README.Rmd

---
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://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![Codecov test coverage](https://codecov.io/gh/traitecoevo/APCalign/branch/master/graph/badge.svg)](https://app.codecov.io/gh/traitecoevo/APCalign?branch=master)
[![R-CMD-check](https://github.com/traitecoevo/APCalign/actions/workflows/R-CMD-check.yaml/badge.svg)](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"/>

'APCalign' uses the [Australian Plant Census (APC)](https://biodiversity.org.au/nsl/services/search/taxonomy) and [Australian Plant Name Index](https://biodiversity.org.au/nsl/services/search/names) to align and update Australian plant taxon name strings. 'APCalign' also supplies information about
the established status (native/introduced) of plant taxa across different states/territories.

## Installation

'APCalign' is current not on CRAN. Install the currently development version: 

```{r install, eval= FALSE}
# install.packages("remotes")
# remotes::install_github("traitecoevo/APCalign", dependencies = TRUE, upgrade = "ask")

library(APCalign)
```

## A quick demo

Generating a look-up table can be done with just one function

```{r,message=FALSE}
# Load APC/APNI resources into R
resources <- load_taxonomic_resources()

# Create lookup 
create_taxonomic_update_lookup( 
  taxa = c(
    "Banksia integrifolia",
    "Acacia longifolia",
    "Commersonia rosea"
    ),
  resources = resources
)
```

## Shiny application

We also developed a shiny application for non-R users to update and align their taxonomic names. You can find the application here: https://unsw.shinyapps.io/APCalign-app

## 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).


## 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!