New Upstream Snapshot - r-cran-natserv
Ready changes
Summary
Merged new upstream version: 1.0.0+git20220909.1.ef8d717+dfsg (was: 1.0.0+dfsg).
Resulting package
Built on 2023-01-19T05:41 (took 13m7s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots r-cran-natserv
Lintian Result
Diff
diff --git a/DESCRIPTION b/DESCRIPTION
index 467fe0c..6bf8135 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,9 +3,9 @@ Title: 'NatureServe' Interface
Description: Interface to 'NatureServe' (<https://www.natureserve.org/>).
Includes methods to get data, image metadata, search taxonomic names,
and make maps.
-Version: 1.0.0
+Version: 1.0.0.91
License: MIT + file LICENSE
-URL: https://docs.ropensci.org/natserv,
+URL: https://docs.ropensci.org/natserv/,
https://github.com/ropensci/natserv
BugReports: https://github.com/ropensci/natserv/issues
Authors@R: c(
@@ -16,21 +16,19 @@ Authors@R: c(
role = "fnd",
comment = "https://ropensci.org/"))
LazyData: true
-VignetteBuilder: knitr
Language: en-US
Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
Depends: R(>= 3.2.1)
Imports: crul (>= 0.7.0), jsonlite, tibble
-Suggests: testthat, knitr, vcr
-RoxygenNote: 7.1.0
+Suggests: testthat, vcr
+RoxygenNote: 7.1.1
X-schema.org-applicationCategory: Taxonomy
X-schema.org-keywords: taxonomy, species, API, web-services,
NatureServe, metadata, maps
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
-Packaged: 2020-05-15 21:02:58 UTC; sckott
+Packaged: 2023-01-19 05:35:26 UTC; root
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
-Repository: CRAN
-Date/Publication: 2020-05-16 22:30:07 UTC
diff --git a/LICENSE b/LICENSE
index d99b2f4..0555ec9 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2020
-COPYRIGHT HOLDER: Scott Chamberlain
+YEAR: 2021
+COPYRIGHT HOLDER: natserv authors
diff --git a/MD5 b/MD5
deleted file mode 100644
index 87f04bb..0000000
--- a/MD5
+++ /dev/null
@@ -1,52 +0,0 @@
-7766597c2fd896bc6833673a1c17d58b *DESCRIPTION
-35bd8606c71dfbfad3ad27387e177ad4 *LICENSE
-aee627b2c6d28b18479b018fe5f4df26 *NAMESPACE
-df909438e8a262c5b624428bc79f2c5d *NEWS.md
-9495e27eac4003c7cbeb500f51982d76 *R/globals.R
-ba0e99dff32bcd7a1776bcc461201bcd *R/http.R
-da8fd42bbe38df64779ffc855d14a152 *R/natserv-package.R
-a9e012039f4c579bf7f9ab21c861fdcd *R/ns_altid.R
-a4214a37db02077d75280bb097f49367 *R/ns_ecohier.R
-2b6954731a13a89a3cf1d56f1c75ad2a *R/ns_export.R
-6bfd4f4e6f9d0548bc29b9d3f174df00 *R/ns_id.R
-47c31719d90923dad276870e1bac8d22 *R/ns_search_comb.R
-0fb835fae00cb6f206f10923eef4d7fc *R/ns_search_eco.R
-c62e1590c00b5b14a86fd26d9de662c7 *R/ns_search_spp.R
-b4a88193b5b7ade50c9edabd338220da *R/search_helpers.R
-9c655c60012e6b52b3e5cd2b1378d876 *R/zzz.R
-e49167c6d95bc150301a90f271fe5432 *README.md
-24d332f2136cec13615ac5eb2e801944 *build/vignette.rds
-4b1a9d05899601061c9c77559b355ea6 *data/sysdata.rda
-ec49ca345b45cdddbf29f3e23b3d46d7 *inst/doc/natserv.Rmd
-38cfc8b776bd6b731ebae8c321ad3542 *inst/doc/natserv.html
-261ab8141a7c1af05f3fb5ae49812e48 *man/figures/plot.states-1.png
-8d931892f247107c1481db419f33bace *man/figures/status.map-1.png
-d92c19a3a9b42e179c0b6048fa7e3ef6 *man/nat_states.Rd
-169ff40c44c8317a3ef66fedb72eb0a1 *man/natserv-package.Rd
-067a3763f5c093956f1a473d924b3d80 *man/ns_altid.Rd
-3cd8ae356e6a631292183c06aa5c3981 *man/ns_ecohier.Rd
-301c309e3837e35d319979960e2d50c4 *man/ns_export.Rd
-df7f1351d3c608fff3dc9dcabc8c4405 *man/ns_id.Rd
-c40f3de17da3378bbd61e3b2fb59cf4c *man/ns_search_comb.Rd
-01868aad8d5ace96042f378537086e87 *man/ns_search_eco.Rd
-9465a0aebde997b3af1116516b09e315 *man/ns_search_spp.Rd
-a8ef46e02db19b8fb9f0fe94b049d6bc *tests/fixtures/ns_altid.yml
-240290805c5b603a97286d5b7befea60 *tests/fixtures/ns_ecohier.yml
-63ecd6029ebb8d6c74bcf5c411c0a2d5 *tests/fixtures/ns_export.yml
-5385adda58f16ad63805fd6220f8f406 *tests/fixtures/ns_export_status.yml
-06a0207f2552c30f983ba4d97791fc9a *tests/fixtures/ns_id.yml
-a0b371a3abd3e43c65cc3cdc2855bd5d *tests/fixtures/ns_search_comb.yml
-a641c9c7113407a16e4d874ba5b00049 *tests/fixtures/ns_search_eco.yml
-a19ce441bbb6696936a534337bccac1d *tests/fixtures/ns_search_spp.yml
-12d4e215a6ba314ad17833f38d1906e9 *tests/test-all.R
-261d034dd036bf8744438521232a4f0f *tests/testthat/helper-natserv.R
-e68b8dbe91386c4c9a51b5bc7a0bad34 *tests/testthat/test-ns_altid.R
-04a66952878fbd50609b3cea681a4af7 *tests/testthat/test-ns_ecohier.R
-7d2bd14cebc3dd7367dd9108937109ab *tests/testthat/test-ns_export.R
-be7236f3cca71736a3d62c72fc68dd2d *tests/testthat/test-ns_id.R
-0655e9382f2b56ea1ac2df96502f9f7e *tests/testthat/test-ns_search_comb.R
-6eec18c9058a66b77f3f55f1951967f7 *tests/testthat/test-ns_search_eco.R
-2286685b5d0df3a749358d410206fa28 *tests/testthat/test-ns_search_spp.R
-6fb26008d86fd24bcbc65ebbc0be05c2 *tests/testthat/test-utils.R
-ec49ca345b45cdddbf29f3e23b3d46d7 *vignettes/natserv.Rmd
-018c95f54183881785c3aed595243d19 *vignettes/natserv.Rmd.og
diff --git a/README-not.md b/README-not.md
new file mode 100644
index 0000000..dc4dd3d
--- /dev/null
+++ b/README-not.md
@@ -0,0 +1,101 @@
+natserv
+=======
+
+
+
+[](https://cranchecks.info/pkgs/natserv)
+[](https://github.com/ropensci/natserv/actions?query=workflow%3AR-check)
+[](https://codecov.io/gh/ropensci/natserv)
+[](https://cran.r-project.org/package=natserv)
+[](https://github.com/metacran/cranlogs.app)
+
+
+`natserv` NatureServe R client
+
+NatureServe is a non-profit organization that provides wildlife conservation related data to various groups including the public.
+
+* NatureServe site: https://services.natureserve.org
+* NatureServe API docs: https://explorer.natureserve.org/api-docs/
+
+All functions in this package are prefixed with `ns_` to prevent
+collision with other pkgs.
+
+You no longer need an API key.
+
+See also the taxize book (https://taxize.dev/) for
+a manual on working with taxonomic data in R, including with NatureServe data.
+
+## Installation
+
+Stable version from CRAN
+
+
+```r
+install.packages("natserv")
+```
+
+Development version
+
+
+```r
+remotes::install_github("ropensci/natserv")
+```
+
+
+```r
+library('natserv')
+```
+
+## Search
+
+
+```r
+ns_search_comb(text = "robin", page = 0, per_page = 5)
+#> $results
+#> # A tibble: 5 x 15
+#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
+#> <chr> <int> <chr> <chr> <chr> <chr>
+#> 1 SPECIES 100637 ELEMENT… /Taxo… ABPBJ… Copsychus sau…
+#> 2 SPECIES 102323 ELEMENT… /Taxo… ABPBJ… Turdus grayi
+#> 3 SPECIES 102179 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
+#> 4 SPECIES 105536 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
+#> 5 SPECIES 105850 ELEMENT… /Taxo… ABPBJ… Turdus rufopa…
+#> # … with 23 more variables: formattedScientificName <chr>,
+#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
+#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
+#> # classificationStatus <chr>, speciesGlobal$usesaCode <lgl>,
+#> # $cosewicCode <lgl>, $saraCode <lgl>, $synonyms <list>,
+#> # $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>, $taxclass <chr>,
+#> # $taxorder <chr>, $family <chr>, $genus <chr>, $taxonomicComments <chr>,
+#> # $informalTaxonomy <chr>, $infraspecies <lgl>, $completeDistribution <lgl>,
+#> # gRank <chr>
+#>
+#> $resultsSummary
+#> name value
+#> 1 page 0
+#> 2 recordsPerPage 5
+#> 3 totalPages 26
+#> 4 totalResults 126
+#> 5 species_total 103
+#> 6 total 23
+#> 7 classes 0
+#> 8 subclasses 0
+#> 9 formations 0
+#> 10 divisions 0
+#> 11 macrogroups 1
+#> 12 groups 1
+#> 13 alliances 3
+#> 14 associations 18
+#> 15 terrestrialEcologicalSystems 0
+```
+
+See the vignette (https://docs.ropensci.org/natserv/articles/natserv.html) for more examples.
+
+## Meta
+
+* Please [report any issues or bugs](https://github.com/ropensci/natserv/issues).
+* License: MIT
+* Get citation information for `natserv` in R doing `citation(package = 'natserv')`
+* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
+
+[](https://ropensci.org)
diff --git a/README.md b/README.md
index f9eb2d6..a09c462 100644
--- a/README.md
+++ b/README.md
@@ -1,103 +1,3 @@
-natserv
-=======
+[](https://www.repostatus.org/#abandoned)
-
-
-[](https://cranchecks.info/pkgs/natserv)
-[](https://travis-ci.org/ropensci/natserv)
-[](https://ci.appveyor.com/project/sckott/natserv)
-[](https://codecov.io/gh/ropensci/natserv)
-[](https://cran.r-project.org/package=natserv)
-[](https://github.com/metacran/cranlogs.app)
-
-
-`natserv` NatureServe R client
-
-NatureServe is a non-profit organization that provides wildlife conservation related data to various groups including the public.
-
-* NatureServe site: https://services.natureserve.org
-* NatureServe API docs: https://explorer.natureserve.org/api-docs/
-
-All functions in this package are prefixed with `ns_` to prevent
-collision with other pkgs.
-
-You no longer need an API key.
-
-See also the taxize book (https://taxize.dev/) for
-a manual on working with taxonomic data in R, including with NatureServe data.
-
-## Installation
-
-Stable version from CRAN
-
-
-```r
-install.packages("natserv")
-```
-
-Development version
-
-
-```r
-remotes::install_github("ropensci/natserv")
-```
-
-
-```r
-library('natserv')
-```
-
-## Search
-
-
-```r
-ns_search_comb(text = "robin", page = 0, per_page = 5)
-#> $results
-#> # A tibble: 5 x 14
-#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
-#> <chr> <int> <chr> <chr> <chr> <chr>
-#> 1 SPECIES 100637 ELEMENT… /Taxo… ABPBJ… Copsychus sau…
-#> 2 SPECIES 102323 ELEMENT… /Taxo… ABPBJ… Turdus grayi
-#> 3 SPECIES 102179 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
-#> 4 SPECIES 105536 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
-#> 5 SPECIES 105850 ELEMENT… /Taxo… ABPBJ… Turdus rufopa…
-#> # … with 22 more variables: formattedScientificName <chr>,
-#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
-#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
-#> # speciesGlobal$usesaCode <lgl>, $cosewicCode <lgl>, $saraCode <lgl>,
-#> # $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>,
-#> # $taxonomicComments <chr>, $informalTaxonomy <chr>, $infraspecies <lgl>,
-#> # $completeDistribution <lgl>, gRank <chr>
-#>
-#> $resultsSummary
-#> name value
-#> 1 page 0
-#> 2 recordsPerPage 5
-#> 3 totalPages 26
-#> 4 totalResults 126
-#> 5 species_total 103
-#> 6 total 23
-#> 7 classes 0
-#> 8 subclasses 0
-#> 9 formations 0
-#> 10 divisions 0
-#> 11 macrogroups 1
-#> 12 groups 1
-#> 13 alliances 3
-#> 14 associations 18
-#> 15 terrestrialEcologicalSystems 0
-```
-
-See the vignette (https://docs.ropensci.org/natserv/articles/natserv.html) for more examples.
-
-## Meta
-
-* Please [report any issues or bugs](https://github.com/ropensci/natserv/issues).
-* License: MIT
-* Get citation information for `natserv` in R doing `citation(package = 'natserv')`
-* Please note that this project is released with a [Contributor Code of Conduct][coc]. By participating in this project you agree to abide by its terms.
-
-[](https://ropensci.org)
-
-[coc]: https://github.com/ropensci/natserv/blob/master/CODE_OF_CONDUCT.md
+This package has been archived. The former README is now in [README-not](README-not.md).<
diff --git a/build/vignette.rds b/build/vignette.rds
deleted file mode 100644
index 5a3f17e..0000000
Binary files a/build/vignette.rds and /dev/null differ
diff --git a/debian/changelog b/debian/changelog
index 58fead3..5e03da1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+r-cran-natserv (1.0.0+git20220909.1.ef8d717+dfsg-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Thu, 19 Jan 2023 05:36:00 -0000
+
r-cran-natserv (1.0.0+dfsg-1) unstable; urgency=medium
* New upstream version
diff --git a/inst/doc/natserv.Rmd b/inst/doc/natserv.Rmd
deleted file mode 100644
index c67897a..0000000
--- a/inst/doc/natserv.Rmd
+++ /dev/null
@@ -1,420 +0,0 @@
----
-title: "natserv introduction"
-author: "Scott Chamberlain"
-date: "2020-05-15"
-output: rmarkdown::html_vignette
-vignette: >
- %\VignetteIndexEntry{natserv introduction}
- %\VignetteEngine{knitr::rmarkdown}
- \usepackage[utf8]{inputenc}
----
-
-
-
-`natserv` is an R package that interacts with the API services of the non-profit organization NatureServe (https://services.natureserve.org/). If you want to read the full API documentation, you can find it at https://explorer.natureserve.org/api-docs/
-
-See also the taxize book (https://taxize.dev/) for
-a manual on working with taxonomic data in R, including with NatureServe data.
-
-This tutorial will walk you through installing `natserv` and using its functions.
-
-## A quick introduction to NatureServe
-
-NatureServe is a non-profit organization that provides biodiversity data freely online.
-They maintain a database comprised of data from natural heritage programs and conservation data centers - this database includes information about the conservation status, taxonomy, geographic distribution, and life history information for over 70,000 species of plants, animals, and fungi in Canada and the United States.
-You can find information about their data coverage (https://explorer.natureserve.org/AboutTheData/DataCoverage), and data sources (https://explorer.natureserve.org/AboutTheData/Sources) on their website. NatureServe also hosts data on ecological communities/systems and their conservation status.
-
-While small amounts of data can be easily collected using their online NatureServe explorer site (http://explorer.natureserve.org/), downloading species data this way would be incredibly slow.
-Thus `natserv` was born.
-This R package can access NatureServe's online API for rapid downloading of conservation data, allows for easy access to multiple species' data sets, and loads the data directly into your R session.
-
-## Installing `natserv` from CRAN or GitHub
-
-Stable version:
-
-
-```r
-install.packages("natserv")
-```
-
-Development version:
-
-
-```r
-remotes::install_github("ropensci/natserv")
-```
-
-After successful installation, load the package into the environment:
-
-
-```r
-library(natserv)
-```
-
-## `natserv` functions
-
-All of `natserv`'s functions are prefixed with `ns_` to avoid confusion with other packages - here are the functions provided by `natserv`:
-
-
-```r
-cat(paste(" -", paste(sprintf("`%s`", sort(getNamespaceExports("natserv"))), collapse = "\n - ")))
-#> - `ns_altid`
-#> - `ns_ecohier`
-#> - `ns_export`
-#> - `ns_export_status`
-#> - `ns_id`
-#> - `ns_search_comb`
-#> - `ns_search_eco`
-#> - `ns_search_spp`
-```
-
-## Search
-
-There's three functions for search:
-
-- combined: supports searching for both species and ecosystems using search criteria which are applicable to both types of records
-- species: supports searching for only species; extends the search criteria available through the Combined Search to include support for additional criteria which are only applicable to species records
-- ecosystem: supports searching for only ecosystems; extends the search criteria available through the Combined Search to include support for additional criteria which are only applicable to ecosystems records
-
-Combined search
-
-
-```r
-ns_search_comb(text = "robin", page = 0, per_page = 5)
-#> $results
-#> # A tibble: 5 x 14
-#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
-#> <chr> <int> <chr> <chr> <chr> <chr>
-#> 1 SPECIES 100637 ELEMENT… /Taxo… ABPBJ… Copsychus sau…
-#> 2 SPECIES 102323 ELEMENT… /Taxo… ABPBJ… Turdus grayi
-#> 3 SPECIES 102179 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
-#> 4 SPECIES 105536 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
-#> 5 SPECIES 105850 ELEMENT… /Taxo… ABPBJ… Turdus rufopa…
-#> # … with 22 more variables: formattedScientificName <chr>,
-#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
-#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
-#> # speciesGlobal$usesaCode <lgl>, $cosewicCode <lgl>, $saraCode <lgl>,
-#> # $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>,
-#> # $taxonomicComments <chr>, $informalTaxonomy <chr>, $infraspecies <lgl>,
-#> # $completeDistribution <lgl>, gRank <chr>
-#>
-#> $resultsSummary
-#> name value
-#> 1 page 0
-#> 2 recordsPerPage 5
-#> 3 totalPages 26
-#> 4 totalResults 126
-#> 5 species_total 103
-#> 6 total 23
-#> 7 classes 0
-#> 8 subclasses 0
-#> 9 formations 0
-#> 10 divisions 0
-#> 11 macrogroups 1
-#> 12 groups 1
-#> 13 alliances 3
-#> 14 associations 18
-#> 15 terrestrialEcologicalSystems 0
-```
-
-Species search
-
-
-```r
-ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Animalia", level = "kingdom"))
-#> $results
-#> # A tibble: 20 x 14
-#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
-#> <chr> <int> <chr> <chr> <chr> <chr>
-#> 1 SPECIES 828458 ELEMENT… /Taxo… AAABC… Acris blancha…
-#> 2 SPECIES 828419 ELEMENT… /Taxo… AAABC… Acris crepita…
-#> 3 SPECIES 103292 ELEMENT… /Taxo… AAABC… Acris gryllus
-#> 4 SPECIES 104324 ELEMENT… /Taxo… AAAAA… Ambystoma ann…
-#> 5 SPECIES 100100 ELEMENT… /Taxo… AAAAA… Ambystoma bar…
-#> 6 SPECIES 802300 ELEMENT… /Taxo… AAAAA… Ambystoma bis…
-#> 7 SPECIES 104488 ELEMENT… /Taxo… AAAAA… Ambystoma cal…
-#> 8 SPECIES 802301 ELEMENT… /Taxo… AAAAA… Ambystoma cin…
-#> 9 SPECIES 103251 ELEMENT… /Taxo… AAAAA… Ambystoma gra…
-#> 10 SPECIES 100401 ELEMENT… /Taxo… AAAAA… Ambystoma jef…
-#> 11 SPECIES 102149 ELEMENT… /Taxo… AAAAA… Ambystoma lat…
-#> 12 SPECIES 1143335 ELEMENT… /Taxo… AAAAA… Ambystoma lat…
-#> 13 SPECIES 1143337 ELEMENT… /Taxo… AAAAA… Ambystoma lat…
-#> 14 SPECIES 101261 ELEMENT… /Taxo… AAAAA… Ambystoma mab…
-#> 15 SPECIES 106403 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 16 SPECIES 101632 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 17 SPECIES 103392 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 18 SPECIES 104239 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 19 SPECIES 100115 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 20 SPECIES 103039 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> # … with 22 more variables: formattedScientificName <chr>,
-#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
-#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
-#> # speciesGlobal$usesaCode <chr>, $cosewicCode <chr>, $saraCode <chr>,
-#> # $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>,
-#> # $taxonomicComments <chr>, $informalTaxonomy <chr>, $infraspecies <lgl>,
-#> # $completeDistribution <lgl>, gRank <chr>
-#>
-#> $resultsSummary
-#> name value
-#> 1 page 0
-#> 2 recordsPerPage 20
-#> 3 totalPages 2586
-#> 4 totalResults 51705
-#> 5 species_total 51705
-```
-
-Ecosystem search
-
-
-```r
-ns_search_eco(ecosystem_taxonomy = "M067")
-#> $results
-#> # A tibble: 20 x 14
-#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
-#> <chr> <int> <chr> <chr> <chr> <chr>
-#> 1 ECOSYSTEM 899525 ELEMENT… /Taxo… A3401 Eleocharis el…
-#> 2 ECOSYSTEM 899121 ELEMENT… /Taxo… A1372 Fimbristylis …
-#> 3 ECOSYSTEM 899126 ELEMENT… /Taxo… A1389 Spartina bake…
-#> 4 ECOSYSTEM 899744 ELEMENT… /Taxo… A3692 Spartina pate…
-#> 5 ECOSYSTEM 899523 ELEMENT… /Taxo… A3399 Typha dominge…
-#> 6 ECOSYSTEM 899526 ELEMENT… /Taxo… A3402 Andropogon ca…
-#> 7 ECOSYSTEM 899517 ELEMENT… /Taxo… A3393 Aristida palu…
-#> 8 ECOSYSTEM 899132 ELEMENT… /Taxo… A1429 Eleocharis sp…
-#> 9 ECOSYSTEM 899512 ELEMENT… /Taxo… A3388 Hypericum cha…
-#> 10 ECOSYSTEM 899133 ELEMENT… /Taxo… A1430 Juncus milita…
-#> 11 ECOSYSTEM 899122 ELEMENT… /Taxo… A1379 Panicum hemit…
-#> 12 ECOSYSTEM 899124 ELEMENT… /Taxo… A1383 Rhynchospora …
-#> 13 ECOSYSTEM 899518 ELEMENT… /Taxo… A3394 Rhynchospora …
-#> 14 ECOSYSTEM 1146914 ELEMENT… /Taxo… A4404 Rhynchospora …
-#> 15 ECOSYSTEM 899521 ELEMENT… /Taxo… A3397 Rhynchospora …
-#> 16 ECOSYSTEM 899125 ELEMENT… /Taxo… A1384 Rhynchospora …
-#> 17 ECOSYSTEM 899530 ELEMENT… /Taxo… A3406 Cladium maris…
-#> 18 ECOSYSTEM 899120 ELEMENT… /Taxo… A1369 Cladium maris…
-#> 19 ECOSYSTEM 899720 ELEMENT… /Taxo… A3668 Hottonia infl…
-#> 20 ECOSYSTEM 900115 ELEMENT… /Taxo… A4065 Orontium aqua…
-#> # … with 18 more variables: formattedScientificName <chr>,
-#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
-#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
-#> # ecosystemGlobal$translatedScientificName <chr>, $taxclassCode <chr>,
-#> # $taxsubclassCode <chr>, $formationCode <chr>, $divisionCode <chr>,
-#> # $macrogroupKey <chr>, $taxgroupKey <chr>, $allianceKey <lgl>,
-#> # $ecosystemType <chr>, $classificationCode <chr>, $parentName <chr>,
-#> # gRank <chr>
-#>
-#> $resultsSummary
-#> name value
-#> 1 page 0
-#> 2 recordsPerPage 20
-#> 3 totalPages 11
-#> 4 totalResults 210
-#> 5 total 210
-#> 6 classes 0
-#> 7 subclasses 0
-#> 8 formations 0
-#> 9 divisions 0
-#> 10 macrogroups 1
-#> 11 groups 6
-#> 12 alliances 33
-#> 13 associations 154
-#> 14 terrestrialEcologicalSystems 16
-```
-
-## Get taxon by id
-
-By UID
-
-
-```r
-w <- ns_id("ELEMENT_GLOBAL.2.154701")
-str(w, max.level = 1)
-#> List of 40
-#> $ elementGlobalId : int 154701
-#> $ circumscripConfidence : NULL
-#> $ classificationLevel :List of 4
-#> $ classificationStatus :List of 4
-#> $ iucn :List of 5
-#> $ nameCategory :List of 6
-#> $ rankMethodUsed :List of 4
-#> $ formattedScientificName : chr "<i>Hydrastis canadensis</i>"
-#> $ scientificName : chr "Hydrastis canadensis"
-#> $ scientificNameAuthor : chr "L."
-#> $ primaryCommonName : chr "Goldenseal"
-#> $ relatedItisNames : chr "<i>Hydrastis canadensis</i> L. (TSN 18781)"
-#> $ uniqueId : chr "ELEMENT_GLOBAL.2.154701"
-#> $ elcode : chr "PDRAN0F010"
-#> $ conceptRefFullCitation : chr "Kartesz, J.T. 1994. A synonymized checklist of the vascular flora of the United States, Canada, and Greenland. "| __truncated__
-#> $ conceptName : chr "<i>Hydrastis canadensis</i>"
-#> $ taxonomicComments : chr "<i>Hydrastis canadensis</i> occurs in eastern North America and is a monotypic genus. In the most current taxon"| __truncated__
-#> $ roundedGRank : chr "G3"
-#> $ conservationStatusFactorsEditionDate : chr "2013-04-29"
-#> $ conservationStatusFactorsEditionAuthors: chr "Oliver, L."
-#> $ primaryCommonNameLanguage : chr "EN"
-#> $ recordType : chr "SPECIES"
-#> $ elementNationals :'data.frame': 2 obs. of 7 variables:
-#> $ lastModified : chr "2020-05-14T04:31:58.480462Z"
-#> $ lastPublished : chr "2020-05-14T02:14:14.569584Z"
-#> $ nsxUrl : chr "/Taxon/ELEMENT_GLOBAL.2.154701/Hydrastis_canadensis"
-#> $ grank : chr "G3G4"
-#> $ grankReviewDate : chr "2012-11-30"
-#> $ grankChangeDate : chr "2012-11-30"
-#> $ grankReasons : chr "Goldenseal, <i>Hydrastis canadensis, </i>an herbaceous understory species of the eastern deciduous forest, with"| __truncated__
-#> $ rankInfo :List of 27
-#> $ animalCharacteristics : NULL
-#> $ occurrenceDelineations :'data.frame': 1 obs. of 17 variables:
-#> $ plantCharacteristics :List of 7
-#> $ elementManagement :List of 14
-#> $ occurrenceViabilities :'data.frame': 1 obs. of 12 variables:
-#> $ references :'data.frame': 97 obs. of 6 variables:
-#> $ otherCommonNames :'data.frame': 6 obs. of 3 variables:
-#> $ speciesGlobal :List of 29
-#> $ speciesCharacteristics :List of 13
-```
-
-By alternate id
-
-
-```r
-x <- ns_altid(uid = "ELEMENT_GLOBAL.2.154701")
-str(x, max.level = 1)
-#> List of 40
-#> $ elementGlobalId : int 154701
-#> $ circumscripConfidence : NULL
-#> $ classificationLevel :List of 4
-#> $ classificationStatus :List of 4
-#> $ iucn :List of 5
-#> $ nameCategory :List of 6
-#> $ rankMethodUsed :List of 4
-#> $ formattedScientificName : chr "<i>Hydrastis canadensis</i>"
-#> $ scientificName : chr "Hydrastis canadensis"
-#> $ scientificNameAuthor : chr "L."
-#> $ primaryCommonName : chr "Goldenseal"
-#> $ relatedItisNames : chr "<i>Hydrastis canadensis</i> L. (TSN 18781)"
-#> $ uniqueId : chr "ELEMENT_GLOBAL.2.154701"
-#> $ elcode : chr "PDRAN0F010"
-#> $ conceptRefFullCitation : chr "Kartesz, J.T. 1994. A synonymized checklist of the vascular flora of the United States, Canada, and Greenland. "| __truncated__
-#> $ conceptName : chr "<i>Hydrastis canadensis</i>"
-#> $ taxonomicComments : chr "<i>Hydrastis canadensis</i> occurs in eastern North America and is a monotypic genus. In the most current taxon"| __truncated__
-#> $ roundedGRank : chr "G3"
-#> $ conservationStatusFactorsEditionDate : chr "2013-04-29"
-#> $ conservationStatusFactorsEditionAuthors: chr "Oliver, L."
-#> $ primaryCommonNameLanguage : chr "EN"
-#> $ recordType : chr "SPECIES"
-#> $ elementNationals :'data.frame': 2 obs. of 7 variables:
-#> $ lastModified : chr "2020-05-14T04:31:58.480462Z"
-#> $ lastPublished : chr "2020-05-14T02:14:14.569584Z"
-#> $ nsxUrl : chr "/Taxon/ELEMENT_GLOBAL.2.154701/Hydrastis_canadensis"
-#> $ grank : chr "G3G4"
-#> $ grankReviewDate : chr "2012-11-30"
-#> $ grankChangeDate : chr "2012-11-30"
-#> $ grankReasons : chr "Goldenseal, <i>Hydrastis canadensis, </i>an herbaceous understory species of the eastern deciduous forest, with"| __truncated__
-#> $ rankInfo :List of 27
-#> $ animalCharacteristics : NULL
-#> $ occurrenceDelineations :'data.frame': 1 obs. of 17 variables:
-#> $ plantCharacteristics :List of 7
-#> $ elementManagement :List of 14
-#> $ occurrenceViabilities :'data.frame': 1 obs. of 12 variables:
-#> $ references :'data.frame': 97 obs. of 6 variables:
-#> $ otherCommonNames :'data.frame': 6 obs. of 3 variables:
-#> $ speciesGlobal :List of 29
-#> $ speciesCharacteristics :List of 13
-```
-
-## Get a summary of the upper level hierarchy for an Ecosystem record
-
-
-```r
-ns_ecohier("ELEMENT_GLOBAL.2.683060")
-#> uniqueId
-#> 1 ELEMENT_GLOBAL.2.860217
-#> 2 ELEMENT_GLOBAL.2.860227
-#> 3 ELEMENT_GLOBAL.2.860241
-#> 4 ELEMENT_GLOBAL.2.860284
-#> 5 ELEMENT_GLOBAL.2.838501
-#> 6 ELEMENT_GLOBAL.2.833279
-#> 7 ELEMENT_GLOBAL.2.899395
-#> name
-#> 1 Forest & Woodland
-#> 2 Temperate & Boreal Forest & Woodland
-#> 3 Cool Temperate Forest & Woodland
-#> 4 Eastern North American Forest & Woodland
-#> 5 Southern & South-Central Oak - Pine Forest & Woodland
-#> 6 South-Central Interior Shortleaf Pine - Oak Forest & Woodland
-#> 7 Ozark-Ouachita Shortleaf Pine - Oak Woodland
-#> nsxUrl
-#> 1 /Taxon/ELEMENT_GLOBAL.2.860217/Mesomorphic_Tree_Vegetation_Class
-#> 2 /Taxon/ELEMENT_GLOBAL.2.860227/Temperate_Boreal_Forest_Woodland_Subclass
-#> 3 /Taxon/ELEMENT_GLOBAL.2.860241/Cool_Temperate_Forest_Woodland_Formation
-#> 4 /Taxon/ELEMENT_GLOBAL.2.860284/Acer_saccharum_-_Fagus_grandifolia_-_Quercus_rubra_Forest_Woodland_Division
-#> 5 /Taxon/ELEMENT_GLOBAL.2.838501/Quercus_alba_-_Quercus_falcata_-_Pinus_echinata_Forest_Woodland_Macrogroup
-#> 6 /Taxon/ELEMENT_GLOBAL.2.833279/Pinus_echinata_-_Quercus_falcata_-_Quercus_stellata_Forest_Woodland_Group
-#> 7 /Taxon/ELEMENT_GLOBAL.2.899395/Pinus_echinata_-_Quercus_stellata_-_Quercus_velutina_Ozark-Ouachita_Woodland_Alliance
-#> ecosystemType classificationCode
-#> 1 CLASS 1
-#> 2 SUBCLASS 1.B
-#> 3 FORMATION 1.B.2
-#> 4 DIVISION 1.B.2.Na
-#> 5 MACROGROUP M016
-#> 6 GROUP G012
-#> 7 ALLIANCE A3271
-```
-
-## Search exports
-
-`ns_export()` uses the same search interface as the `ns_search*` functions, but instead of downloading data immediately, `ns_export()` creates a "download job", which eventually provides a compressed JSON file that you can download.
-
-
-```r
-x <- ns_export(text = "robin")
-x
-#> [1] "7a107bea-b98d-4b5a-87b3-456ea2194f07"
-```
-
-You can pass the output of `ns_export()` to `ns_export_status()` to get the status of the job
-
-
-```r
-res <- ns_export_status(x)
-#> $state
-#> [1] "Finished"
-#>
-#> $data
-#> $data$success
-#> [1] TRUE
-#> $percentComplete
-#> [1] 100
-#> $successful
-#> [1] TRUE
-#> $error
-#> ...
-```
-
-When state equals "Finished", you can read the data into R, e.g, with `jsonlite`:
-
-
-```r
-res$data$url
-#> [1] "https://explorer-downloads.natureserve.org/shortTerm/explorer/taxaSearchExports/2020-05-15/7a107bea-b98d-4b5a-87b3-456ea2194f07.json"
-tibble::as_tibble(jsonlite::fromJSON(res$data$url))
-#> # A tibble: 126 x 14
-#> elementGlobalId uniqueId nsxUrl elcode scientificName formattedScient… primaryCommonNa… primaryCommonNa… roundedGRank
-#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
-#> 1 100637 ELEMENT… /Taxo… ABPBJ… Copsychus sau… <i>Copsychus sa… Oriental Magpie… EN G5
-#> 2 102323 ELEMENT… /Taxo… ABPBJ… Turdus grayi <i>Turdus grayi… Clay-colored Th… EN G5
-#> 3 102179 ELEMENT… /Taxo… ABPBJ… Turdus migrat… <i>Turdus migra… American Robin EN G5
-#> 4 105536 ELEMENT… /Taxo… ABPBJ… Turdus migrat… <i>Turdus migra… Western America… EN TU
-#> 5 105850 ELEMENT… /Taxo… ABPBJ… Turdus rufopa… <i>Turdus rufop… Rufous-backed R… EN G5
-#> 6 100589 ELEMENT… /Taxo… AFC4B… Peristedion g… <i>Peristedion … Slender Searobin EN GNR
-#> 7 105826 ELEMENT… /Taxo… AFC4B… Prionotus ala… <i>Prionotus al… Spiny Searobin EN GNR
-#> 8 101394 ELEMENT… /Taxo… AFC4B… Prionotus car… <i>Prionotus ca… Northern Searob… EN G5
-#> 9 100276 ELEMENT… /Taxo… AFC4B… Prionotus evo… <i>Prionotus ev… Striped Searobin EN G5
-#> 10 103595 ELEMENT… /Taxo… AFC4B… Prionotus lon… <i>Prionotus lo… Bigeye Searobin EN G5
-#> # … with 116 more rows, and 29 more variables: nations <list>, lastModified <chr>, speciesGlobal$usesaCode <chr>,
-#> # $cosewicCode <chr>, $saraCode <chr>, $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>, $taxonomicComments <chr>, $informalTaxonomy <chr>,
-#> # $infraspecies <lgl>, $completeDistribution <lgl>, gRank <chr>, ecosystemGlobal$translatedScientificName <chr>,
-#> # $taxclassCode <chr>, $taxsubclassCode <chr>, $formationCode <chr>, $divisionCode <chr>, $macrogroupKey <chr>,
-#> # $taxgroupKey <chr>, $allianceKey <chr>, $ecosystemType <chr>, $classificationCode <chr>, $parentName <chr>
-```
-
diff --git a/tests/testthat/helper-natserv.R b/tests/testthat/helper-natserv.R
index ddeed28..7cd190a 100644
--- a/tests/testthat/helper-natserv.R
+++ b/tests/testthat/helper-natserv.R
@@ -1,3 +1,3 @@
library("vcr")
-vcr_configure(dir = "../fixtures")
-check_cassette_names()
+vcr::vcr_configure(dir = "../fixtures")
+vcr::check_cassette_names()
diff --git a/vignettes/natserv.Rmd b/vignettes/natserv.Rmd
deleted file mode 100644
index c67897a..0000000
--- a/vignettes/natserv.Rmd
+++ /dev/null
@@ -1,420 +0,0 @@
----
-title: "natserv introduction"
-author: "Scott Chamberlain"
-date: "2020-05-15"
-output: rmarkdown::html_vignette
-vignette: >
- %\VignetteIndexEntry{natserv introduction}
- %\VignetteEngine{knitr::rmarkdown}
- \usepackage[utf8]{inputenc}
----
-
-
-
-`natserv` is an R package that interacts with the API services of the non-profit organization NatureServe (https://services.natureserve.org/). If you want to read the full API documentation, you can find it at https://explorer.natureserve.org/api-docs/
-
-See also the taxize book (https://taxize.dev/) for
-a manual on working with taxonomic data in R, including with NatureServe data.
-
-This tutorial will walk you through installing `natserv` and using its functions.
-
-## A quick introduction to NatureServe
-
-NatureServe is a non-profit organization that provides biodiversity data freely online.
-They maintain a database comprised of data from natural heritage programs and conservation data centers - this database includes information about the conservation status, taxonomy, geographic distribution, and life history information for over 70,000 species of plants, animals, and fungi in Canada and the United States.
-You can find information about their data coverage (https://explorer.natureserve.org/AboutTheData/DataCoverage), and data sources (https://explorer.natureserve.org/AboutTheData/Sources) on their website. NatureServe also hosts data on ecological communities/systems and their conservation status.
-
-While small amounts of data can be easily collected using their online NatureServe explorer site (http://explorer.natureserve.org/), downloading species data this way would be incredibly slow.
-Thus `natserv` was born.
-This R package can access NatureServe's online API for rapid downloading of conservation data, allows for easy access to multiple species' data sets, and loads the data directly into your R session.
-
-## Installing `natserv` from CRAN or GitHub
-
-Stable version:
-
-
-```r
-install.packages("natserv")
-```
-
-Development version:
-
-
-```r
-remotes::install_github("ropensci/natserv")
-```
-
-After successful installation, load the package into the environment:
-
-
-```r
-library(natserv)
-```
-
-## `natserv` functions
-
-All of `natserv`'s functions are prefixed with `ns_` to avoid confusion with other packages - here are the functions provided by `natserv`:
-
-
-```r
-cat(paste(" -", paste(sprintf("`%s`", sort(getNamespaceExports("natserv"))), collapse = "\n - ")))
-#> - `ns_altid`
-#> - `ns_ecohier`
-#> - `ns_export`
-#> - `ns_export_status`
-#> - `ns_id`
-#> - `ns_search_comb`
-#> - `ns_search_eco`
-#> - `ns_search_spp`
-```
-
-## Search
-
-There's three functions for search:
-
-- combined: supports searching for both species and ecosystems using search criteria which are applicable to both types of records
-- species: supports searching for only species; extends the search criteria available through the Combined Search to include support for additional criteria which are only applicable to species records
-- ecosystem: supports searching for only ecosystems; extends the search criteria available through the Combined Search to include support for additional criteria which are only applicable to ecosystems records
-
-Combined search
-
-
-```r
-ns_search_comb(text = "robin", page = 0, per_page = 5)
-#> $results
-#> # A tibble: 5 x 14
-#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
-#> <chr> <int> <chr> <chr> <chr> <chr>
-#> 1 SPECIES 100637 ELEMENT… /Taxo… ABPBJ… Copsychus sau…
-#> 2 SPECIES 102323 ELEMENT… /Taxo… ABPBJ… Turdus grayi
-#> 3 SPECIES 102179 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
-#> 4 SPECIES 105536 ELEMENT… /Taxo… ABPBJ… Turdus migrat…
-#> 5 SPECIES 105850 ELEMENT… /Taxo… ABPBJ… Turdus rufopa…
-#> # … with 22 more variables: formattedScientificName <chr>,
-#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
-#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
-#> # speciesGlobal$usesaCode <lgl>, $cosewicCode <lgl>, $saraCode <lgl>,
-#> # $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>,
-#> # $taxonomicComments <chr>, $informalTaxonomy <chr>, $infraspecies <lgl>,
-#> # $completeDistribution <lgl>, gRank <chr>
-#>
-#> $resultsSummary
-#> name value
-#> 1 page 0
-#> 2 recordsPerPage 5
-#> 3 totalPages 26
-#> 4 totalResults 126
-#> 5 species_total 103
-#> 6 total 23
-#> 7 classes 0
-#> 8 subclasses 0
-#> 9 formations 0
-#> 10 divisions 0
-#> 11 macrogroups 1
-#> 12 groups 1
-#> 13 alliances 3
-#> 14 associations 18
-#> 15 terrestrialEcologicalSystems 0
-```
-
-Species search
-
-
-```r
-ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Animalia", level = "kingdom"))
-#> $results
-#> # A tibble: 20 x 14
-#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
-#> <chr> <int> <chr> <chr> <chr> <chr>
-#> 1 SPECIES 828458 ELEMENT… /Taxo… AAABC… Acris blancha…
-#> 2 SPECIES 828419 ELEMENT… /Taxo… AAABC… Acris crepita…
-#> 3 SPECIES 103292 ELEMENT… /Taxo… AAABC… Acris gryllus
-#> 4 SPECIES 104324 ELEMENT… /Taxo… AAAAA… Ambystoma ann…
-#> 5 SPECIES 100100 ELEMENT… /Taxo… AAAAA… Ambystoma bar…
-#> 6 SPECIES 802300 ELEMENT… /Taxo… AAAAA… Ambystoma bis…
-#> 7 SPECIES 104488 ELEMENT… /Taxo… AAAAA… Ambystoma cal…
-#> 8 SPECIES 802301 ELEMENT… /Taxo… AAAAA… Ambystoma cin…
-#> 9 SPECIES 103251 ELEMENT… /Taxo… AAAAA… Ambystoma gra…
-#> 10 SPECIES 100401 ELEMENT… /Taxo… AAAAA… Ambystoma jef…
-#> 11 SPECIES 102149 ELEMENT… /Taxo… AAAAA… Ambystoma lat…
-#> 12 SPECIES 1143335 ELEMENT… /Taxo… AAAAA… Ambystoma lat…
-#> 13 SPECIES 1143337 ELEMENT… /Taxo… AAAAA… Ambystoma lat…
-#> 14 SPECIES 101261 ELEMENT… /Taxo… AAAAA… Ambystoma mab…
-#> 15 SPECIES 106403 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 16 SPECIES 101632 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 17 SPECIES 103392 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 18 SPECIES 104239 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 19 SPECIES 100115 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> 20 SPECIES 103039 ELEMENT… /Taxo… AAAAA… Ambystoma mac…
-#> # … with 22 more variables: formattedScientificName <chr>,
-#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
-#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
-#> # speciesGlobal$usesaCode <chr>, $cosewicCode <chr>, $saraCode <chr>,
-#> # $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>,
-#> # $taxonomicComments <chr>, $informalTaxonomy <chr>, $infraspecies <lgl>,
-#> # $completeDistribution <lgl>, gRank <chr>
-#>
-#> $resultsSummary
-#> name value
-#> 1 page 0
-#> 2 recordsPerPage 20
-#> 3 totalPages 2586
-#> 4 totalResults 51705
-#> 5 species_total 51705
-```
-
-Ecosystem search
-
-
-```r
-ns_search_eco(ecosystem_taxonomy = "M067")
-#> $results
-#> # A tibble: 20 x 14
-#> recordType elementGlobalId uniqueId nsxUrl elcode scientificName
-#> <chr> <int> <chr> <chr> <chr> <chr>
-#> 1 ECOSYSTEM 899525 ELEMENT… /Taxo… A3401 Eleocharis el…
-#> 2 ECOSYSTEM 899121 ELEMENT… /Taxo… A1372 Fimbristylis …
-#> 3 ECOSYSTEM 899126 ELEMENT… /Taxo… A1389 Spartina bake…
-#> 4 ECOSYSTEM 899744 ELEMENT… /Taxo… A3692 Spartina pate…
-#> 5 ECOSYSTEM 899523 ELEMENT… /Taxo… A3399 Typha dominge…
-#> 6 ECOSYSTEM 899526 ELEMENT… /Taxo… A3402 Andropogon ca…
-#> 7 ECOSYSTEM 899517 ELEMENT… /Taxo… A3393 Aristida palu…
-#> 8 ECOSYSTEM 899132 ELEMENT… /Taxo… A1429 Eleocharis sp…
-#> 9 ECOSYSTEM 899512 ELEMENT… /Taxo… A3388 Hypericum cha…
-#> 10 ECOSYSTEM 899133 ELEMENT… /Taxo… A1430 Juncus milita…
-#> 11 ECOSYSTEM 899122 ELEMENT… /Taxo… A1379 Panicum hemit…
-#> 12 ECOSYSTEM 899124 ELEMENT… /Taxo… A1383 Rhynchospora …
-#> 13 ECOSYSTEM 899518 ELEMENT… /Taxo… A3394 Rhynchospora …
-#> 14 ECOSYSTEM 1146914 ELEMENT… /Taxo… A4404 Rhynchospora …
-#> 15 ECOSYSTEM 899521 ELEMENT… /Taxo… A3397 Rhynchospora …
-#> 16 ECOSYSTEM 899125 ELEMENT… /Taxo… A1384 Rhynchospora …
-#> 17 ECOSYSTEM 899530 ELEMENT… /Taxo… A3406 Cladium maris…
-#> 18 ECOSYSTEM 899120 ELEMENT… /Taxo… A1369 Cladium maris…
-#> 19 ECOSYSTEM 899720 ELEMENT… /Taxo… A3668 Hottonia infl…
-#> 20 ECOSYSTEM 900115 ELEMENT… /Taxo… A4065 Orontium aqua…
-#> # … with 18 more variables: formattedScientificName <chr>,
-#> # primaryCommonName <chr>, primaryCommonNameLanguage <chr>,
-#> # roundedGRank <chr>, nations <list>, lastModified <chr>,
-#> # ecosystemGlobal$translatedScientificName <chr>, $taxclassCode <chr>,
-#> # $taxsubclassCode <chr>, $formationCode <chr>, $divisionCode <chr>,
-#> # $macrogroupKey <chr>, $taxgroupKey <chr>, $allianceKey <lgl>,
-#> # $ecosystemType <chr>, $classificationCode <chr>, $parentName <chr>,
-#> # gRank <chr>
-#>
-#> $resultsSummary
-#> name value
-#> 1 page 0
-#> 2 recordsPerPage 20
-#> 3 totalPages 11
-#> 4 totalResults 210
-#> 5 total 210
-#> 6 classes 0
-#> 7 subclasses 0
-#> 8 formations 0
-#> 9 divisions 0
-#> 10 macrogroups 1
-#> 11 groups 6
-#> 12 alliances 33
-#> 13 associations 154
-#> 14 terrestrialEcologicalSystems 16
-```
-
-## Get taxon by id
-
-By UID
-
-
-```r
-w <- ns_id("ELEMENT_GLOBAL.2.154701")
-str(w, max.level = 1)
-#> List of 40
-#> $ elementGlobalId : int 154701
-#> $ circumscripConfidence : NULL
-#> $ classificationLevel :List of 4
-#> $ classificationStatus :List of 4
-#> $ iucn :List of 5
-#> $ nameCategory :List of 6
-#> $ rankMethodUsed :List of 4
-#> $ formattedScientificName : chr "<i>Hydrastis canadensis</i>"
-#> $ scientificName : chr "Hydrastis canadensis"
-#> $ scientificNameAuthor : chr "L."
-#> $ primaryCommonName : chr "Goldenseal"
-#> $ relatedItisNames : chr "<i>Hydrastis canadensis</i> L. (TSN 18781)"
-#> $ uniqueId : chr "ELEMENT_GLOBAL.2.154701"
-#> $ elcode : chr "PDRAN0F010"
-#> $ conceptRefFullCitation : chr "Kartesz, J.T. 1994. A synonymized checklist of the vascular flora of the United States, Canada, and Greenland. "| __truncated__
-#> $ conceptName : chr "<i>Hydrastis canadensis</i>"
-#> $ taxonomicComments : chr "<i>Hydrastis canadensis</i> occurs in eastern North America and is a monotypic genus. In the most current taxon"| __truncated__
-#> $ roundedGRank : chr "G3"
-#> $ conservationStatusFactorsEditionDate : chr "2013-04-29"
-#> $ conservationStatusFactorsEditionAuthors: chr "Oliver, L."
-#> $ primaryCommonNameLanguage : chr "EN"
-#> $ recordType : chr "SPECIES"
-#> $ elementNationals :'data.frame': 2 obs. of 7 variables:
-#> $ lastModified : chr "2020-05-14T04:31:58.480462Z"
-#> $ lastPublished : chr "2020-05-14T02:14:14.569584Z"
-#> $ nsxUrl : chr "/Taxon/ELEMENT_GLOBAL.2.154701/Hydrastis_canadensis"
-#> $ grank : chr "G3G4"
-#> $ grankReviewDate : chr "2012-11-30"
-#> $ grankChangeDate : chr "2012-11-30"
-#> $ grankReasons : chr "Goldenseal, <i>Hydrastis canadensis, </i>an herbaceous understory species of the eastern deciduous forest, with"| __truncated__
-#> $ rankInfo :List of 27
-#> $ animalCharacteristics : NULL
-#> $ occurrenceDelineations :'data.frame': 1 obs. of 17 variables:
-#> $ plantCharacteristics :List of 7
-#> $ elementManagement :List of 14
-#> $ occurrenceViabilities :'data.frame': 1 obs. of 12 variables:
-#> $ references :'data.frame': 97 obs. of 6 variables:
-#> $ otherCommonNames :'data.frame': 6 obs. of 3 variables:
-#> $ speciesGlobal :List of 29
-#> $ speciesCharacteristics :List of 13
-```
-
-By alternate id
-
-
-```r
-x <- ns_altid(uid = "ELEMENT_GLOBAL.2.154701")
-str(x, max.level = 1)
-#> List of 40
-#> $ elementGlobalId : int 154701
-#> $ circumscripConfidence : NULL
-#> $ classificationLevel :List of 4
-#> $ classificationStatus :List of 4
-#> $ iucn :List of 5
-#> $ nameCategory :List of 6
-#> $ rankMethodUsed :List of 4
-#> $ formattedScientificName : chr "<i>Hydrastis canadensis</i>"
-#> $ scientificName : chr "Hydrastis canadensis"
-#> $ scientificNameAuthor : chr "L."
-#> $ primaryCommonName : chr "Goldenseal"
-#> $ relatedItisNames : chr "<i>Hydrastis canadensis</i> L. (TSN 18781)"
-#> $ uniqueId : chr "ELEMENT_GLOBAL.2.154701"
-#> $ elcode : chr "PDRAN0F010"
-#> $ conceptRefFullCitation : chr "Kartesz, J.T. 1994. A synonymized checklist of the vascular flora of the United States, Canada, and Greenland. "| __truncated__
-#> $ conceptName : chr "<i>Hydrastis canadensis</i>"
-#> $ taxonomicComments : chr "<i>Hydrastis canadensis</i> occurs in eastern North America and is a monotypic genus. In the most current taxon"| __truncated__
-#> $ roundedGRank : chr "G3"
-#> $ conservationStatusFactorsEditionDate : chr "2013-04-29"
-#> $ conservationStatusFactorsEditionAuthors: chr "Oliver, L."
-#> $ primaryCommonNameLanguage : chr "EN"
-#> $ recordType : chr "SPECIES"
-#> $ elementNationals :'data.frame': 2 obs. of 7 variables:
-#> $ lastModified : chr "2020-05-14T04:31:58.480462Z"
-#> $ lastPublished : chr "2020-05-14T02:14:14.569584Z"
-#> $ nsxUrl : chr "/Taxon/ELEMENT_GLOBAL.2.154701/Hydrastis_canadensis"
-#> $ grank : chr "G3G4"
-#> $ grankReviewDate : chr "2012-11-30"
-#> $ grankChangeDate : chr "2012-11-30"
-#> $ grankReasons : chr "Goldenseal, <i>Hydrastis canadensis, </i>an herbaceous understory species of the eastern deciduous forest, with"| __truncated__
-#> $ rankInfo :List of 27
-#> $ animalCharacteristics : NULL
-#> $ occurrenceDelineations :'data.frame': 1 obs. of 17 variables:
-#> $ plantCharacteristics :List of 7
-#> $ elementManagement :List of 14
-#> $ occurrenceViabilities :'data.frame': 1 obs. of 12 variables:
-#> $ references :'data.frame': 97 obs. of 6 variables:
-#> $ otherCommonNames :'data.frame': 6 obs. of 3 variables:
-#> $ speciesGlobal :List of 29
-#> $ speciesCharacteristics :List of 13
-```
-
-## Get a summary of the upper level hierarchy for an Ecosystem record
-
-
-```r
-ns_ecohier("ELEMENT_GLOBAL.2.683060")
-#> uniqueId
-#> 1 ELEMENT_GLOBAL.2.860217
-#> 2 ELEMENT_GLOBAL.2.860227
-#> 3 ELEMENT_GLOBAL.2.860241
-#> 4 ELEMENT_GLOBAL.2.860284
-#> 5 ELEMENT_GLOBAL.2.838501
-#> 6 ELEMENT_GLOBAL.2.833279
-#> 7 ELEMENT_GLOBAL.2.899395
-#> name
-#> 1 Forest & Woodland
-#> 2 Temperate & Boreal Forest & Woodland
-#> 3 Cool Temperate Forest & Woodland
-#> 4 Eastern North American Forest & Woodland
-#> 5 Southern & South-Central Oak - Pine Forest & Woodland
-#> 6 South-Central Interior Shortleaf Pine - Oak Forest & Woodland
-#> 7 Ozark-Ouachita Shortleaf Pine - Oak Woodland
-#> nsxUrl
-#> 1 /Taxon/ELEMENT_GLOBAL.2.860217/Mesomorphic_Tree_Vegetation_Class
-#> 2 /Taxon/ELEMENT_GLOBAL.2.860227/Temperate_Boreal_Forest_Woodland_Subclass
-#> 3 /Taxon/ELEMENT_GLOBAL.2.860241/Cool_Temperate_Forest_Woodland_Formation
-#> 4 /Taxon/ELEMENT_GLOBAL.2.860284/Acer_saccharum_-_Fagus_grandifolia_-_Quercus_rubra_Forest_Woodland_Division
-#> 5 /Taxon/ELEMENT_GLOBAL.2.838501/Quercus_alba_-_Quercus_falcata_-_Pinus_echinata_Forest_Woodland_Macrogroup
-#> 6 /Taxon/ELEMENT_GLOBAL.2.833279/Pinus_echinata_-_Quercus_falcata_-_Quercus_stellata_Forest_Woodland_Group
-#> 7 /Taxon/ELEMENT_GLOBAL.2.899395/Pinus_echinata_-_Quercus_stellata_-_Quercus_velutina_Ozark-Ouachita_Woodland_Alliance
-#> ecosystemType classificationCode
-#> 1 CLASS 1
-#> 2 SUBCLASS 1.B
-#> 3 FORMATION 1.B.2
-#> 4 DIVISION 1.B.2.Na
-#> 5 MACROGROUP M016
-#> 6 GROUP G012
-#> 7 ALLIANCE A3271
-```
-
-## Search exports
-
-`ns_export()` uses the same search interface as the `ns_search*` functions, but instead of downloading data immediately, `ns_export()` creates a "download job", which eventually provides a compressed JSON file that you can download.
-
-
-```r
-x <- ns_export(text = "robin")
-x
-#> [1] "7a107bea-b98d-4b5a-87b3-456ea2194f07"
-```
-
-You can pass the output of `ns_export()` to `ns_export_status()` to get the status of the job
-
-
-```r
-res <- ns_export_status(x)
-#> $state
-#> [1] "Finished"
-#>
-#> $data
-#> $data$success
-#> [1] TRUE
-#> $percentComplete
-#> [1] 100
-#> $successful
-#> [1] TRUE
-#> $error
-#> ...
-```
-
-When state equals "Finished", you can read the data into R, e.g, with `jsonlite`:
-
-
-```r
-res$data$url
-#> [1] "https://explorer-downloads.natureserve.org/shortTerm/explorer/taxaSearchExports/2020-05-15/7a107bea-b98d-4b5a-87b3-456ea2194f07.json"
-tibble::as_tibble(jsonlite::fromJSON(res$data$url))
-#> # A tibble: 126 x 14
-#> elementGlobalId uniqueId nsxUrl elcode scientificName formattedScient… primaryCommonNa… primaryCommonNa… roundedGRank
-#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
-#> 1 100637 ELEMENT… /Taxo… ABPBJ… Copsychus sau… <i>Copsychus sa… Oriental Magpie… EN G5
-#> 2 102323 ELEMENT… /Taxo… ABPBJ… Turdus grayi <i>Turdus grayi… Clay-colored Th… EN G5
-#> 3 102179 ELEMENT… /Taxo… ABPBJ… Turdus migrat… <i>Turdus migra… American Robin EN G5
-#> 4 105536 ELEMENT… /Taxo… ABPBJ… Turdus migrat… <i>Turdus migra… Western America… EN TU
-#> 5 105850 ELEMENT… /Taxo… ABPBJ… Turdus rufopa… <i>Turdus rufop… Rufous-backed R… EN G5
-#> 6 100589 ELEMENT… /Taxo… AFC4B… Peristedion g… <i>Peristedion … Slender Searobin EN GNR
-#> 7 105826 ELEMENT… /Taxo… AFC4B… Prionotus ala… <i>Prionotus al… Spiny Searobin EN GNR
-#> 8 101394 ELEMENT… /Taxo… AFC4B… Prionotus car… <i>Prionotus ca… Northern Searob… EN G5
-#> 9 100276 ELEMENT… /Taxo… AFC4B… Prionotus evo… <i>Prionotus ev… Striped Searobin EN G5
-#> 10 103595 ELEMENT… /Taxo… AFC4B… Prionotus lon… <i>Prionotus lo… Bigeye Searobin EN G5
-#> # … with 116 more rows, and 29 more variables: nations <list>, lastModified <chr>, speciesGlobal$usesaCode <chr>,
-#> # $cosewicCode <chr>, $saraCode <chr>, $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>, $taxonomicComments <chr>, $informalTaxonomy <chr>,
-#> # $infraspecies <lgl>, $completeDistribution <lgl>, gRank <chr>, ecosystemGlobal$translatedScientificName <chr>,
-#> # $taxclassCode <chr>, $taxsubclassCode <chr>, $formationCode <chr>, $divisionCode <chr>, $macrogroupKey <chr>,
-#> # $taxgroupKey <chr>, $allianceKey <chr>, $ecosystemType <chr>, $classificationCode <chr>, $parentName <chr>
-```
-
diff --git a/vignettes/natserv.Rmd.og b/vignettes/natserv.Rmd.og
deleted file mode 100644
index dd9eac6..0000000
--- a/vignettes/natserv.Rmd.og
+++ /dev/null
@@ -1,172 +0,0 @@
----
-title: "natserv introduction"
-author: "Scott Chamberlain"
-date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
-vignette: >
- %\VignetteIndexEntry{natserv introduction}
- %\VignetteEngine{knitr::rmarkdown}
- \usepackage[utf8]{inputenc}
----
-
-```{r, echo = FALSE, warning = FALSE, message = FALSE}
-NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")
-knitr::opts_chunk$set(
- collapse = TRUE,
- comment = "#>",
- warning = FALSE,
- message = FALSE,
- purl = NOT_CRAN,
- eval = NOT_CRAN,
- fig.path = "../man/figures/"
-)
-```
-
-`natserv` is an R package that interacts with the API services of the non-profit organization NatureServe (https://services.natureserve.org/). If you want to read the full API documentation, you can find it at https://explorer.natureserve.org/api-docs/
-
-See also the taxize book (https://taxize.dev/) for
-a manual on working with taxonomic data in R, including with NatureServe data.
-
-This tutorial will walk you through installing `natserv` and using its functions.
-
-## A quick introduction to NatureServe
-
-NatureServe is a non-profit organization that provides biodiversity data freely online.
-They maintain a database comprised of data from natural heritage programs and conservation data centers - this database includes information about the conservation status, taxonomy, geographic distribution, and life history information for over 70,000 species of plants, animals, and fungi in Canada and the United States.
-You can find information about their data coverage (https://explorer.natureserve.org/AboutTheData/DataCoverage), and data sources (https://explorer.natureserve.org/AboutTheData/Sources) on their website. NatureServe also hosts data on ecological communities/systems and their conservation status.
-
-While small amounts of data can be easily collected using their online NatureServe explorer site (http://explorer.natureserve.org/), downloading species data this way would be incredibly slow.
-Thus `natserv` was born.
-This R package can access NatureServe's online API for rapid downloading of conservation data, allows for easy access to multiple species' data sets, and loads the data directly into your R session.
-
-## Installing `natserv` from CRAN or GitHub
-
-Stable version:
-
-```{r eval=FALSE}
-install.packages("natserv")
-```
-
-Development version:
-
-```{r eval=FALSE}
-remotes::install_github("ropensci/natserv")
-```
-
-After successful installation, load the package into the environment:
-
-```{r}
-library(natserv)
-```
-
-## `natserv` functions
-
-All of `natserv`'s functions are prefixed with `ns_` to avoid confusion with other packages - here are the functions provided by `natserv`:
-
-```{r}
-cat(paste(" -", paste(sprintf("`%s`", sort(getNamespaceExports("natserv"))), collapse = "\n - ")))
-```
-
-## Search
-
-There's three functions for search:
-
-- combined: supports searching for both species and ecosystems using search criteria which are applicable to both types of records
-- species: supports searching for only species; extends the search criteria available through the Combined Search to include support for additional criteria which are only applicable to species records
-- ecosystem: supports searching for only ecosystems; extends the search criteria available through the Combined Search to include support for additional criteria which are only applicable to ecosystems records
-
-Combined search
-
-```{r}
-ns_search_comb(text = "robin", page = 0, per_page = 5)
-```
-
-Species search
-
-```{r}
-ns_search_spp(species_taxonomy = list(scientificTaxonomy = "Animalia", level = "kingdom"))
-```
-
-Ecosystem search
-
-```{r}
-ns_search_eco(ecosystem_taxonomy = "M067")
-```
-
-## Get taxon by id
-
-By UID
-
-```{r}
-w <- ns_id("ELEMENT_GLOBAL.2.154701")
-str(w, max.level = 1)
-```
-
-By alternate id
-
-```{r}
-x <- ns_altid(uid = "ELEMENT_GLOBAL.2.154701")
-str(x, max.level = 1)
-```
-
-## Get a summary of the upper level hierarchy for an Ecosystem record
-
-```{r}
-ns_ecohier("ELEMENT_GLOBAL.2.683060")
-```
-
-## Search exports
-
-`ns_export()` uses the same search interface as the `ns_search*` functions, but instead of downloading data immediately, `ns_export()` creates a "download job", which eventually provides a compressed JSON file that you can download.
-
-```{r eval=FALSE}
-x <- ns_export(text = "robin")
-x
-#> [1] "7a107bea-b98d-4b5a-87b3-456ea2194f07"
-```
-
-You can pass the output of `ns_export()` to `ns_export_status()` to get the status of the job
-
-```{r eval=FALSE}
-res <- ns_export_status(x)
-#> $state
-#> [1] "Finished"
-#>
-#> $data
-#> $data$success
-#> [1] TRUE
-#> $percentComplete
-#> [1] 100
-#> $successful
-#> [1] TRUE
-#> $error
-#> ...
-```
-
-When state equals "Finished", you can read the data into R, e.g, with `jsonlite`:
-
-```{r eval=FALSE}
-res$data$url
-#> [1] "https://explorer-downloads.natureserve.org/shortTerm/explorer/taxaSearchExports/2020-05-15/7a107bea-b98d-4b5a-87b3-456ea2194f07.json"
-tibble::as_tibble(jsonlite::fromJSON(res$data$url))
-#> # A tibble: 126 x 14
-#> elementGlobalId uniqueId nsxUrl elcode scientificName formattedScient… primaryCommonNa… primaryCommonNa… roundedGRank
-#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
-#> 1 100637 ELEMENT… /Taxo… ABPBJ… Copsychus sau… <i>Copsychus sa… Oriental Magpie… EN G5
-#> 2 102323 ELEMENT… /Taxo… ABPBJ… Turdus grayi <i>Turdus grayi… Clay-colored Th… EN G5
-#> 3 102179 ELEMENT… /Taxo… ABPBJ… Turdus migrat… <i>Turdus migra… American Robin EN G5
-#> 4 105536 ELEMENT… /Taxo… ABPBJ… Turdus migrat… <i>Turdus migra… Western America… EN TU
-#> 5 105850 ELEMENT… /Taxo… ABPBJ… Turdus rufopa… <i>Turdus rufop… Rufous-backed R… EN G5
-#> 6 100589 ELEMENT… /Taxo… AFC4B… Peristedion g… <i>Peristedion … Slender Searobin EN GNR
-#> 7 105826 ELEMENT… /Taxo… AFC4B… Prionotus ala… <i>Prionotus al… Spiny Searobin EN GNR
-#> 8 101394 ELEMENT… /Taxo… AFC4B… Prionotus car… <i>Prionotus ca… Northern Searob… EN G5
-#> 9 100276 ELEMENT… /Taxo… AFC4B… Prionotus evo… <i>Prionotus ev… Striped Searobin EN G5
-#> 10 103595 ELEMENT… /Taxo… AFC4B… Prionotus lon… <i>Prionotus lo… Bigeye Searobin EN G5
-#> # … with 116 more rows, and 29 more variables: nations <list>, lastModified <chr>, speciesGlobal$usesaCode <chr>,
-#> # $cosewicCode <chr>, $saraCode <chr>, $synonyms <list>, $otherCommonNames <list>, $kingdom <chr>, $phylum <chr>,
-#> # $taxclass <chr>, $taxorder <chr>, $family <chr>, $genus <chr>, $taxonomicComments <chr>, $informalTaxonomy <chr>,
-#> # $infraspecies <lgl>, $completeDistribution <lgl>, gRank <chr>, ecosystemGlobal$translatedScientificName <chr>,
-#> # $taxclassCode <chr>, $taxsubclassCode <chr>, $formationCode <chr>, $divisionCode <chr>, $macrogroupKey <chr>,
-#> # $taxgroupKey <chr>, $allianceKey <chr>, $ecosystemType <chr>, $classificationCode <chr>, $parentName <chr>
-```
-
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/lib/R/site-library/natserv/Meta/vignette.rds -rw-r--r-- root/root /usr/lib/R/site-library/natserv/doc/index.html -rw-r--r-- root/root /usr/lib/R/site-library/natserv/doc/natserv.Rmd
Control files: lines which differ (wdiff format)
Depends: r-base-core (>= 4.1.3.20220413-2~jan+lint1), 4.2.2.20221110-1), r-api-4.0, r-cran-crul (>= 0.7.0), r-cran-jsonlite, r-cran-tibble
Suggests: r-cran-knitr