From 042e558033767d54d16e40773c6929cda6e92e3b Mon Sep 17 00:00:00 2001 From: wcornwell Date: Tue, 28 Jan 2025 05:55:31 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20traiteco?= =?UTF-8?q?evo/APCalign@59ae1eeb062e5583044c9053e6e36baec21a9b98=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/APCalign.html | 2 +- articles/data-providers.html | 2 +- articles/reproducibility.html | 4 +-- articles/updating-taxon-names.html | 2 +- authors.html | 2 +- news/index.html | 2 +- pkgdown.yml | 2 +- reference/APCalign.html | 2 +- reference/align_taxa.html | 2 +- .../create_species_state_origin_matrix.html | 32 +++++++++---------- reference/create_taxonomic_update_lookup.html | 6 ++-- reference/default_version.html | 4 +-- reference/gbif_lite.html | 2 +- reference/get_apc_genus_family_lookup.html | 2 +- reference/get_versions.html | 25 ++++++++------- reference/load_taxonomic_resources.html | 5 ++- reference/native_anywhere_in_australia.html | 2 +- reference/reexports.html | 2 +- reference/standardise_names.html | 2 +- reference/standardise_taxon_rank.html | 2 +- reference/state_diversity_counts.html | 10 +++--- reference/strip_names.html | 2 +- reference/strip_names_extra.html | 2 +- reference/update_taxonomy.html | 2 +- search.json | 2 +- 25 files changed, 63 insertions(+), 59 deletions(-) diff --git a/articles/APCalign.html b/articles/APCalign.html index 2e60288..6f7f66c 100644 --- a/articles/APCalign.html +++ b/articles/APCalign.html @@ -62,7 +62,7 @@

APCalign

- Source: vignettes/APCalign.Rmd + Source: vignettes/APCalign.Rmd
APCalign.Rmd
diff --git a/articles/data-providers.html b/articles/data-providers.html index 1fc6ebc..fdcda12 100644 --- a/articles/data-providers.html +++ b/articles/data-providers.html @@ -62,7 +62,7 @@

Data Providers

- Source: vignettes/articles/data-providers.Rmd + Source: vignettes/articles/data-providers.Rmd
data-providers.Rmd
diff --git a/articles/reproducibility.html b/articles/reproducibility.html index 768c33f..b190973 100644 --- a/articles/reproducibility.html +++ b/articles/reproducibility.html @@ -62,7 +62,7 @@

How to be more reproducible with APCalign

- Source: vignettes/articles/reproducibility.Rmd + Source: vignettes/articles/reproducibility.Rmd
reproducibility.Rmd
@@ -118,7 +118,7 @@

Taxonomic Resources
 default_version()
-#> [1] "2024-10-11"
+#> [1] "2025-01-28"

Then copying and pasting the output into load_taxonomic_resources() directly. This way makes the version of taxonomic resources more explicit in your code.

diff --git a/articles/updating-taxon-names.html b/articles/updating-taxon-names.html index 2fea7ff..b4dbd9c 100644 --- a/articles/updating-taxon-names.html +++ b/articles/updating-taxon-names.html @@ -62,7 +62,7 @@

Methods for updating taxon names in APCalign

- Source: vignettes/updating-taxon-names.Rmd + Source: vignettes/updating-taxon-names.Rmd
updating-taxon-names.Rmd
diff --git a/authors.html b/authors.html index ddb89d1..889f413 100644 --- a/authors.html +++ b/authors.html @@ -65,7 +65,7 @@

Authors

Citation

-

Source: inst/CITATION

+

Source: inst/CITATION

Wenk E, Cornwell W, Fuchs A, Kar F, Monro A, Sauquet H, Stephens R, Falster D (2024). “APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census.” diff --git a/news/index.html b/news/index.html index 1b31536..0039332 100644 --- a/news/index.html +++ b/news/index.html @@ -36,7 +36,7 @@

Changelog

- Source: NEWS.md + Source: NEWS.md
diff --git a/pkgdown.yml b/pkgdown.yml index c7350e9..935e009 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: articles/data-providers: data-providers.html articles/reproducibility: reproducibility.html updating-taxon-names: updating-taxon-names.html -last_built: 2025-01-28T05:49Z +last_built: 2025-01-28T05:53Z urls: reference: https://traitecoevo.github.io/APCalign/reference article: https://traitecoevo.github.io/APCalign/articles diff --git a/reference/APCalign.html b/reference/APCalign.html index 5c6fb1f..5c93cad 100644 --- a/reference/APCalign.html +++ b/reference/APCalign.html @@ -44,7 +44,7 @@

Standardising Taxonomic Names in Australian Plants

- Source: R/APCalign-package.R + Source: R/APCalign-package.R
APCalign.Rd
diff --git a/reference/align_taxa.html b/reference/align_taxa.html index eb9978e..3d03faa 100644 --- a/reference/align_taxa.html +++ b/reference/align_taxa.html @@ -52,7 +52,7 @@

Align Australian plant scientific names to the APC or APNI

- Source: R/align_taxa.R + Source: R/align_taxa.R
align_taxa.Rd
diff --git a/reference/create_species_state_origin_matrix.html b/reference/create_species_state_origin_matrix.html index 936c531..6d4b57f 100644 --- a/reference/create_species_state_origin_matrix.html +++ b/reference/create_species_state_origin_matrix.html @@ -42,7 +42,7 @@

State level native and introduced origin status

- Source: R/create_species_state_origin_matrix.R + Source: R/create_species_state_origin_matrix.R
create_species_state_origin_matrix.Rd
@@ -88,22 +88,22 @@

Examples#> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done -#> # A tibble: 26,273 × 19 -#> species NT Qld WA ChI NSW SA Vic Tas ACT NI LHI +#> # A tibble: 26,509 × 19 +#> species WA NT Qld SA NSW Vic Tas ChI LHI CoI NI #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> -#> 1 Cycas angu… nati… nati… not … not … not … not … not … not … not … not … not … -#> 2 Cycas aren… nati… not … not … not … not … not … not … not … not … not … not … -#> 3 Cycas arms… nati… not … not … not … not … not … not … not … not … not … not … -#> 4 Cycas arnh… nati… not … not … not … not … not … not … not … not … not … not … -#> 5 Cycas bade… not … nati… not … not … not … not … not … not … not … not … not … -#> 6 Cycas basa… not … not … nati… not … not … not … not … not … not … not … not … -#> 7 Cycas brun… nati… nati… not … not … not … not … not … not … not … not … not … -#> 8 Cycas cair… not … nati… not … not … not … not … not … not … not … not … not … -#> 9 Cycas calc… nati… not … not … not … not … not … not … not … not … not … not … -#> 10 Cycas cana… nati… not … not … not … not … not … not … not … not … not … not … -#> # ℹ 26,263 more rows -#> # ℹ 7 more variables: MI <chr>, HI <chr>, MDI <chr>, CoI <chr>, CSI <chr>, -#> # AR <chr>, CaI <chr> +#> 1 Acanthus e… nati… nati… nati… not … not … not … not … not … not … not … not … +#> 2 Acanthus i… not … nati… nati… not … not … not … not … not … not … not … not … +#> 3 Acanthus m… natu… not … doub… natu… natu… natu… natu… not … not … not … not … +#> 4 Andrograph… not … natu… doub… not … not … not … not … nati… not … not … not … +#> 5 Asystasia … not … not … not … not … not … not … not … nati… not … not … not … +#> 6 Asystasia … not … not … nati… not … not … not … not … not … not … not … not … +#> 7 Asystasia … natu… natu… natu… not … natu… not … not … natu… not … not … not … +#> 8 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … +#> 9 Asystasia … not … not … nati… not … not … not … not … not … not … not … not … +#> 10 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … +#> # ℹ 26,499 more rows +#> # ℹ 7 more variables: ACT <chr>, CSI <chr>, AR <chr>, MI <chr>, HI <chr>, +#> # MDI <chr>, CaI <chr> diff --git a/reference/create_taxonomic_update_lookup.html b/reference/create_taxonomic_update_lookup.html index 1b182a3..d1388c2 100644 --- a/reference/create_taxonomic_update_lookup.html +++ b/reference/create_taxonomic_update_lookup.html @@ -44,7 +44,7 @@

Create a table with the best-possible scientific name match for Australian plant names

- Source: R/create_taxonomic_update_lookup.R + Source: R/create_taxonomic_update_lookup.R
create_taxonomic_update_lookup.Rd
@@ -286,7 +286,7 @@

Examples#> 3 Banksia cerrata Banksia sp. [Bank… NA Banksia sp. [… Bank… Prote… #> 4 Banksea serrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 5 Banksia serrrrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… -#> 6 Dryandra Dryandra sp. [Dry… NA Banksia sp. [… Bank… Prote… +#> 6 Dryandra Dryandra sp. [Dry… NA Dryandra sp. … Drya… Eupho… #> # ℹ 15 more variables: taxon_rank <chr>, taxonomic_dataset <chr>, #> # taxonomic_status <chr>, taxonomic_status_aligned <chr>, #> # aligned_reason <chr>, update_reason <chr>, subclass <chr>, @@ -317,7 +317,7 @@

Examples#> 3 Banksee serrate Banksia ser… Banksia serr… Banksia serra… Bank… Prote… #> 4 Banksia cerrata Banksia sp.… NA Banksia sp. [… Bank… Prote… #> 5 Banksia sp. Banksia sp.… NA Banksia sp. [… Bank… Prote… -#> 6 Dryandra sp. Dryandra sp… NA Banksia sp. [… Bank… Prote… +#> 6 Dryandra sp. Dryandra sp… NA Dryandra sp. … Drya… Eupho… #> 7 Argyrodendron (Whyanb… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 8 Argyrodendron ssp. (W… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 9 Argyrodendron Whyanbe… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… diff --git a/reference/default_version.html b/reference/default_version.html index 447c9b2..86d518d 100644 --- a/reference/default_version.html +++ b/reference/default_version.html @@ -38,7 +38,7 @@

Get the default version for stable data

- Source: R/load_taxonomic_resources.R + Source: R/load_taxonomic_resources.R
default_version.Rd
@@ -60,7 +60,7 @@

Value

Examples

default_version()
-#> [1] "2024-10-11"
+#> [1] "2025-01-28"

diff --git a/reference/gbif_lite.html b/reference/gbif_lite.html index f146c3e..1dd013b 100644 --- a/reference/gbif_lite.html +++ b/reference/gbif_lite.html @@ -36,7 +36,7 @@

GBIF Australian Plant Data

- Source: R/data.R + Source: R/data.R
gbif_lite.Rd
diff --git a/reference/get_apc_genus_family_lookup.html b/reference/get_apc_genus_family_lookup.html index b6bbf9c..20f06a7 100644 --- a/reference/get_apc_genus_family_lookup.html +++ b/reference/get_apc_genus_family_lookup.html @@ -38,7 +38,7 @@

Lookup Family by Genus from APC

- Source: R/state_diversity_counts.R + Source: R/state_diversity_counts.R
get_apc_genus_family_lookup.Rd
diff --git a/reference/get_versions.html b/reference/get_versions.html index 15cd91b..b7ebd16 100644 --- a/reference/get_versions.html +++ b/reference/get_versions.html @@ -36,7 +36,7 @@

Which versions of taxonomic resources are available?

- Source: R/load_taxonomic_resources.R + Source: R/load_taxonomic_resources.R
get_versions.Rd
@@ -57,19 +57,20 @@

Value

Examples

get_versions()
-#> # A tibble: 10 × 1
+#> # A tibble: 11 × 1
 #>    versions  
 #>    <chr>     
-#>  1 2024-10-11
-#>  2 2024-09-25
-#>  3 2024-09-05
-#>  4 2024-07-31
-#>  5 2024-05-29
-#>  6 2024-05-10
-#>  7 2024-04-29
-#>  8 2024-04-11
-#>  9 2023-04-18
-#> 10 2023-02-28
+#>  1 2025-01-28
+#>  2 2024-10-11
+#>  3 2024-09-25
+#>  4 2024-09-05
+#>  5 2024-07-31
+#>  6 2024-05-29
+#>  7 2024-05-10
+#>  8 2024-04-29
+#>  9 2024-04-11
+#> 10 2023-04-18
+#> 11 2023-02-28