From dea7a44fbbd9841a7a9774f9f9c47e9f76965d73 Mon Sep 17 00:00:00 2001 From: wcornwell Date: Mon, 6 May 2024 05:33:31 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20traiteco?= =?UTF-8?q?evo/APCalign@41b4a786817bbd622ccbabad11b9e956fb314a5d=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 20 +- LICENSE-text.html | 18 +- articles/APCalign.html | 22 +- articles/articles/reproducibility.html | 8 + articles/data-providers.html | 24 +- articles/index.html | 24 +- articles/reproducibility.html | 210 ++++++++++++++ articles/updating-taxon-names.html | 91 +++++- authors.html | 36 ++- deps/bootstrap-5.3.1/bootstrap.min.css | 2 +- index.html | 114 +++++--- news/index.html | 58 +++- pkgdown.js | 8 +- pkgdown.yml | 7 +- reference/APCalign.html | 21 +- reference/align_taxa.html | 266 +++++++++++++----- .../create_species_state_origin_matrix.html | 45 +-- reference/create_taxonomic_update_lookup.html | 259 +++++++++++++---- reference/default_version.html | 120 ++++---- reference/gbif_lite.html | 18 +- reference/index.html | 75 +++-- reference/load_taxonomic_resources.html | 89 ++++-- reference/native_anywhere_in_australia.html | 60 ++-- reference/reexports.html | 102 +++++++ reference/standardise_names.html | 53 ++-- reference/standardise_taxon_rank.html | 111 ++++++++ reference/state_diversity_counts.html | 57 ++-- reference/strip_names.html | 43 +-- reference/strip_names_extra.html | 125 ++++++++ reference/update_taxonomy.html | 157 +++++++---- search.json | 2 +- sitemap.xml | 18 +- 32 files changed, 1670 insertions(+), 593 deletions(-) create mode 100644 articles/articles/reproducibility.html create mode 100644 articles/reproducibility.html create mode 100644 reference/reexports.html create mode 100644 reference/standardise_taxon_rank.html create mode 100644 reference/strip_names_extra.html diff --git a/404.html b/404.html index 187d0254..8342c938 100644 --- a/404.html +++ b/404.html @@ -10,7 +10,7 @@ - + License • APCalignLicense • APCalign @@ -10,7 +10,7 @@ APCalign - 0.1.4 + 1.0.0 + + + + + +
+ + + + +
+
+

How to be more reproducible with APCalign

+ + + Source: vignettes/articles/reproducibility.Rmd +
reproducibility.Rmd
+
+ + + +

The article will show you how to use APCalign to update +and align your plant taxonomic names in a more reproducible manner. The +tips offered below will be particularly useful if you used our package +and will share your code and data in your research paper or report.

+

There are two components that we need to cited and their versions +determined:

+
    +
  • The APCalign package itself
    • +
  • The taxonomic resources used by APCalign for aligning +and updating your plant taxon names
    • +
+

Both of these components are updated for bug fixes, or to incorporate +new taxonomic information and decisions.

+

First let’s load APCalign

+ +
+

APCalign R package version +

+

To determine the version of the APCalign package +itself:

+
+packageVersion("APCalign")
+
+
+

Taxonomic Resources +

+

APCalign allows users to load static downloads of +taxonomic resources the APC and APNI or the latest version from the +National Species List website. This functionality is specified using the +stable_or_current_data argument of +load_taxonomic_resources().

+

If you want your taxonomic alignment and update to be reproducible, +we recommend to always use +stable_or_current_data = "stable". The default value is +stable_or_current_data = "stable". These static downloads +are version controlled and stored in our repository as releases.

+
+load_taxonomic_resources(stable_or_current_data = "stable")
+

By default, load_taxonomic_resources() will load the +latest version of the static downloads.

+
+load_taxonomic_resources(
+  stable_or_current_data = "stable",
+  version = default_version()
+)
+

In order to be more transparent, we recommend you to check what is +the latest default_version before each alignment

+
+default_version()
+#> [1] "0.0.5.9000"
+

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

+

To ensure the specific version of taxonomic resources is availabe for +subsequent functions make sure to assign them to an object:

+
+resources_0.0.4.9000 <- load_taxonomic_resources(
+  stable_or_current_data = "stable",
+  version = "0.0.4.9000"
+)
+

Then during alignment and update, make sure you supply your version +of taxonomic resources using the resources argument:

+
+# Align taxa
+aligned_taxa <- align_taxa(gbif_lite$species, resources = resources_0.0.4.9000)
+
+# Update taxonomy 
+updated_taxa <- update_taxonomy(aligned_taxa, resources = resources_0.0.4.9000)
+
+# Align and update all-in-one
+aligned_updated_taxa <- create_taxonomic_update_lookup(gbif_lite$species, resources = resources_0.0.4.9000)
+
+
+

Citing the R package +

+

For completion, you can also cite the R package by calling +citation(). We also have a research article introducing the +APCalign, we will share the details of its citation when it +is in press.

+
+citation("APCalign")
+#> To cite package 'APCalign' in publications use:
+#> 
+#>   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." R
+#>   package version: 1.0.0,
+#>   <https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1>.
+#> 
+#> A BibTeX entry for LaTeX users is
+#> 
+#>   @Unpublished{,
+#>     title = {APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census},
+#>     author = {Elizabeth Wenk and Will Cornwell and Ann Fuchs and Fonti Kar and Anna Monro and Herve Sauquet and Ruby Stephens and Daniel Falster},
+#>     year = {2024},
+#>     note = {R package version: 1.0.0},
+#>     url = {https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1},
+#>   }
+
+
+
+ + + +
+

Developed by Daniel Falster, Elizabeth Wenk, Will Cornwell, Fonti Kar.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+
+ + + + + + + diff --git a/articles/updating-taxon-names.html b/articles/updating-taxon-names.html index 51c53fa8..9e4f5671 100644 --- a/articles/updating-taxon-names.html +++ b/articles/updating-taxon-names.html @@ -11,7 +11,7 @@ - + Authors and Citation • APCalignAuthors and Citation • APCalign @@ -10,7 +10,7 @@ APCalign - 0.1.4 + 1.0.0 - - ausflora - 0.0.2.9000 - - +
+
+
+

Get the default version for stable data

+ Source: R/load_taxonomic_resources.R +
default_version.Rd
-
+

This function returns the default version for stable data, which is used when no -version is specified. The default version is "0.0.1.9000".

+version is specified.

-
+
+

Usage

default_version()
-
-

Value

+
+

Value

A character string representing the default version for stable data.

-
-

See also

-

align_taxa

-
-
-

Examples

- 
default_version()
-#> [1] "0.0.2.9000"
-
-
-
-
- -
+
-
-

Developed by Daniel Falster.

+
+

Developed by Daniel Falster, Elizabeth Wenk, Will Cornwell, Fonti Kar.

-
-

Site built with pkgdown 2.0.7.

+
+

Site built with pkgdown 2.0.9.

-
+
- diff --git a/reference/gbif_lite.html b/reference/gbif_lite.html index bc594fa9..17f7ec75 100644 --- a/reference/gbif_lite.html +++ b/reference/gbif_lite.html @@ -1,5 +1,5 @@ -GBIF Australian Plant Data — gbif_lite • APCalignGBIF Australian Plant Data — gbif_lite • APCalign @@ -10,7 +10,7 @@ APCalign - 0.1.4 + 1.0.0 + + + + + +
+
+
+

Objects exported from other packages

+ Source: R/reexports.R +
reexports.Rd
+
+ +
+

These objects are imported from other packages. Follow the links +below to see their documentation.

+
dplyr
+

%>%

+ + +
+ + + +
+ + +
+

Developed by Daniel Falster, Elizabeth Wenk, Will Cornwell, Fonti Kar.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + diff --git a/reference/standardise_names.html b/reference/standardise_names.html index 0b96497d..7590cf70 100644 --- a/reference/standardise_names.html +++ b/reference/standardise_names.html @@ -1,11 +1,13 @@ -Standardises taxon names by performing a series of text substitutions to remove common inconsistencies in taxonomic nomenclature. — standardise_names • APCalignStandardise taxon names — standardise_names • APCalign @@ -16,7 +18,7 @@ APCalign - 0.1.4 + 1.0.0 + + + + + +
+
+
+

Standardise taxon ranks

+ Source: R/standardise_names.R +
standardise_taxon_rank.Rd
+
+ +
+

Standardise taxon ranks from Latin into English.

+
+ +
+

Usage

+ 
standardise_taxon_rank(taxon_rank)
+
+ +
+

Arguments

+
taxon_rank
+

A character vector of Latin taxon ranks.

+ +
+
+

Value

+ + +

A character vector of English taxon ranks.

+
+
+

Details

+

The function takes a character vector of Latin taxon ranks as input and +returns a character vector of taxon ranks using standardised English terms.

+
+ +
+

Examples

+ 
standardise_taxon_rank(c("regnum", "kingdom", "classis", "class"))
+#> [1] "kingdom" "kingdom" "class"   "class"  
+
+
+
+ + +
+

Developed by Daniel Falster, Elizabeth Wenk, Will Cornwell, Fonti Kar.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + diff --git a/reference/state_diversity_counts.html b/reference/state_diversity_counts.html index 5437e743..659a2206 100644 --- a/reference/state_diversity_counts.html +++ b/reference/state_diversity_counts.html @@ -1,7 +1,9 @@ -For Australian states and territories, use data from the APC to calculate state-level diversity for native, introduced, and more complicated species origins — state_diversity_counts • APCalignState- and territory-level diversity — state_diversity_counts • APCalign @@ -12,7 +14,7 @@ APCalign - 0.1.4 + 1.0.0 + + + + + +
+
+
+

Strip taxon names, extra

+ Source: R/strip_names.R +
strip_names_extra.Rd
+
+ +
+

Strip taxonomic names of sp. and hybrid symbols. This function assumes +that a character function has already been run through strip_names.

+
+ +
+

Usage

+ 
strip_names_extra(taxon_names)
+
+ +
+

Arguments

+
taxon_names
+

A character vector of taxonomic names to be stripped.

+ +
+
+

Value

+ + +

A character vector of stripped taxonomic names, +with sp. and hybrid symbols removed.

+
+
+

Details

+

Given a vector of taxonomic names, this function removes additional filler +words (" x " for hybrid taxa, "sp.") not removed by the function +strip_names

+
+ +
+

Examples

+ 
strip_names_extra(c("Abies lasiocarpa subsp. lasiocarpa",
+              "Quercus kelloggii",
+              "Pinus contorta var. latifolia",
+              "Acacia sp.",
+              "Lepidium sp. Tanguin Hill (K.R.Newbey 10501)"))
+#> [1] "Abies lasiocarpa subsp. lasiocarpa"          
+#> [2] "Quercus kelloggii"                           
+#> [3] "Pinus contorta var. latifolia"               
+#> [4] "Acacia sp."                                  
+#> [5] "Lepidium sp. Tanguin Hill (K.R.Newbey 10501)"
+
+
+
+
+ + +
+

Developed by Daniel Falster, Elizabeth Wenk, Will Cornwell, Fonti Kar.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + diff --git a/reference/update_taxonomy.html b/reference/update_taxonomy.html index 0956ebca..7d894dea 100644 --- a/reference/update_taxonomy.html +++ b/reference/update_taxonomy.html @@ -1,11 +1,9 @@ -For a list of taxon names aligned to the APC, update the name to an accepted taxon concept per the APC and add scientific name and taxon concept metadata to names aligned to either the APC or APNI. — update_taxonomy • APCalignUpdate to currently accepted APC name and add APC/APNI name metadata — update_taxonomy • APCalign @@ -16,7 +14,7 @@ APCalign - 0.1.4 + 1.0.0