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APCalign

R package for accessing, matching and updating species names of Australian flora

https://github.com/traitecoevo/apcalign

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 10 committers (30.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.9%) to scientific vocabulary

Keywords

r-package
Last synced: 7 months ago · JSON representation

Repository

R package for accessing, matching and updating species names of Australian flora

Basic Info
Statistics
  • Stars: 5
  • Watchers: 8
  • Forks: 6
  • Open Issues: 3
  • Releases: 15
Topics
r-package
Created over 5 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
editor_options: 
  chunk_output_type: console
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

library(APCalign)
```


[![](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![](https://www.r-pkg.org/badges/version/APCalign?color=orange)](https://cran.r-project.org/package=APCalign)
[![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)


# APCalign 

`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 names. '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.

DOI: https://doi.org/10.1071/BT24014 

## 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")
```

## 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"
    )
)
```

If you're going to use `APCalign` more than once, it will save you time to load the taxonomic resources into memory first:

```{r,message=FALSE}
tax_resources <- load_taxonomic_resources()

create_taxonomic_update_lookup( 
  taxa = c(
    "Banksia integrifolia",
    "Acacia longifolia",
    "Commersonia rosea",
    "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)

```

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)
```

## Cheatsheet



## 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!

Owner

  • Name: Trait Ecology and Evolution
  • Login: traitecoevo
  • Kind: organization
  • Location: Australia

GitHub Events

Total
  • Create event: 20
  • Release event: 5
  • Issues event: 19
  • Delete event: 8
  • Issue comment event: 18
  • Push event: 53
  • Pull request review comment event: 10
  • Pull request review event: 21
  • Pull request event: 22
Last Year
  • Create event: 20
  • Release event: 5
  • Issues event: 19
  • Delete event: 8
  • Issue comment event: 18
  • Push event: 53
  • Pull request review comment event: 10
  • Pull request review event: 21
  • Pull request event: 22

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 141
  • Total Committers: 10
  • Avg Commits per committer: 14.1
  • Development Distribution Score (DDS): 0.624
Past Year
  • Commits: 108
  • Committers: 6
  • Avg Commits per committer: 18.0
  • Development Distribution Score (DDS): 0.62
Top Committers
Name Email Commits
Will Cornwell w****l@u****u 53
Will Cornwell w****l@g****m 30
Elizabeth Wenk e****k@g****m 24
Daniel Falster d****r@u****u 15
Fonti Kar f****r@u****u 14
Fabrice Samonte f****e@F****l 1
FabriceSamonte f****e@o****m 1
rubysaltbush s****y@g****m 1
yangsophieee s****7@g****m 1
Ruby E Stephens 6****h 1
Committer Domains (Top 20 + Academic)
unsw.edu.au: 3

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 108
  • Total pull requests: 151
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 10
  • Total pull request authors: 5
  • Average comments per issue: 3.45
  • Average comments per pull request: 0.67
  • Merged pull requests: 128
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 11
  • Pull requests: 21
  • Average time to close issues: 7 days
  • Average time to close pull requests: 2 days
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 0.91
  • Average comments per pull request: 0.29
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • fontikar (40)
  • wcornwell (30)
  • ehwenk (17)
  • dfalster (12)
  • rubysaltbush (3)
  • yangsophieee (2)
  • a-orn (1)
  • tmesaglio (1)
  • elijahmagistrado (1)
  • T-LeB (1)
Pull Request Authors
  • ehwenk (53)
  • wcornwell (52)
  • fontikar (36)
  • dfalster (8)
  • slager (2)
Top Labels
Issue Labels
enhancement (5) question (3) bug (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 536 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: APCalign

Resolving Plant Taxon Names Using the Australian Plant Census

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 536 Last month
Rankings
Dependent packages count: 27.8%
Dependent repos count: 36.9%
Average: 50.3%
Downloads: 86.1%
Maintainers (1)
daniel.falster@unsw.edu.au
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1.0 depends
  • crayon * imports
  • datastorr >= 0.0.3 imports
  • dplyr * imports
  • forcats * imports
  • magrittr * imports
  • readr * imports
  • stringr * imports
  • tibble * imports
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite