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---
output: github_document
editor_options:
chunk_output_type: console
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
library(APCalign)
```
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://cran.r-project.org/package=APCalign)
[](https://app.codecov.io/gh/traitecoevo/APCalign?branch=master)
[](https://github.com/traitecoevo/APCalign/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
# APCalign <img src="man/figures/APCalign_hex_2.svg" align="right" width="120"/>
When working with biodiversity data, it is important to verify taxonomic names with an authoritative list and correct any out-of-date names or names with typos.
The 'APCalign' package simplifies this process by:
- Accessing up-to-date taxonomic information from the [Australian Plant Census](https://biodiversity.org.au/nsl/services/search/taxonomy) and the [Australia Plant Name Index](https://biodiversity.org.au/nsl/services/search/names).
- Aligning authoritative names to your taxonomic names using our [fuzzy matching algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html)
- Updating your taxonomic names in a transparent, reproducible manner
- Because APCalign was developed explicitly for the Australian flora it handles phrase names and aligns disparate phrase name syntax
- Indicating when a split leads to uncertainty in a name alignment
'APCalign' also supplies information about the established status (i.e., native/introduced) of plant taxa within different states/territories as compiled by the APC. It's useful for updating species list and intersecting them with the APC consensus for both taxonomy and establishment status.
Read the [APCalign paper](https://doi.org/10.1071/BT24014) to learn more about the motivations for this project and our fuzzy matching and aligning algorithms.
## Installation 🛠️
From CRAN:
```{r install, eval= FALSE}
install.packages("APCalign")
library(APCalign)
```
OR for the GitHub version:
```{r install2, eval= FALSE}
install.packages("remotes")
remotes::install_github("traitecoevo/APCalign")
```
Or for the ShinyApp head to [unsw.shinyapps.io/APCalign-app](https://unsw.shinyapps.io/APCalign-app/)
## A quick demo
Generating a look-up table can be done with just one function:
```{r,message=FALSE}
create_taxonomic_update_lookup(
taxa = c(
"Banksia integrifolia",
"Acacia longifolia",
"Commersonia rosea"
)
)
```
You can alternatively load the taxonomic resources into memory first:
```{r,message=FALSE}
tax_resources <- load_taxonomic_resources()
create_taxonomic_update_lookup(
taxa = c(
"Banksia integrifolia",
"Banksya integrifolla",
"Banksya integriifolla",
"Banksyya integriifolla",
"Banksia red flowers",
"Banksia sp.",
"Banksia catoglypta",
"Dryandra catoglypta",
"Dryandra cataglypta",
"Dryandra australis",
"Acacia longifolia",
"Commersonia rosea",
"Panicum sp. Hairy glumes (C.R.Michell 4192)",
"Panicum sp. Hairy glumes (Michell)",
"Panicum sp. Hairy glumes",
"not a species"
),
resources = tax_resources
)
```
Checking for a list of species to see if they are classified as Australian natives:
```{r, message=FALSE}
native_anywhere_in_australia(c("Eucalyptus globulus","Pinus radiata"), resources = tax_resources)
```
Determining the number of species present in NSW and their establishment means:
```{r, message=FALSE}
state_diversity_counts("NSW", resources = tax_resources)
```
The related function `create_species_state_origin_matrix()` generates a table for all taxa in Australia, indicating their distribution and establishment means, by state.
Getting a family lookup table for genera from the specified taxonomy:
```{r, message=FALSE}
get_apc_genus_family_lookup(c("Eucalyptus",
"Pinus",
"Actinotus",
"Banksia",
"Acacia",
"Triodia"),
resources = tax_resources)
```
Compiling a list of outdated synonyms for currently accepted names:
```{r, message=FALSE}
names_to_check <- c("Acacia aneura", "Banksia nivea", "Cardamine gunnii", "Stenocarpus sinuatus")
synonyms_for_accepted_names(resources = tax_resources, accepted_names = names_to_check, collapse = T)
```
## Cheatsheet
<a href="https://github.com/traitecoevo/APCalign/blob/master/inst/cheatsheet/APCalign-cheatsheet.pdf"><img src="man/figures/APCalign-cheatsheet.png" width="60%"/></a>
## Learn more 📚
Highly recommend looking at our [Getting Started](https://traitecoevo.github.io/APCalign/articles/APCalign.html) vignette to learn about how to use `APCalign`. You can also learn more about our [taxa matching algorithm](https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html).
## Show us support 💛
Please consider citing our work, we are really proud of it!
```{r}
citation("APCalign")
```
## Found a bug? 🐛
Did you come across an unexpected taxon name change? Elusive error you can't debug - [submit an issue](https://github.com/traitecoevo/APCalign/issues) and we will try our best to help.
## Comments and contributions
We welcome any comments and contributions to the package, start by [submit an issue](https://github.com/traitecoevo/APCalign/issues) and we can take it from there!