austraits

R package for accessing the AusTraits Plant database, an open-source, harmonized database of Australian plant trait data.
https://github.com/traitecoevo/austraits

Category: Biosphere
Sub Category: Plants and Vegetation

Keywords

australia database plants traits

Last synced: about 24 hours ago
JSON representation

Repository metadata

R package for accessing the AusTraits Plant database and working with traits.build databases

• Host: GitHub
• URL: https://github.com/traitecoevo/austraits
• Owner: traitecoevo
• License: mit
• Created: 2021-04-27T01:17:27.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2025-03-29T22:43:07.000Z (29 days ago)
• Last Synced: 2025-04-20T06:30:02.344Z (7 days ago)
• Topics: australia, database, plants, traits
• Language: R
• Homepage: https://traitecoevo.github.io/austraits/
• Size: 50.5 MB
• Stars: 23
• Watchers: 9
• Forks: 3
• Open Issues: 8
• Releases: 4
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: 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%",
  message = FALSE,
  warning = FALSE
)

library(austraits) 
library(stringr)
library(dplyr)
```


# austraits 


[![R-CMD-check](https://github.com/traitecoevo/austraits/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/traitecoevo/austraits/actions/workflows/R-CMD-check.yml)
[![codecov](https://codecov.io/gh/traitecoevo/austraits/branch/master/graph/badge.svg?token=JT1M0AMZ44)](https://codecov.io/gh/traitecoevo/austraits)
[![](https://img.shields.io/badge/doi-10.1038/s41597--021--01006--6-blue.svg)](https://doi.org/10.1038/s41597-021-01006-6)
[![](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![Codecov test coverage](https://codecov.io/gh/traitecoevo/austraits/branch/master/graph/badge.svg)](https://app.codecov.io/gh/traitecoevo/austraits?branch=master)


`austraits` allow users to **access, explore and wrangle data** from [traits.build](https://github.com/traitecoevo/traits.build) relational databases. It is also an R interface to [AusTraits](https://austraits.org/), the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with `traits.build` databases.

### Installation

This package is not on CRAN yet and is still under active development. For the current stable release of `austraits`, which has full capabilities of the functions used in vignettes (e.g. plotting functions), use: 

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

library(austraits) 
```

For a lightweight installation where dependencies for plotting and producing the vignettes will not be installed, use:

```{r light, results = 'hide', eval = FALSE}
remotes::install_github("traitecoevo/austraits", upgrade = "ask")
```

### Details for AusTraits users

#### Retrieve AusTraits data

- **For R users**, the AusTraits database can be accessed through the `austraits` package using `load_austraits()`

- **For Python or other users**, the [Zenodo download](https://zenodo.org/record/5112001#collapseTwo) includes a `.zip` file containing all the data in plain text (`.csv` files) and associated meta-data 

#### Backwards compatibility with past AusTraits versions

From September 2024, `austraits` functions were revamped to support all [traits.build](https://github.com/traitecoevo/traits.build) compiled databases, rather than being linked to [austraits.build](https://github.com/traitecoevo/austraits.build).

Versions of `austraits.build` (the AusTraits plant trait database) **< 5.0 are no longer supported** by the latest version of the package. If you are working with an older version of AusTraits, please install an older version of austraits:

For `austraits.build` versions 4.2 and older: 

```{r backwards, results = 'hide', eval = FALSE}
#install.packages("remotes")
remotes::install_github("traitecoevo/[email protected]", dependencies = TRUE, upgrade = "ask")

library(austraits)
```

Note, if you are unsure what version of AusTraits you are working with, run:

```{r version, results = 'hide', eval = FALSE}
austraits$build_info$version
```

### Getting started  `r emo::ji("eyes")`

We highly recommend taking a look at our [Getting Started tutorial](https://traitecoevo.github.io/austraits/) on our website before jumping into the `austraits` R package!

If you prefer to view this vignette in R, we recommend installing the package with `build_vignettes = TRUE`. 

```{r, eval = FALSE}
remotes::install_github("traitecoevo/austraits", 
                        dependencies = TRUE, upgrade = "ask", 
                        build_vignettes = TRUE)

vignette("austraits")
```

### Cheat sheet



### Learn more about AusTraits

AusTraits is a relational database, you can learn more about it's structure from the [traits.build book](https://traitecoevo.github.io/traits.build-book/AusTraits_tutorial.html).  

You can also learn about the definitions of each plant trait with the [AusTraits Plant Dictionary!](https://w3id.org/APD)

### Show us some support `r emo::ji("green heart")`

Please consider citing `austraits`, we would super appreciate it! 

```{r}
citation("austraits")
```

### Behind the scenes `r emo::ji("spanner")`

Check out [austraits.build](https://github.com/traitecoevo/austraits.build?tab=readme-ov-file), if you are interested in how AusTraits the database is managed and created

### Find a bug? `r emo::ji("bug")`

Thank you for finding it! Head over to the GitHub Issues tab and let us know about it! We will try to get to it as soon as we can! 



        

---

Owner metadata

• Name: Trait Ecology and Evolution
• Login: traitecoevo
• Email:
• Kind: organization
• Description:
• Website:
• Location: Australia
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/11747619?v=4
• Repositories: 64
• Last ynced at: 2023-06-03T21:10:14.705Z
• Profile URL: https://github.com/traitecoevo

---

GitHub Events

Total

• Issues event: 49
• Watch event: 4
• Delete event: 30
• Issue comment event: 32
• Push event: 138
• Pull request review event: 48
• Pull request review comment event: 27
• Pull request event: 55
• Fork event: 2
• Create event: 29

Last Year

• Issues event: 49
• Watch event: 4
• Delete event: 30
• Issue comment event: 32
• Push event: 138
• Pull request review event: 48
• Pull request review comment event: 27
• Pull request event: 55
• Fork event: 2
• Create event: 29

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Committers metadata

Last synced: 5 days ago

Name	Email	Commits
Fonti Kar	f****r@u****u	345
Daniel Falster	d****r@u****u	15
Dony Indiarto	d****o@s****u	1
runner	r****r@M****l	1
runner	r****r@M****l	1
runner	r****r@M****l	1
runner	r****r@M****l	1

Committer domains:

• unsw.edu.au: 2
• student.unsw.edu.au: 1

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Issue and Pull Request metadata

Last synced: 2 days ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/traitecoevo/austraits

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Dependencies

Score: 5.37989735354046