austraits

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

https://github.com/traitecoevo/austraits

Keywords

Repository

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

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/austraits@v2.2.2", 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/articles/austraits.html) 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! 

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