources.R | 2 +-
R/parent_tsn.R | 2 +-
R/publications.R | 5 +-
R/rank_name.R | 2 +-
R/rank_names.R | 2 +-
R/record.R | 2 +-
R/review_year.R | 2 +-
R/scientific_name.R | 2 +-
R/search_any_match_paged.R | 2 +-
R/search_anymatch.R | 5 +-
R/search_common.R | 25 +++--
R/search_scientific.R | 2 +-
R/synonym_names.R | 2 +-
R/taxon_authorship.R | 2 +-
R/terms.R | 12 ++-
R/tsn2lsid.R | 2 +-
R/tsn_by_vernacular_language.R | 2 +-
R/unacceptability_reason.R | 2 +-
R/usage.R | 2 +-
R/vernacular_languages.R | 2 +-
R/zzz.R | 29 ++++--
build/vignette.rds | Bin 208 -> 208 bytes
man/accepted_names.Rd | 3 +-
man/any_match_count.Rd | 3 +-
man/comment_detail.Rd | 5 +-
man/common_names.Rd | 3 +-
man/core_metadata.Rd | 3 +-
man/coverage.Rd | 3 +-
man/credibility.Rd | 7 +-
man/currency.Rd | 3 +-
man/date_data.Rd | 3 +-
man/description.Rd | 3 +-
man/experts.Rd | 3 +-
man/full_record.Rd | 3 +-
man/geographic_divisions.Rd | 3 +-
man/geographic_values.Rd | 3 +-
man/global_species_completeness.Rd | 3 +-
man/hierarchy.Rd | 20 ++--
man/itis_facet.Rd | 1 -
man/itis_group.Rd | 1 -
man/itis_highlight.Rd | 1 -
man/itis_search.Rd | 1 -
man/jurisdiction.Rd | 17 ++--
man/kingdoms.Rd | 9 +-
man/last_change_date.Rd | 3 +-
man/lsid2tsn.Rd | 3 +-
man/other_sources.Rd | 3 +-
man/parent_tsn.Rd | 3 +-
man/publications.Rd | 6 +-
man/rank_name.Rd | 3 +-
man/rank_names.Rd | 13 ++-
man/record.Rd | 7 +-
man/review_year.Rd | 3 +-
man/ritis-package.Rd | 4 +-
man/scientific_name.Rd | 7 +-
man/search_any_match_paged.Rd | 3 +-
man/search_anymatch.Rd | 3 +-
man/search_common.Rd | 17 ++--
man/search_scientific.Rd | 3 +-
man/solr.Rd | 8 +-
man/synonym_names.Rd | 3 +-
man/taxon_authorship.Rd | 3 +-
man/terms.Rd | 7 +-
man/tsn2lsid.Rd | 3 +-
man/tsn_by_vernacular_language.Rd | 3 +-
man/unacceptability_reason.Rd | 3 +-
man/usage.Rd | 3 +-
man/vernacular_languages.Rd | 3 +-
tests/testthat/test-hierarchy.R | 16 +--
tests/testthat/test-itis_facet.R | 5 +-
tests/testthat/test-jurisdiction.R | 6 +-
tests/testthat/test-kingdoms.R | 6 +-
tests/testthat/test-publications.R | 6 +-
101 files changed, 344 insertions(+), 352 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 133d6dd..4d35906 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,22 +2,22 @@ Package: ritis
Title: Integrated Taxonomic Information System Client
Description: An interface to the Integrated Taxonomic Information System ('ITIS')
(<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST
- 'API' methods (<https://www.itis.gov/ws_description.html>), as well as the
+ API methods (<https://www.itis.gov/ws_description.html>), as well as the
'Solr' web service (<https://www.itis.gov/solr_documentation.html>).
-Version: 0.5.4
+Version: 0.6.0
License: MIT + file LICENSE
URL: https://github.com/ropensci/ritis
BugReports: https://github.com/ropensci/ritis/issues
Authors at R: c(person("Scott", "Chamberlain", role = c("aut", "cre"),
email = "myrmecocystus at gmail.com"))
VignetteBuilder: knitr
-Imports: solrium (>= 0.3.0), httr (>= 1.2.0), jsonlite (>= 0.9.22),
+Imports: solrium (>= 0.3.0), crul (>= 0.3.8), jsonlite (>= 0.9.22),
data.table (>= 1.9.6), tibble (>= 1.0)
-Suggests: roxygen2 (>= 5.0.1), testthat, knitr, covr
-RoxygenNote: 5.0.1
+Suggests: roxygen2 (>= 6.0.1), testthat, knitr
+RoxygenNote: 6.0.1
NeedsCompilation: no
-Packaged: 2016-10-12 18:17:40 UTC; sacmac
+Packaged: 2017-09-27 05:34:59 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus at gmail.com>
Repository: CRAN
-Date/Publication: 2016-10-13 00:02:09
+Date/Publication: 2017-09-27 20:35:53 UTC
diff --git a/LICENSE b/LICENSE
index d044f7e..37ee2c7 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2016
+YEAR: 2017
COPYRIGHT HOLDER: Scott Chamberlain
diff --git a/MD5 b/MD5
index 45194bf..fead52b 100644
--- a/MD5
+++ b/MD5
@@ -1,117 +1,117 @@
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+07c2b60c86cdbb7f07ae9ef0471c122d *man/search_common.Rd
+b9f2eb978b2ed794f4e4cfcb4ca10060 *man/search_scientific.Rd
+be22e8c42c7deaff439e663559f809e4 *man/solr.Rd
+f5adf95f0cef804e6d89644ca192c522 *man/synonym_names.Rd
+39bf9901a673fd9292cef751653d16c9 *man/taxon_authorship.Rd
+501020759b9f5f328c378e5e109e5b9d *man/terms.Rd
+1eed21e24b257a202ed106fc530b74ef *man/tsn2lsid.Rd
+f12a99b007e75c5937a676cc1983ef75 *man/tsn_by_vernacular_language.Rd
+b3e26d27add39358353fffa0a5ca8a74 *man/unacceptability_reason.Rd
+81d90c720d511de76e9afcb38ca8ad58 *man/usage.Rd
+f8a48aa42210f6e5ef37725e8b875ff1 *man/vernacular_languages.Rd
680535a7e7ba6856cc630af23d88f514 *tests/test-all.R
6de6bfda4529c5811788f56ef88d257b *tests/testthat/helper.R
16d6cb8e540be05d6dd4b9c38b1dc29c *tests/testthat/test-any_match_count.R
-4b547c91008c9efac895d337c3ff71a8 *tests/testthat/test-hierarchy.R
-b0561ba2ea6c83a65e524f3f78429d17 *tests/testthat/test-itis_facet.R
+fe3efb1dc47b16fcc31016d5fbbb899f *tests/testthat/test-hierarchy.R
+40830184ec4355aeba4c067f2af3ec86 *tests/testthat/test-itis_facet.R
8f0cc9f23a1b5d1d63e57c5b79102f19 *tests/testthat/test-itis_group.R
7b947d7b545d2ea498fe387b0fd8cfef *tests/testthat/test-itis_highlight.R
b8d1e69d7cf3eec4ffa405bb73f3773a *tests/testthat/test-itis_search.R
-0407e978bab82d55666645ede78576f7 *tests/testthat/test-jurisdiction.R
-baeaa8f253f86f82fece2028e4fe70f0 *tests/testthat/test-kingdoms.R
-1a57fe5de59133d0ef3961b3d7d5163b *tests/testthat/test-publications.R
+1f9a7d5cae81492d825c0b80407aafa4 *tests/testthat/test-jurisdiction.R
+6c7c1dc2a53bce55306459126d9236b4 *tests/testthat/test-kingdoms.R
+163f8698f56add6d111def5025c871da *tests/testthat/test-publications.R
fb9dc6f954548aecc6c83ee5d36249cd *tests/testthat/test-record.R
d79f700bcedff969a0ad09b8ad4c9771 *tests/testthat/test-search_common.R
b64e1e75d67150bc6c8790d4403821ed *tests/testthat/test-search_scientific.R
diff --git a/NEWS.md b/NEWS.md
index 096a670..c7a8325 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,18 @@
+ritis 0.6.0
+===========
+
+### NEW FEATURES
+
+* Now using `crul` as underlying HTTP client (#5)
+
+### BUG FIXES
+
+* Base URL change for Solr service from `http` to `https` (#8)
+* Fixed JSON parsing problem (#6)
+
+
ritis 0.5.4
-===============
+===========
### BUG FIXES
@@ -8,7 +21,7 @@ requests, but not others. Changed to `https` (#4)
ritis 0.5.0
-===============
+===========
### NEW FEATURES
@@ -20,7 +33,7 @@ interface via use of `solrium`
ritis 0.0.3
-===============
+===========
### BUG FIXES
@@ -28,7 +41,7 @@ ritis 0.0.3
ritis 0.0.2
-===============
+===========
### BUG FIXES
@@ -36,7 +49,7 @@ ritis 0.0.2
ritis 0.0.1
-===============
+===========
### NEW FEATURES
diff --git a/R/accepted_names.R b/R/accepted_names.R
index b62b26b..b78fe8f 100644
--- a/R/accepted_names.R
+++ b/R/accepted_names.R
@@ -1,7 +1,10 @@
#' Get accepted names from tsn
#'
#' @export
-#' @template common
+#' @param wt (character) One of "json" or "xml". Required.
+#' @param raw (logical) Return raw JSON or XML as character string. Required.
+#' Default: `FALSE`
+#' @param ... curl options passed on to [crul::HttpClient]
#' @template tsn
#' @return Zero row data.frame if the name is accepted, otherwise a data.frame
#' with information on the currently accepted name
@@ -19,5 +22,9 @@ accepted_names <- function(tsn, wt = "json", raw = FALSE, ...) {
out <- itis_GET("getAcceptedNamesFromTSN", list(tsn = tsn), wt, ...)
if (raw || wt == "xml") return(out)
tmp <- parse_raw(out)
- if (all(is.na(tmp$acceptedNames))) tibble::data_frame() else dr_op(tibble::as_data_frame(tmp$acceptedNames), "class")
+ if (all(is.na(tmp$acceptedNames))) {
+ tibble::data_frame()
+ } else {
+ dr_op(tibble::as_data_frame(tmp$acceptedNames), "class")
+ }
}
diff --git a/R/any_match_count.R b/R/any_match_count.R
index 8739db4..b19f20e 100644
--- a/R/any_match_count.R
+++ b/R/any_match_count.R
@@ -1,8 +1,8 @@
#' Get any match count.
#'
#' @export
-#' @template common
#' @param x text or taxonomic serial number (TSN) (character or numeric)
+#' @inheritParams accepted_names
#' @return An integer containing the number of matches the search will return.
#' @examples \dontrun{
#' any_match_count(x = 202385)
diff --git a/R/comment_detail.R b/R/comment_detail.R
index 49d82fe..4d81420 100644
--- a/R/comment_detail.R
+++ b/R/comment_detail.R
@@ -2,13 +2,11 @@
#'
#' @export
#' @template tsn
-#' @template common
+#' @inheritParams accepted_names
#' @return A data.frame with results.
#' @examples \dontrun{
#' comment_detail(tsn=180543)
#' comment_detail(tsn=180543, wt = "xml")
-#' library(httr)
-#' comment_detail(tsn=180543)
#' }
comment_detail <- function(tsn, wt = "json", raw = FALSE, ...) {
out <- itis_GET("getCommentDetailFromTSN", list(tsn = tsn), wt, ...)
diff --git a/R/common_names.R b/R/common_names.R
index 77178ca..4d034f5 100644
--- a/R/common_names.R
+++ b/R/common_names.R
@@ -1,8 +1,8 @@
#' Get common names from tsn
#'
#' @export
-#' @template common
#' @template tsn
+#' @inheritParams accepted_names
#' @return a data.frame
#' @examples \dontrun{
#' common_names(tsn=183833)
diff --git a/R/core_metadata.R b/R/core_metadata.R
index 5849eb7..649c507 100644
--- a/R/core_metadata.R
+++ b/R/core_metadata.R
@@ -1,8 +1,8 @@
#' Get core metadata from tsn
#'
#' @export
-#' @template common
#' @template tsn
+#' @inheritParams accepted_names
#' @examples \dontrun{
#' # coverage and currrency data
#' core_metadata(tsn=28727)
diff --git a/R/coverage.R b/R/coverage.R
index 097a375..b02b81a 100644
--- a/R/coverage.R
+++ b/R/coverage.R
@@ -1,8 +1,8 @@
#' Get coverge from tsn
#'
#' @export
-#' @template common
#' @template tsn
+#' @inheritParams accepted_names
#' @examples \dontrun{
#' # coverage data
#' coverage(tsn=28727)
diff --git a/R/credibility.R b/R/credibility.R
index 98d29f0..18affb5 100644
--- a/R/credibility.R
+++ b/R/credibility.R
@@ -2,8 +2,8 @@
#'
#' @export
#' @name credibility
-#' @template common
#' @template tsn
+#' @inheritParams accepted_names
#' @return a data.frame
#' @details methods:
#' \itemize{
diff --git a/R/currency.R b/R/currency.R
index 96cd2f4..37eb8fd 100644
--- a/R/currency.R
+++ b/R/currency.R
@@ -1,8 +1,8 @@
#' Get currency from tsn
#'
#' @export
-#' @template common
#' @template tsn
+#' @inheritParams accepted_names
#' @return a data.frame
#' @examples \dontrun{
#' # currency data
diff --git a/R/date_data.R b/R/date_data.R
index 0907e80..5678f0c 100644
--- a/R/date_data.R
+++ b/R/date_data.R
@@ -1,8 +1,8 @@
#' Get date data from tsn
#'
#' @export
-#' @template common
#' @template tsn
+#' @inheritParams accepted_names
#' @examples \dontrun{
#' date_data(tsn = 180543)
#' date_data(180543, wt = "xml")
diff --git a/R/description.R b/R/description.R
index 5452563..20ff0e4 100644
--- a/R/description.R
+++ b/R/description.R
@@ -1,13 +1,13 @@
#' Get description of the ITIS service
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @return a string, the ITIS web service description
#' @examples \dontrun{
#' description()
#' description(wt = "xml")
#' }
-description <- function(wt = "json", raw = FALSE, ...){
+description <- function(wt = "json", raw = FALSE, ...) {
out <- itis_GET("getDescription", list(), wt, ...)
if (raw || wt == "xml") return(out)
parse_raw(out)$description
diff --git a/R/experts.R b/R/experts.R
index da91111..4f631b3 100644
--- a/R/experts.R
+++ b/R/experts.R
@@ -1,7 +1,7 @@
#' Get expert information for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @examples \dontrun{
#' experts(tsn = 180544)
diff --git a/R/full_record.R b/R/full_record.R
index 30662ef..8ff7f49 100644
--- a/R/full_record.R
+++ b/R/full_record.R
@@ -16,8 +16,12 @@
#' full_record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
#' full_record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
#' }
-full_record <- function(tsn = NULL, lsid = NULL, wt = "json", raw = FALSE, ...) {
- if (!xor(is.null(tsn), is.null(lsid))) stop("Pass only one of `tsn` or `lsid`", call. = FALSE)
+full_record <- function(tsn = NULL, lsid = NULL, wt = "json", raw = FALSE,
+ ...) {
+
+ if (!xor(is.null(tsn), is.null(lsid))) {
+ stop("Pass only one of `tsn` or `lsid`", call. = FALSE)
+ }
if (!is.null(tsn)) {
verb <- "getFullRecordFromTSN"
args <- list(tsn = tsn)
diff --git a/R/geographic_divisions.R b/R/geographic_divisions.R
index 325dddf..4494aa2 100644
--- a/R/geographic_divisions.R
+++ b/R/geographic_divisions.R
@@ -1,8 +1,8 @@
#' Get geographic divisions from tsn
#'
#' @export
-#' @template common
#' @template tsn
+#' @inheritParams accepted_names
#' @examples \dontrun{
#' geographic_divisions(tsn = 180543)
#'
diff --git a/R/geographic_values.R b/R/geographic_values.R
index dd3031b..9ce115d 100644
--- a/R/geographic_values.R
+++ b/R/geographic_values.R
@@ -1,7 +1,7 @@
#' Get all possible geographic values
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @return character vector of geographic names
#' @examples \dontrun{
#' geographic_values()
diff --git a/R/global_species_completeness.R b/R/global_species_completeness.R
index acace69..609e3c5 100644
--- a/R/global_species_completeness.R
+++ b/R/global_species_completeness.R
@@ -1,15 +1,18 @@
#' Get global species completeness from tsn
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @examples \dontrun{
#' global_species_completeness(tsn = 180541)
#' global_species_completeness(180541, wt = "xml")
#' global_species_completeness(180541, wt = "json", raw = TRUE)
#' }
-global_species_completeness <- function(tsn, wt = "json", raw = FALSE, ...) {
- out <- itis_GET("getGlobalSpeciesCompletenessFromTSN", list(tsn = tsn), wt, ...)
+global_species_completeness <- function(tsn, wt = "json", raw = FALSE,
+ ...) {
+
+ out <- itis_GET("getGlobalSpeciesCompletenessFromTSN", list(tsn = tsn),
+ wt, ...)
if (raw || wt == "xml") return(out)
tibble::as_data_frame(
tc(pick_cols(parse_raw(out), c("completeness","rankId","tsn")))
diff --git a/R/hierarchy.R b/R/hierarchy.R
index dbf20ed..6288448 100644
--- a/R/hierarchy.R
+++ b/R/hierarchy.R
@@ -2,7 +2,7 @@
#'
#' @export
#' @name hierarchy
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @details Hierarchy methods:
#' \itemize{
@@ -11,22 +11,26 @@
#' \item hierarchy_full: Get full hierarchy from tsn
#' }
#' @examples \dontrun{
-#' ## Full down
-#' hierarchy_down(tsn=161030)
+#' ## Full down (class Mammalia)
+#' hierarchy_down(tsn=179913)
#'
-#' ## Full up
+#' ## Full up (genus Agoseris)
#' hierarchy_up(tsn=36485)
#'
#' ## Full hierarchy
+#' ### genus Liatris
#' hierarchy_full(tsn=37906)
+#' ### get raw data back
#' hierarchy_full(tsn=37906, raw = TRUE)
+#' ### genus Baetis, get xml back
#' hierarchy_full(100800, wt = "xml")
#' }
hierarchy_down <- function(tsn, wt = "json", raw = FALSE, ...) {
out <- itis_GET("getHierarchyDownFromTSN", list(tsn = tsn), wt, ...)
if (raw || wt == "xml") return(out)
tibble::as_data_frame(
- pick_cols(parse_raw(out)$hierarchyList, c("parentName","parentTsn","rankName","taxonName","tsn"))
+ pick_cols(parse_raw(out)$hierarchyList, c("parentName","parentTsn",
+ "rankName","taxonName","tsn"))
)
}
@@ -35,7 +39,8 @@ hierarchy_down <- function(tsn, wt = "json", raw = FALSE, ...) {
hierarchy_up <- function(tsn, wt = "json", raw = FALSE, ...) {
out <- itis_GET("getHierarchyUpFromTSN", list(tsn = tsn), wt, ...)
if (raw || wt == "xml") return(out)
- res <- tc(pick_cols(parse_raw(out), c("parentName","parentTsn","rankName","taxonName","tsn")))
+ res <- tc(pick_cols(parse_raw(out), c("parentName","parentTsn","rankName",
+ "taxonName","tsn")))
tibble::as_data_frame(
if (length(names(res)) != 1) res else NULL
)
diff --git a/R/itis_facet.R b/R/itis_facet.R
index e00fd44..d7e6f9a 100644
--- a/R/itis_facet.R
+++ b/R/itis_facet.R
@@ -11,6 +11,6 @@
#' head(x$facet_pivot$`nameWInd,vernacular`)
#' }
itis_facet <- function(...) {
- invisible(solrium::solr_connect(url = "http://services.itis.gov"))
+ invisible(solrium::solr_connect(url = itis_solr_url()))
solrium::solr_facet(...)
}
diff --git a/R/itis_group.R b/R/itis_group.R
index f6703b9..864f6f1 100644
--- a/R/itis_group.R
+++ b/R/itis_group.R
@@ -8,6 +8,6 @@
#' head(x)
#' }
itis_group <- function(...) {
- invisible(solrium::solr_connect(url = "http://services.itis.gov"))
+ invisible(solrium::solr_connect(url = itis_solr_url()))
solrium::solr_group(...)
}
diff --git a/R/itis_highlight.R b/R/itis_highlight.R
index 5d09c51..12d3828 100644
--- a/R/itis_highlight.R
+++ b/R/itis_highlight.R
@@ -6,6 +6,6 @@
#' itis_highlight(q = "rank:Species", hl.fl = 'rank', rows=10)
#' }
itis_highlight <- function(...) {
- invisible(solrium::solr_connect(url = "http://services.itis.gov"))
+ invisible(solrium::solr_connect(url = itis_solr_url()))
solrium::solr_highlight(...)
}
diff --git a/R/itis_search.R b/R/itis_search.R
index e79f5e0..ad60a0d 100644
--- a/R/itis_search.R
+++ b/R/itis_search.R
@@ -24,6 +24,6 @@
#' fl = c('nameWInd', 'tsn'))
#' }
itis_search <- function(...) {
- invisible(solrium::solr_connect(url = "http://services.itis.gov"))
+ invisible(solrium::solr_connect(url = itis_solr_url()))
solrium::solr_search(...)
}
diff --git a/R/jurisdiction.R b/R/jurisdiction.R
index 28ae018..a1567cd 100644
--- a/R/jurisdiction.R
+++ b/R/jurisdiction.R
@@ -2,7 +2,7 @@
#'
#' @export
#' @name jurisdiction
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return
#' \itemize{
@@ -29,7 +29,8 @@ jurisdictional_origin <- function(tsn, wt = "json", raw = FALSE, ...) {
if (raw || wt == "xml") return(out)
z <- parse_raw(out)
tibble::as_data_frame(
- pick_cols(z$jurisdictionalOrigins, c("jurisdictionValue", "origin", "updateDate"))
+ pick_cols(z$jurisdictionalOrigins, c("jurisdictionValue", "origin",
+ "updateDate"))
)
}
diff --git a/R/kingdoms.R b/R/kingdoms.R
index b3c96a4..07e6c69 100644
--- a/R/kingdoms.R
+++ b/R/kingdoms.R
@@ -2,7 +2,7 @@
#'
#' @export
#' @name kingdoms
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @details
#' \itemize{
diff --git a/R/last_change_date.R b/R/last_change_date.R
index 51a9623..e0acb92 100644
--- a/R/last_change_date.R
+++ b/R/last_change_date.R
@@ -1,7 +1,7 @@
#' Provides the date the ITIS database was last updated
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @return character value with a date
#' @examples \dontrun{
#' last_change_date()
diff --git a/R/lsid2tsn.R b/R/lsid2tsn.R
index 92ee4b5..39e1845 100644
--- a/R/lsid2tsn.R
+++ b/R/lsid2tsn.R
@@ -1,7 +1,7 @@
#' Gets the TSN corresponding to the LSID, or an empty result if there is no match.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @param lsid (character) lsid for a taxonomic group. Required.
#' @examples \dontrun{
#' lsid2tsn(lsid="urn:lsid:itis.gov:itis_tsn:28726")
diff --git a/R/other_sources.R b/R/other_sources.R
index 05ffc8b..53d4253 100644
--- a/R/other_sources.R
+++ b/R/other_sources.R
@@ -1,7 +1,7 @@
#' Returns a list of the other sources used for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @examples \dontrun{
#' other_sources(tsn=182662)
diff --git a/R/parent_tsn.R b/R/parent_tsn.R
index ab9d6cf..ec24b7a 100644
--- a/R/parent_tsn.R
+++ b/R/parent_tsn.R
@@ -1,7 +1,7 @@
#' Returns the parent TSN for the entered TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a data.frame
#' @examples \dontrun{
diff --git a/R/publications.R b/R/publications.R
index 1844177..82de9ad 100644
--- a/R/publications.R
+++ b/R/publications.R
@@ -1,15 +1,14 @@
#' Returns a list of the pulications used for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a data.frame
#' @examples \dontrun{
#' publications(tsn = 70340)
#' publications(tsn = 70340, wt = "xml")
#'
-#' library(httr)
-#' publications(tsn = 70340, config = verbose())
+#' publications(tsn = 70340, verbose = TRUE)
#' }
publications <- function(tsn, wt = "json", raw = FALSE, ...) {
out <- itis_GET("getPublicationsFromTSN", list(tsn = tsn), wt, ...)
diff --git a/R/rank_name.R b/R/rank_name.R
index 34dc9d2..cfc1344 100644
--- a/R/rank_name.R
+++ b/R/rank_name.R
@@ -1,7 +1,7 @@
#' Returns the kingdom and rank information for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a data.frame, with rank name and other info
#' @examples \dontrun{
diff --git a/R/rank_names.R b/R/rank_names.R
index 58e9f59..e67f6e1 100644
--- a/R/rank_names.R
+++ b/R/rank_names.R
@@ -2,7 +2,7 @@
#' their kingdom and rank ID values.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @return a data.frame, with columns:
#' \itemize{
#' \item kingdomname
diff --git a/R/record.R b/R/record.R
index 75c5c48..eb8203e 100644
--- a/R/record.R
+++ b/R/record.R
@@ -1,7 +1,7 @@
#' Gets a record from an LSID
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @param lsid lsid for a taxonomic group (character). Required.
#' @details Gets the partial ITIS record for the TSN in the LSID, found by comparing the
#' TSN in the search key to the TSN field. Returns an empty result set if
diff --git a/R/review_year.R b/R/review_year.R
index 48c143a..3e4a272 100644
--- a/R/review_year.R
+++ b/R/review_year.R
@@ -1,7 +1,7 @@
#' Returns the review year for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a data.frame
#' @examples \dontrun{
diff --git a/R/scientific_name.R b/R/scientific_name.R
index 9c8d85c..afb41e5 100644
--- a/R/scientific_name.R
+++ b/R/scientific_name.R
@@ -2,7 +2,7 @@
#' (names and indicators) of the scientific name.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a data.frame
#' @examples \dontrun{
diff --git a/R/search_any_match_paged.R b/R/search_any_match_paged.R
index 5694fec..73a2a1f 100644
--- a/R/search_any_match_paged.R
+++ b/R/search_any_match_paged.R
@@ -1,7 +1,7 @@
#' Search for any matched page
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @inheritParams any_match_count
#' @return a data.frame
#' @param pagesize An integer containing the page size (numeric)
diff --git a/R/search_anymatch.R b/R/search_anymatch.R
index 1a3d5a4..d65bced 100644
--- a/R/search_anymatch.R
+++ b/R/search_anymatch.R
@@ -1,7 +1,7 @@
#' Search for any match
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @inheritParams any_match_count
#' @return a data.frame
#' @seealso \code{\link{search_any_match_paged}}
@@ -17,7 +17,8 @@ search_anymatch <- function(x, wt = "json", raw = FALSE, ...) {
names(tmp) <- paste0("common_", names(tmp))
x <- suppressWarnings(
cbind(
- dr_op(x, c("commonNameList.commonNames", "commonNameList.class", "commonNameList.tsn", "class")),
+ dr_op(x, c("commonNameList.commonNames", "commonNameList.class",
+ "commonNameList.tsn", "class")),
tmp
)
)
diff --git a/R/search_common.R b/R/search_common.R
index 1894662..ccdfd44 100644
--- a/R/search_common.R
+++ b/R/search_common.R
@@ -1,20 +1,20 @@
#' Search for tsn by common name
#'
#' @export
-#' @template common
#' @param x text or taxonomic serial number (TSN) (character or numeric)
#' @param from (character) One of "all", "begin", or "end". See Details.
-#' @details The \code{from} parameter:
+#' @inheritParams accepted_names
+#' @details The `from` parameter:
#' \itemize{
-#' \item all - Search against the \code{searchByCommonName} API route, which
+#' \item all - Search against the `searchByCommonName` API route, which
#' searches entire name string
-#' \item begin - Search against the \code{searchByCommonNameBeginsWith} API route, which
-#' searches for a match at the beginning of a name string
-#' \item end - Search against the \code{searchByCommonNameEndsWith} API route, which
-#' searches for a match at the end of a name string
+#' \item begin - Search against the `searchByCommonNameBeginsWith` API
+#' route, which searches for a match at the beginning of a name string
+#' \item end - Search against the `searchByCommonNameEndsWith` API route,
+#' which searches for a match at the end of a name string
#' }
#' @return a data.frame
-#' @seealso \code{\link{search_scientific}}
+#' @seealso [search_scientific()]
#' @examples \dontrun{
#' search_common("american bullfrog")
#' search_common("ferret-badger")
@@ -28,10 +28,13 @@
#' # end
#' search_common("snake", from = "end")
#' }
-search_common <- function(x, from = "all", wt = "json", raw = FALSE, ...) {
- verb <- switch(from, all = "searchByCommonName", begin = "searchByCommonNameBeginsWith",
+search_common <- function(x, from = "all", wt = "json", raw = FALSE,
+ ...) {
+ verb <- switch(from,
+ all = "searchByCommonName",
+ begin = "searchByCommonNameBeginsWith",
end = "searchByCommonNameEndsWith")
- out <- itis_GET(verb, list(srchKey = x), wt, ...)
+ out <- itis_GET(endpt = verb, args = list(srchKey = x), wt, ...)
if (raw || wt == "xml") return(out)
tibble::as_data_frame(dr_op(parse_raw(out)$commonNames, "class"))
}
diff --git a/R/search_scientific.R b/R/search_scientific.R
index f157cc0..163d7b8 100644
--- a/R/search_scientific.R
+++ b/R/search_scientific.R
@@ -1,7 +1,7 @@
#' Search by scientific name
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @inheritParams any_match_count
#' @return a data.frame
#' @seealso \code{\link{search_common}}
diff --git a/R/synonym_names.R b/R/synonym_names.R
index fb723ff..d929354 100644
--- a/R/synonym_names.R
+++ b/R/synonym_names.R
@@ -1,7 +1,7 @@
#' Returns a list of the synonyms (if any) for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a data.frame
#' @examples \dontrun{
diff --git a/R/taxon_authorship.R b/R/taxon_authorship.R
index ce7cfb7..987baa3 100644
--- a/R/taxon_authorship.R
+++ b/R/taxon_authorship.R
@@ -1,7 +1,7 @@
#' Returns the author information for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a data.frame
#' @examples \dontrun{
diff --git a/R/terms.R b/R/terms.R
index 8cb937b..5245cbd 100644
--- a/R/terms.R
+++ b/R/terms.R
@@ -1,10 +1,10 @@
#' Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @param query One or more common or scientific names, or partial names
-#' @param what One of both (search common and scientific names), common (search just
-#' common names), or scientific (search just scientific names)
+#' @param what One of both (search common and scientific names), common
+#' (search just common names), or scientific (search just scientific names)
#' @examples \dontrun{
#' # Get terms searching both common and scientific names
#' terms(query='bear')
@@ -22,8 +22,10 @@ terms <- function(query, what = "both", wt = "json", raw = FALSE, ...) {
what <- match.arg(what, c('both', 'scientific', 'common'))
temp <- switch(what,
both = lapply(query, function(x) itisterms(x, wt, raw, ...)),
- common = lapply(query, function(x) itistermsfromcommonname(x, wt, raw, ...)),
- scientific = lapply(query, function(x) itistermsfromscientificname(x, wt, raw, ...)))
+ common = lapply(query, function(x)
+ itistermsfromcommonname(x, wt, raw, ...)),
+ scientific = lapply(query, function(x)
+ itistermsfromscientificname(x, wt, raw, ...)))
if (length(query) == 1) {
temp[[1]]
} else {
diff --git a/R/tsn2lsid.R b/R/tsn2lsid.R
index a387c55..c27f4fe 100644
--- a/R/tsn2lsid.R
+++ b/R/tsn2lsid.R
@@ -1,7 +1,7 @@
#' Gets the unique LSID for the TSN, or an empty result if there is no match.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @return a character string, an LSID, or \code{NULL} if nothing found
#' @examples \dontrun{
diff --git a/R/tsn_by_vernacular_language.R b/R/tsn_by_vernacular_language.R
index e3e2949..52d9b57 100644
--- a/R/tsn_by_vernacular_language.R
+++ b/R/tsn_by_vernacular_language.R
@@ -1,7 +1,7 @@
#' Get tsn by vernacular language
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @param language A string containing the language. This is a language string,
#' not the international language code (character)
#' @return a data.frame
diff --git a/R/unacceptability_reason.R b/R/unacceptability_reason.R
index 48f5500..7434ad4 100644
--- a/R/unacceptability_reason.R
+++ b/R/unacceptability_reason.R
@@ -1,7 +1,7 @@
#' Returns the unacceptability reason, if any, for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @examples \dontrun{
#' unacceptability_reason(tsn = 183671)
diff --git a/R/usage.R b/R/usage.R
index 100226c..014544c 100644
--- a/R/usage.R
+++ b/R/usage.R
@@ -1,7 +1,7 @@
#' Returns the usage information for the TSN.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @template tsn
#' @examples \dontrun{
#' usage(tsn = 526852)
diff --git a/R/vernacular_languages.R b/R/vernacular_languages.R
index 4e80280..5cc4b92 100644
--- a/R/vernacular_languages.R
+++ b/R/vernacular_languages.R
@@ -1,7 +1,7 @@
#' Provides a list of the unique languages used in the vernacular table.
#'
#' @export
-#' @template common
+#' @inheritParams accepted_names
#' @return a character vector of verncular names
#' @examples \dontrun{
#' vernacular_languages()
diff --git a/R/zzz.R b/R/zzz.R
index 5003ddf..1a91407 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,5 +1,3 @@
-con_utf8 <- function(x) rawToChar(httr::content(x, "raw", encoding = "UTF-8"))
-
tc <- function(l) Filter(Negate(is.null), l)
argsnull <- function(x) {
@@ -16,6 +14,7 @@ nmslwr <- function(x) {
itbase <- function() 'https://www.itis.gov/ITISWebService/services/ITISService/'
itjson <- function() 'https://www.itis.gov/ITISWebService/jsonservice/'
+itis_solr_url <- function() "https://services.itis.gov"
iturl <- function(x) {
if (!tolower(x) %in% c('json', 'xml')) {
stop("'wt' must be one of 'json' or 'xml'", call. = FALSE)
@@ -47,14 +46,30 @@ dr_op.list <- function(x, y) {
itis_GET <- function(endpt, args, wt, ...){
args <- argsnull(args)
- tt <- httr::GET(paste0(iturl(wt), endpt), query = args, ...)
- httr::stop_for_status(tt)
- #err_handle(tt)
- con_utf8(tt)
+ cli <- crul::HttpClient$new(
+ url = paste0(iturl(wt), endpt),
+ opts = list(...)
+ )
+ tt <- cli$get(query = args)
+ tt$raise_for_status()
+
+ # sort out encoding - if not found, parse differently
+ encoding <- NULL
+ if (!is.null(tt$response_headers$`content-type`)) {
+ encoding <- strsplit(
+ strsplit(tt$response_headers$`content-type`, ";")[[1]][2],
+ "="
+ )[[1]][2]
+ }
+ if (is.null(encoding) || !nzchar(encoding)) {
+ readBin(tt$content, character())
+ } else {
+ tt$parse(encoding)
+ }
}
parse_raw <- function(x) {
- if (inherits(x, "character") && !nzchar(x)) {
+ if ((inherits(x, "character") && !nzchar(x)) || is.na(x)) {
return(tibble::as_data_frame())
}
jsonlite::fromJSON(x, flatten = TRUE)
diff --git a/build/vignette.rds b/build/vignette.rds
index 100219f..f65562a 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/man/accepted_names.Rd b/man/accepted_names.Rd
index 95feae6..373b447 100644
--- a/man/accepted_names.Rd
+++ b/man/accepted_names.Rd
@@ -14,7 +14,7 @@ accepted_names(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
Zero row data.frame if the name is accepted, otherwise a data.frame
@@ -35,4 +35,3 @@ accepted_names(tsn = 504239)
accepted_names(tsn = 208527, raw = TRUE)
}
}
-
diff --git a/man/any_match_count.Rd b/man/any_match_count.Rd
index b50d50c..40adf31 100644
--- a/man/any_match_count.Rd
+++ b/man/any_match_count.Rd
@@ -14,7 +14,7 @@ any_match_count(x, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
An integer containing the number of matches the search will return.
@@ -29,4 +29,3 @@ any_match_count(x = "dolphin")
any_match_count(x = "dolphin", wt = "xml")
}
}
-
diff --git a/man/comment_detail.Rd b/man/comment_detail.Rd
index b4b120a..76f4b69 100644
--- a/man/comment_detail.Rd
+++ b/man/comment_detail.Rd
@@ -14,7 +14,7 @@ comment_detail(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
A data.frame with results.
@@ -26,8 +26,5 @@ Get comment detail from TSN
\dontrun{
comment_detail(tsn=180543)
comment_detail(tsn=180543, wt = "xml")
-library(httr)
-comment_detail(tsn=180543)
}
}
-
diff --git a/man/common_names.Rd b/man/common_names.Rd
index 3837136..c8c1db5 100644
--- a/man/common_names.Rd
+++ b/man/common_names.Rd
@@ -14,7 +14,7 @@ common_names(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -28,4 +28,3 @@ common_names(tsn=183833)
common_names(tsn=183833, wt = "xml")
}
}
-
diff --git a/man/core_metadata.Rd b/man/core_metadata.Rd
index f7db931..851f55a 100644
--- a/man/core_metadata.Rd
+++ b/man/core_metadata.Rd
@@ -14,7 +14,7 @@ core_metadata(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get core metadata from tsn
@@ -29,4 +29,3 @@ core_metadata(183671)
core_metadata(183671, wt = "xml")
}
}
-
diff --git a/man/coverage.Rd b/man/coverage.Rd
index 7e272f3..2fa6632 100644
--- a/man/coverage.Rd
+++ b/man/coverage.Rd
@@ -14,7 +14,7 @@ coverage(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get coverge from tsn
@@ -28,4 +28,3 @@ coverage(526852)
coverage(526852, wt = "xml")
}
}
-
diff --git a/man/credibility.Rd b/man/credibility.Rd
index b90d157..e69fe5f 100644
--- a/man/credibility.Rd
+++ b/man/credibility.Rd
@@ -18,7 +18,7 @@ credibility_ratings(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -29,8 +29,8 @@ Get credibility rating from tsn
\details{
methods:
\itemize{
- \item credibility_rating: Get credibility rating for a tsn
- \item credibility_ratings: Get possible credibility ratings
+\item credibility_rating: Get credibility rating for a tsn
+\item credibility_ratings: Get possible credibility ratings
}
}
\examples{
@@ -44,4 +44,3 @@ credibility_ratings(wt = "xml")
credibility_ratings(raw = TRUE)
}
}
-
diff --git a/man/currency.Rd b/man/currency.Rd
index 43366c8..3cf82e8 100644
--- a/man/currency.Rd
+++ b/man/currency.Rd
@@ -14,7 +14,7 @@ currency(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -32,4 +32,3 @@ currency(526852)
currency(526852, raw = TRUE)
}
}
-
diff --git a/man/date_data.Rd b/man/date_data.Rd
index c465bc6..15a1836 100644
--- a/man/date_data.Rd
+++ b/man/date_data.Rd
@@ -14,7 +14,7 @@ date_data(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get date data from tsn
@@ -26,4 +26,3 @@ date_data(180543, wt = "xml")
date_data(180543, wt = "json", raw = TRUE)
}
}
-
diff --git a/man/description.Rd b/man/description.Rd
index ee37014..8fa250b 100644
--- a/man/description.Rd
+++ b/man/description.Rd
@@ -12,7 +12,7 @@ description(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a string, the ITIS web service description
@@ -26,4 +26,3 @@ description()
description(wt = "xml")
}
}
-
diff --git a/man/experts.Rd b/man/experts.Rd
index 88a7c80..e5513d0 100644
--- a/man/experts.Rd
+++ b/man/experts.Rd
@@ -14,7 +14,7 @@ experts(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get expert information for the TSN.
@@ -26,4 +26,3 @@ experts(180544, wt = "xml")
experts(180544, raw = TRUE)
}
}
-
diff --git a/man/full_record.Rd b/man/full_record.Rd
index b30657a..1b34671 100644
--- a/man/full_record.Rd
+++ b/man/full_record.Rd
@@ -16,7 +16,7 @@ full_record(tsn = NULL, lsid = NULL, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get full record from TSN or lsid
@@ -36,4 +36,3 @@ full_record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
full_record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
}
}
-
diff --git a/man/geographic_divisions.Rd b/man/geographic_divisions.Rd
index c588b68..7a0abd0 100644
--- a/man/geographic_divisions.Rd
+++ b/man/geographic_divisions.Rd
@@ -14,7 +14,7 @@ geographic_divisions(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get geographic divisions from tsn
@@ -28,4 +28,3 @@ geographic_divisions(tsn = 180543, wt = "xml")
geographic_divisions(tsn = 180543, wt = "json", raw = TRUE)
}
}
-
diff --git a/man/geographic_values.Rd b/man/geographic_values.Rd
index 541ebc4..0bc01ed 100644
--- a/man/geographic_values.Rd
+++ b/man/geographic_values.Rd
@@ -12,7 +12,7 @@ geographic_values(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
character vector of geographic names
@@ -27,4 +27,3 @@ geographic_values(wt = "xml")
geographic_values(wt = "json", raw = TRUE)
}
}
-
diff --git a/man/global_species_completeness.Rd b/man/global_species_completeness.Rd
index 1d861bb..ae45dd3 100644
--- a/man/global_species_completeness.Rd
+++ b/man/global_species_completeness.Rd
@@ -14,7 +14,7 @@ global_species_completeness(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get global species completeness from tsn
@@ -26,4 +26,3 @@ global_species_completeness(180541, wt = "xml")
global_species_completeness(180541, wt = "json", raw = TRUE)
}
}
-
diff --git a/man/hierarchy.Rd b/man/hierarchy.Rd
index 4333b54..16ebaae 100644
--- a/man/hierarchy.Rd
+++ b/man/hierarchy.Rd
@@ -3,8 +3,8 @@
\name{hierarchy}
\alias{hierarchy}
\alias{hierarchy_down}
-\alias{hierarchy_full}
\alias{hierarchy_up}
+\alias{hierarchy_full}
\title{Get hierarchy down from tsn}
\usage{
hierarchy_down(tsn, wt = "json", raw = FALSE, ...)
@@ -21,7 +21,7 @@ hierarchy_full(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get hierarchy down from tsn
@@ -29,23 +29,25 @@ Get hierarchy down from tsn
\details{
Hierarchy methods:
\itemize{
- \item hierarchy_down: Get hierarchy down from tsn
- \item hierarchy_up: Get hierarchy up from tsn
- \item hierarchy_full: Get full hierarchy from tsn
+\item hierarchy_down: Get hierarchy down from tsn
+\item hierarchy_up: Get hierarchy up from tsn
+\item hierarchy_full: Get full hierarchy from tsn
}
}
\examples{
\dontrun{
-## Full down
-hierarchy_down(tsn=161030)
+## Full down (class Mammalia)
+hierarchy_down(tsn=179913)
-## Full up
+## Full up (genus Agoseris)
hierarchy_up(tsn=36485)
## Full hierarchy
+### genus Liatris
hierarchy_full(tsn=37906)
+### get raw data back
hierarchy_full(tsn=37906, raw = TRUE)
+### genus Baetis, get xml back
hierarchy_full(100800, wt = "xml")
}
}
-
diff --git a/man/itis_facet.Rd b/man/itis_facet.Rd
index 6d02af0..e2f426f 100644
--- a/man/itis_facet.Rd
+++ b/man/itis_facet.Rd
@@ -22,4 +22,3 @@ x <- itis_facet(q = "hierarchySoFar:*$Aves$* AND rank:Species AND usage:valid",
head(x$facet_pivot$`nameWInd,vernacular`)
}
}
-
diff --git a/man/itis_group.Rd b/man/itis_group.Rd
index f9b783a..b23ebd9 100644
--- a/man/itis_group.Rd
+++ b/man/itis_group.Rd
@@ -19,4 +19,3 @@ x <- itis_group(q = "nameWOInd:/[A-Za-z0-9]*[\%20]{1,1}[A-Za-z0-9]*/",
head(x)
}
}
-
diff --git a/man/itis_highlight.Rd b/man/itis_highlight.Rd
index b51b4a7..afaf7e1 100644
--- a/man/itis_highlight.Rd
+++ b/man/itis_highlight.Rd
@@ -17,4 +17,3 @@ ITIS Solr highlight
itis_highlight(q = "rank:Species", hl.fl = 'rank', rows=10)
}
}
-
diff --git a/man/itis_search.Rd b/man/itis_search.Rd
index fe5fb1b..3c0e700 100644
--- a/man/itis_search.Rd
+++ b/man/itis_search.Rd
@@ -35,4 +35,3 @@ itis_search(q = "nameWOInd:/[A-Za-z0-9]*[\%20]{0,0}*/",
fl = c('nameWInd', 'tsn'))
}
}
-
diff --git a/man/jurisdiction.Rd b/man/jurisdiction.Rd
index 641e756..fc6c27b 100644
--- a/man/jurisdiction.Rd
+++ b/man/jurisdiction.Rd
@@ -2,9 +2,9 @@
% Please edit documentation in R/jurisdiction.R
\name{jurisdiction}
\alias{jurisdiction}
+\alias{jurisdictional_origin}
\alias{jurisdiction_origin_values}
\alias{jurisdiction_values}
-\alias{jurisdictional_origin}
\title{Get jurisdictional origin from tsn}
\usage{
jurisdictional_origin(tsn, wt = "json", raw = FALSE, ...)
@@ -21,13 +21,13 @@ jurisdiction_values(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
\itemize{
- \item jurisdictional_origin: data.frame
- \item jurisdiction_origin_values: data.frame
- \item jurisdiction_values: character vector
+\item jurisdictional_origin: data.frame
+\item jurisdiction_origin_values: data.frame
+\item jurisdiction_values: character vector
}
}
\description{
@@ -36,9 +36,9 @@ Get jurisdictional origin from tsn
\details{
Jurisdiction methods:
\itemize{
- \item jurisdictional_origin: Get jurisdictional origin from tsn
- \item jurisdiction_origin_values: Get jurisdiction origin values
- \item jurisdiction_values: Get all possible jurisdiction values
+\item jurisdictional_origin: Get jurisdictional origin from tsn
+\item jurisdiction_origin_values: Get jurisdiction origin values
+\item jurisdiction_values: Get all possible jurisdiction values
}
}
\examples{
@@ -51,4 +51,3 @@ jurisdiction_origin_values()
jurisdiction_values()
}
}
-
diff --git a/man/kingdoms.Rd b/man/kingdoms.Rd
index 90c9b2a..d977564 100644
--- a/man/kingdoms.Rd
+++ b/man/kingdoms.Rd
@@ -1,9 +1,9 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/kingdoms.R
\name{kingdoms}
+\alias{kingdoms}
\alias{kingdom_name}
\alias{kingdom_names}
-\alias{kingdoms}
\title{Get kingdom names from tsn}
\usage{
kingdom_name(tsn, wt = "json", raw = FALSE, ...)
@@ -18,15 +18,15 @@ kingdom_names(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get kingdom names from tsn
}
\details{
\itemize{
- \item kingdom_name: Get kingdom name for a TSN
- \item kingdom_names: Get all possible kingdom names
+\item kingdom_name: Get kingdom name for a TSN
+\item kingdom_names: Get all possible kingdom names
}
}
\examples{
@@ -36,4 +36,3 @@ kingdom_name(202385, wt = "xml")
kingdom_names()
}
}
-
diff --git a/man/last_change_date.Rd b/man/last_change_date.Rd
index b853002..ed811ac 100644
--- a/man/last_change_date.Rd
+++ b/man/last_change_date.Rd
@@ -12,7 +12,7 @@ last_change_date(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
character value with a date
@@ -26,4 +26,3 @@ last_change_date()
last_change_date(wt = "xml")
}
}
-
diff --git a/man/lsid2tsn.Rd b/man/lsid2tsn.Rd
index a6e1673..38c8070 100644
--- a/man/lsid2tsn.Rd
+++ b/man/lsid2tsn.Rd
@@ -14,7 +14,7 @@ lsid2tsn(lsid, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
@@ -27,4 +27,3 @@ lsid2tsn("urn:lsid:itis.gov:itis_tsn:0")
lsid2tsn("urn:lsid:itis.gov:itis_tsn:0", wt = "xml")
}
}
-
diff --git a/man/other_sources.Rd b/man/other_sources.Rd
index 033db41..ec2a147 100644
--- a/man/other_sources.Rd
+++ b/man/other_sources.Rd
@@ -14,7 +14,7 @@ other_sources(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Returns a list of the other sources used for the TSN.
@@ -25,4 +25,3 @@ other_sources(tsn=182662)
other_sources(tsn=182662, wt = "xml")
}
}
-
diff --git a/man/parent_tsn.Rd b/man/parent_tsn.Rd
index 1ca3fcb..4a80882 100644
--- a/man/parent_tsn.Rd
+++ b/man/parent_tsn.Rd
@@ -14,7 +14,7 @@ parent_tsn(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -29,4 +29,3 @@ parent_tsn(tsn = 202385, raw = TRUE)
parent_tsn(tsn = 202385, wt = "xml")
}
}
-
diff --git a/man/publications.Rd b/man/publications.Rd
index 408be19..e1257a5 100644
--- a/man/publications.Rd
+++ b/man/publications.Rd
@@ -14,7 +14,7 @@ publications(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -27,8 +27,6 @@ Returns a list of the pulications used for the TSN.
publications(tsn = 70340)
publications(tsn = 70340, wt = "xml")
-library(httr)
-publications(tsn = 70340, config = verbose())
+publications(tsn = 70340, verbose = TRUE)
}
}
-
diff --git a/man/rank_name.Rd b/man/rank_name.Rd
index 96e866c..feff32c 100644
--- a/man/rank_name.Rd
+++ b/man/rank_name.Rd
@@ -14,7 +14,7 @@ rank_name(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame, with rank name and other info
@@ -27,4 +27,3 @@ Returns the kingdom and rank information for the TSN.
rank_name(tsn = 202385)
}
}
-
diff --git a/man/rank_names.Rd b/man/rank_names.Rd
index df79e97..c019c51 100644
--- a/man/rank_names.Rd
+++ b/man/rank_names.Rd
@@ -3,7 +3,7 @@
\name{rank_names}
\alias{rank_names}
\title{Provides a list of all the unique rank names contained in the database and
- their kingdom and rank ID values.}
+their kingdom and rank ID values.}
\usage{
rank_names(wt = "json", raw = FALSE, ...)
}
@@ -13,23 +13,22 @@ rank_names(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame, with columns:
\itemize{
- \item kingdomname
- \item rankid
- \item rankname
+\item kingdomname
+\item rankid
+\item rankname
}
}
\description{
Provides a list of all the unique rank names contained in the database and
- their kingdom and rank ID values.
+their kingdom and rank ID values.
}
\examples{
\dontrun{
rank_names()
}
}
-
diff --git a/man/record.Rd b/man/record.Rd
index 4de4e96..0b0b406 100644
--- a/man/record.Rd
+++ b/man/record.Rd
@@ -14,7 +14,7 @@ record(lsid, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -24,12 +24,11 @@ Gets a record from an LSID
}
\details{
Gets the partial ITIS record for the TSN in the LSID, found by comparing the
- TSN in the search key to the TSN field. Returns an empty result set if
- there is no match or the TSN is invalid.
+TSN in the search key to the TSN field. Returns an empty result set if
+there is no match or the TSN is invalid.
}
\examples{
\dontrun{
record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
}
}
-
diff --git a/man/review_year.Rd b/man/review_year.Rd
index 2eb91de..651bfba 100644
--- a/man/review_year.Rd
+++ b/man/review_year.Rd
@@ -14,7 +14,7 @@ review_year(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -27,4 +27,3 @@ Returns the review year for the TSN.
review_year(tsn = 180541)
}
}
-
diff --git a/man/ritis-package.Rd b/man/ritis-package.Rd
index 1a5fe3d..b10e869 100644
--- a/man/ritis-package.Rd
+++ b/man/ritis-package.Rd
@@ -2,8 +2,8 @@
% Please edit documentation in R/ritis-package.R
\docType{package}
\name{ritis-package}
-\alias{ritis}
\alias{ritis-package}
+\alias{ritis}
\title{Interface to Integrated Taxonomic Information (ITIS)}
\description{
Interface to Integrated Taxonomic Information (ITIS)
@@ -25,7 +25,7 @@ string, or list. You can get raw JSON as a character string back,
or raw XML as a character string, and then parse yourself with
\pkg{jsonlite} or \pkg{xml2}
}
+
\author{
Scott Chamberlain \email{myrmecocystus at gmail.com}
}
-
diff --git a/man/scientific_name.Rd b/man/scientific_name.Rd
index 5f4b1c1..d611fae 100644
--- a/man/scientific_name.Rd
+++ b/man/scientific_name.Rd
@@ -3,7 +3,7 @@
\name{scientific_name}
\alias{scientific_name}
\title{Returns the scientific name for the TSN. Also returns the component parts
- (names and indicators) of the scientific name.}
+(names and indicators) of the scientific name.}
\usage{
scientific_name(tsn, wt = "json", raw = FALSE, ...)
}
@@ -15,18 +15,17 @@ scientific_name(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
}
\description{
Returns the scientific name for the TSN. Also returns the component parts
- (names and indicators) of the scientific name.
+(names and indicators) of the scientific name.
}
\examples{
\dontrun{
scientific_name(tsn = 531894)
}
}
-
diff --git a/man/search_any_match_paged.Rd b/man/search_any_match_paged.Rd
index aff79d2..f73748f 100644
--- a/man/search_any_match_paged.Rd
+++ b/man/search_any_match_paged.Rd
@@ -22,7 +22,7 @@ for descending (logical)}
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -41,4 +41,3 @@ search_any_match_paged(x="Zy", pagesize=100, pagenum=1, ascend=FALSE)
\seealso{
\code{\link{search_anymatch}}
}
-
diff --git a/man/search_anymatch.Rd b/man/search_anymatch.Rd
index d73bd86..551fd07 100644
--- a/man/search_anymatch.Rd
+++ b/man/search_anymatch.Rd
@@ -14,7 +14,7 @@ search_anymatch(x, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -31,4 +31,3 @@ search_anymatch(x = "dolphin")
\seealso{
\code{\link{search_any_match_paged}}
}
-
diff --git a/man/search_common.Rd b/man/search_common.Rd
index 962cc7a..3c7d583 100644
--- a/man/search_common.Rd
+++ b/man/search_common.Rd
@@ -16,7 +16,7 @@ search_common(x, from = "all", wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -27,12 +27,12 @@ Search for tsn by common name
\details{
The \code{from} parameter:
\itemize{
- \item all - Search against the \code{searchByCommonName} API route, which
- searches entire name string
- \item begin - Search against the \code{searchByCommonNameBeginsWith} API route, which
- searches for a match at the beginning of a name string
- \item end - Search against the \code{searchByCommonNameEndsWith} API route, which
- searches for a match at the end of a name string
+\item all - Search against the \code{searchByCommonName} API route, which
+searches entire name string
+\item begin - Search against the \code{searchByCommonNameBeginsWith} API
+route, which searches for a match at the beginning of a name string
+\item end - Search against the \code{searchByCommonNameEndsWith} API route,
+which searches for a match at the end of a name string
}
}
\examples{
@@ -51,6 +51,5 @@ search_common("snake", from = "end")
}
}
\seealso{
-\code{\link{search_scientific}}
+\code{\link[=search_scientific]{search_scientific()}}
}
-
diff --git a/man/search_scientific.Rd b/man/search_scientific.Rd
index 88cc407..c3bfb6f 100644
--- a/man/search_scientific.Rd
+++ b/man/search_scientific.Rd
@@ -14,7 +14,7 @@ search_scientific(x, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -31,4 +31,3 @@ search_scientific("Quercus douglasii")
\seealso{
\code{\link{search_common}}
}
-
diff --git a/man/solr.Rd b/man/solr.Rd
index 6b245a1..1335d0e 100644
--- a/man/solr.Rd
+++ b/man/solr.Rd
@@ -11,10 +11,10 @@ interace to ITIS data as you have access to a very flexible query interface.
\section{Functions}{
\itemize{
- \item \code{\link{itis_search}} - Search
- \item \code{\link{itis_group}} - Group
- \item \code{\link{itis_highlight}} - Highlight
- \item \code{\link{itis_facet}} - Facet
+\item \code{\link{itis_search}} - Search
+\item \code{\link{itis_group}} - Group
+\item \code{\link{itis_highlight}} - Highlight
+\item \code{\link{itis_facet}} - Facet
}
}
diff --git a/man/synonym_names.Rd b/man/synonym_names.Rd
index 960cc04..3dc8d3b 100644
--- a/man/synonym_names.Rd
+++ b/man/synonym_names.Rd
@@ -14,7 +14,7 @@ synonym_names(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -28,4 +28,3 @@ synonym_names(tsn=183671) # tsn not accepted
synonym_names(tsn=526852) # tsn accepted
}
}
-
diff --git a/man/taxon_authorship.Rd b/man/taxon_authorship.Rd
index d39394e..1544d29 100644
--- a/man/taxon_authorship.Rd
+++ b/man/taxon_authorship.Rd
@@ -14,7 +14,7 @@ taxon_authorship(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -27,4 +27,3 @@ Returns the author information for the TSN.
taxon_authorship(tsn = 183671)
}
}
-
diff --git a/man/terms.Rd b/man/terms.Rd
index 0fcc615..1cb72b8 100644
--- a/man/terms.Rd
+++ b/man/terms.Rd
@@ -9,15 +9,15 @@ terms(query, what = "both", wt = "json", raw = FALSE, ...)
\arguments{
\item{query}{One or more common or scientific names, or partial names}
-\item{what}{One of both (search common and scientific names), common (search just
-common names), or scientific (search just scientific names)}
+\item{what}{One of both (search common and scientific names), common
+(search just common names), or scientific (search just scientific names)}
\item{wt}{(character) One of "json" or "xml". Required.}
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
@@ -37,4 +37,3 @@ terms(query='Poa annua', "scientific")
terms(query=c('Poa annua', 'Pinus contorta'), "scientific")
}
}
-
diff --git a/man/tsn2lsid.Rd b/man/tsn2lsid.Rd
index e538908..f3c81db 100644
--- a/man/tsn2lsid.Rd
+++ b/man/tsn2lsid.Rd
@@ -14,7 +14,7 @@ tsn2lsid(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a character string, an LSID, or \code{NULL} if nothing found
@@ -30,4 +30,3 @@ tsn2lsid(155166, raw = TRUE)
tsn2lsid(155166, wt = "xml")
}
}
-
diff --git a/man/tsn_by_vernacular_language.Rd b/man/tsn_by_vernacular_language.Rd
index 1eef8ad..dcd8e94 100644
--- a/man/tsn_by_vernacular_language.Rd
+++ b/man/tsn_by_vernacular_language.Rd
@@ -15,7 +15,7 @@ not the international language code (character)}
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a data.frame
@@ -28,4 +28,3 @@ Get tsn by vernacular language
tsn_by_vernacular_language(language = "french")
}
}
-
diff --git a/man/unacceptability_reason.Rd b/man/unacceptability_reason.Rd
index 52a8588..ab4cbff 100644
--- a/man/unacceptability_reason.Rd
+++ b/man/unacceptability_reason.Rd
@@ -14,7 +14,7 @@ unacceptability_reason(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Returns the unacceptability reason, if any, for the TSN.
@@ -24,4 +24,3 @@ Returns the unacceptability reason, if any, for the TSN.
unacceptability_reason(tsn = 183671)
}
}
-
diff --git a/man/usage.Rd b/man/usage.Rd
index 4ba25c1..14fec45 100644
--- a/man/usage.Rd
+++ b/man/usage.Rd
@@ -14,7 +14,7 @@ usage(tsn, wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\description{
Returns the usage information for the TSN.
@@ -26,4 +26,3 @@ usage(tsn = 526852, raw = TRUE)
usage(tsn = 526852, wt = "xml")
}
}
-
diff --git a/man/vernacular_languages.Rd b/man/vernacular_languages.Rd
index 522319e..1b91396 100644
--- a/man/vernacular_languages.Rd
+++ b/man/vernacular_languages.Rd
@@ -12,7 +12,7 @@ vernacular_languages(wt = "json", raw = FALSE, ...)
\item{raw}{(logical) Return raw JSON or XML as character string. Required.
Default: \code{FALSE}}
-\item{...}{Curl options passed on to \code{\link[httr]{GET}}}
+\item{...}{curl options passed on to \link[crul:HttpClient]{crul::HttpClient}}
}
\value{
a character vector of verncular names
@@ -25,4 +25,3 @@ Provides a list of the unique languages used in the vernacular table.
vernacular_languages()
}
}
-
diff --git a/tests/testthat/test-hierarchy.R b/tests/testthat/test-hierarchy.R
index de3f13b..a3540cc 100644
--- a/tests/testthat/test-hierarchy.R
+++ b/tests/testthat/test-hierarchy.R
@@ -3,7 +3,7 @@ context("hierarchy functions")
test_that("hierarchy_down basic functionality works", {
skip_on_cran()
- aa <- hierarchy_down(tsn = 161030)
+ aa <- hierarchy_down(tsn = 179913)
expect_is(aa, "data.frame")
expect_is(aa, "tbl_df")
@@ -43,16 +43,10 @@ test_that("hierarchy functions fail well", {
expect_error(hierarchy_up(), "\"tsn\" is missing")
expect_error(hierarchy_full(), "\"tsn\" is missing")
- # tsn's not found lead to 0 row data.frame's
- tmp <- hierarchy_down(tsn = "Asdfasdfa")
- expect_is(tmp, "tbl_df")
- expect_equal(NROW(tmp), 0)
+ # tsn's not found gives 404
+ expect_error(hierarchy_down(tsn = "Asdfasdfa"), "Not Found")
- tmp <- hierarchy_up(tsn = "Asdfasdfa")
- expect_is(tmp, "tbl_df")
- expect_equal(NROW(tmp), 0)
+ expect_error(hierarchy_up(tsn = "Asdfasdfa"), "Not Found")
- tmp <- hierarchy_full(tsn = "Asdfasdfa")
- expect_is(tmp, "tbl_df")
- expect_equal(NROW(tmp), 0)
+ expect_error(hierarchy_full(tsn = "Asdfasdfa"), "Not Found")
})
diff --git a/tests/testthat/test-itis_facet.R b/tests/testthat/test-itis_facet.R
index f1f861a..14d9565 100644
--- a/tests/testthat/test-itis_facet.R
+++ b/tests/testthat/test-itis_facet.R
@@ -20,10 +20,7 @@ test_that("itis_facet basic functionality works", {
test_that("itis_facet fails well", {
skip_on_cran()
- expect_identical(
- sm(itis_facet(foo = "bar")),
- sm(itis_facet())
- )
+ expect_null(sm(itis_facet(foo = "bar")))
expect_error(sm(itis_facet(wt = "asdfaddf")))
})
diff --git a/tests/testthat/test-jurisdiction.R b/tests/testthat/test-jurisdiction.R
index 10869dd..4556357 100644
--- a/tests/testthat/test-jurisdiction.R
+++ b/tests/testthat/test-jurisdiction.R
@@ -42,8 +42,6 @@ test_that("jurisdiction functions fail well", {
expect_error(jurisdiction_values(wt = "ffa"), "'wt' must be one of")
- # lsid's not found lead to 0 row data.frame's
- tmp <- jurisdictional_origin(tsn = "asdfasdf")
- expect_is(tmp, "tbl_df")
- expect_equal(NROW(tmp), 0)
+ # lsid's not found lead 404
+ expect_error(jurisdictional_origin(tsn = "asdfasdf"), "Not Found")
})
diff --git a/tests/testthat/test-kingdoms.R b/tests/testthat/test-kingdoms.R
index 1694b79..aa00618 100644
--- a/tests/testthat/test-kingdoms.R
+++ b/tests/testthat/test-kingdoms.R
@@ -34,8 +34,6 @@ test_that("kingdom functions fail well", {
expect_error(kingdom_names(wt = "ffa"), "'wt' must be one of")
- # tsn's not found lead to 0 row data.frame's
- tmp <- kingdom_name(tsn = "Asdfasdfa")
- expect_is(tmp, "tbl_df")
- expect_equal(NROW(tmp), 0)
+ # tsn's not found lead to 404
+ expect_error(kingdom_name(tsn = "Asdfasdfa"), "Not Found")
})
diff --git a/tests/testthat/test-publications.R b/tests/testthat/test-publications.R
index 127c877..748ac58 100644
--- a/tests/testthat/test-publications.R
+++ b/tests/testthat/test-publications.R
@@ -37,8 +37,6 @@ test_that("publications fails well", {
expect_error(publications(tsn = 70340, wt = "ffa"), "'wt' must be one of")
- # tsn's not found lead to 0 row data.frame's
- tmp <- publications(tsn = "Asdfasdfa")
- expect_is(tmp, "tbl_df")
- expect_equal(NROW(tmp), 0)
+ # tsn's not found lead to 404
+ expect_error(publications(tsn = "Asdfasdfa"), "Not Found")
})
--
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