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and Vegetation","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"---\noutput: github_document\neditor_options: \n  chunk_output_type: console\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\",\n  message = FALSE,\n  warning = FALSE\n)\n\nlibrary(austraits) \nlibrary(stringr)\nlibrary(dplyr)\n```\n\n\n# austraits \u003cimg src=\"man/figures/austraits_hex.png\" align=\"right\" alt=\"\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![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)\n[![codecov](https://codecov.io/gh/traitecoevo/austraits/branch/master/graph/badge.svg?token=JT1M0AMZ44)](https://codecov.io/gh/traitecoevo/austraits)\n[![](https://img.shields.io/badge/doi-10.1038/s41597--021--01006--6-blue.svg)](https://doi.org/10.1038/s41597-021-01006-6)\n[![](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![Codecov test coverage](https://codecov.io/gh/traitecoevo/austraits/branch/master/graph/badge.svg)](https://app.codecov.io/gh/traitecoevo/austraits?branch=master)\n\u003c!-- badges: end --\u003e\n\n`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.\n\n### Installation\n\nThis 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: \n\n```{r setup, results = 'hide', eval = FALSE}\n#install.packages(\"remotes\")\nremotes::install_github(\"traitecoevo/austraits\", dependencies = TRUE, upgrade = \"ask\")\n\nlibrary(austraits) \n```\n\nFor a lightweight installation where dependencies for plotting and producing the vignettes will not be installed, use:\n\n```{r light, results = 'hide', eval = FALSE}\nremotes::install_github(\"traitecoevo/austraits\", upgrade = \"ask\")\n```\n\n### Details for AusTraits users\n\n#### Retrieve AusTraits data\n\n- **For R users**, the AusTraits database can be accessed through the `austraits` package using `load_austraits()`\n\n- **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 \n\n#### Backwards compatibility with past AusTraits versions\n\nFrom 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).\n\nVersions of `austraits.build` (the AusTraits plant trait database) **\u003c 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:\n\nFor `austraits.build` versions 4.2 and older: \n\n```{r backwards, results = 'hide', eval = FALSE}\n#install.packages(\"remotes\")\nremotes::install_github(\"traitecoevo/austraits@v2.2.2\", dependencies = TRUE, upgrade = \"ask\")\n\nlibrary(austraits)\n```\n\nNote, if you are unsure what version of AusTraits you are working with, run:\n\n```{r version, results = 'hide', eval = FALSE}\naustraits$build_info$version\n```\n\n### Getting started  `r emo::ji(\"eyes\")`\n\nWe 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!\n\nIf you prefer to view this vignette in R, we recommend installing the package with `build_vignettes = TRUE`. \n\n```{r, eval = FALSE}\nremotes::install_github(\"traitecoevo/austraits\", \n                        dependencies = TRUE, upgrade = \"ask\", \n                        build_vignettes = TRUE)\n\nvignette(\"austraits\")\n```\n\n### Cheat sheet\n\n\u003ca href=\"https://github.com/traitecoevo/austraits/tree/master/inst/cheatsheet/austraits-cheatsheet.pdf\"\u003e\u003cimg src=\"man/figures/austraits-cheatsheet.png\" width=\"60%\"/\u003e\u003c/a\u003e\n\n### Learn more about AusTraits\n\nAusTraits 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).  \n\nYou can also learn about the definitions of each plant trait with the [AusTraits Plant Dictionary!](https://w3id.org/APD)\n\n### Show us some support `r emo::ji(\"green heart\")`\n\nPlease consider citing `austraits`, we would super appreciate it! \n\n```{r}\ncitation(\"austraits\")\n```\n\n### Behind the scenes `r emo::ji(\"spanner\")`\n\nCheck 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\n\n### Find a bug? `r emo::ji(\"bug\")`\n\nThank 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! \n\n\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1038/s41597-021-01006-6"],"works":{"https://doi.org/10.1038/s41597-021-01006-6":{"id":"https://openalex.org/W3202927809","doi":"https://doi.org/10.1038/s41597-021-01006-6","title":"AusTraits, a curated plant trait database for the Australian flora","display_name":"AusTraits, a curated plant trait database for the Australian flora","publication_year":2021,"publication_date":"2021-09-30","ids":{"openalex":"https://openalex.org/W3202927809","doi":"https://doi.org/10.1038/s41597-021-01006-6","mag":"3202927809","pmid":"https://pubmed.ncbi.nlm.nih.gov/34593819","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8484355"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41597-021-01006-6","pdf_url":"https://www.nature.com/articles/s41597-021-01006-6.pdf","source":{"id":"https://openalex.org/S2607323502","display_name":"Scientific Data","issn_l":"2052-4463","issn":["2052-4463"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.nature.com/articles/s41597-021-01006-6.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087681406","display_name":"Daniel S. Falster","orcid":"https://orcid.org/0000-0002-9814-092X"},"institutions":[{"id":"https://openalex.org/I4210163172","display_name":"Environmental Earth Sciences","ror":"https://ror.org/04rnwed46","country_code":"AU","type":"other","lineage":["https://openalex.org/I4210163172"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Daniel Falster","raw_affiliation_string":"Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia","raw_affiliation_strings":["Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039749882","display_name":"Rachael V. Gallagher","orcid":"https://orcid.org/0000-0002-4680-8115"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]},{"id":"https://openalex.org/I63525965","display_name":"Western Sydney University","ror":"https://ror.org/03t52dk35","country_code":"AU","type":"education","lineage":["https://openalex.org/I63525965"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Rachael Gallagher","raw_affiliation_string":"Department of Biological Sciences, Macquarie University, Sydney, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia","raw_affiliation_strings":["Department of Biological Sciences, Macquarie University, Sydney, Australia","Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049852469","display_name":"Elizabeth Wenk","orcid":"https://orcid.org/0000-0001-5640-5910"},"institutions":[{"id":"https://openalex.org/I4210163172","display_name":"Environmental Earth Sciences","ror":"https://ror.org/04rnwed46","country_code":"AU","type":"other","lineage":["https://openalex.org/I4210163172"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Elizabeth H. Wenk","raw_affiliation_string":"Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia","raw_affiliation_strings":["Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028139677","display_name":"Ian J. Wright","orcid":"https://orcid.org/0000-0001-8338-9143"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ian J. Wright","raw_affiliation_string":"Department of Biological Sciences, Macquarie University, Sydney, Australia","raw_affiliation_strings":["Department of Biological Sciences, Macquarie University, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056835915","display_name":"Dony Indiarto","orcid":"https://orcid.org/0000-0001-9546-8201"},"institutions":[{"id":"https://openalex.org/I4210163172","display_name":"Environmental Earth Sciences","ror":"https://ror.org/04rnwed46","country_code":"AU","type":"other","lineage":["https://openalex.org/I4210163172"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Dony Indiarto","raw_affiliation_string":"Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia","raw_affiliation_strings":["Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033149229","display_name":"Samuel C. Andrew","orcid":"https://orcid.org/0000-0003-4589-2746"},"institutions":[{"id":"https://openalex.org/I4210161554","display_name":"CSIRO Land and Water","ror":"https://ror.org/057xz1h85","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1292875679","https://openalex.org/I4210161554"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Samuel C. Andrew","raw_affiliation_string":"CSIRO Land and Water, Canberra, Australia","raw_affiliation_strings":["CSIRO Land and Water, Canberra, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012984115","display_name":"Caitlan Baxter","orcid":null},"institutions":[{"id":"https://openalex.org/I4210163172","display_name":"Environmental Earth Sciences","ror":"https://ror.org/04rnwed46","country_code":"AU","type":"other","lineage":["https://openalex.org/I4210163172"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Caitlan Baxter","raw_affiliation_string":"Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia","raw_affiliation_strings":["Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056416373","display_name":"James R. Lawson","orcid":null},"institutions":[{"id":"https://openalex.org/I2801559191","display_name":"New South Wales Department of Primary Industries","ror":"https://ror.org/050khh066","country_code":"AU","type":"government","lineage":["https://openalex.org/I2801351115","https://openalex.org/I2801559191"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"James Lawson","raw_affiliation_string":"NSW Department of Primary Industries, Orange, Australia","raw_affiliation_strings":["NSW Department of Primary Industries, Orange, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016583253","display_name":"Stuart Allen","orcid":"https://orcid.org/0000-0003-1640-6884"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Stuart Allen","raw_affiliation_string":"Department of Biological Sciences, Macquarie University, Sydney, Australia","raw_affiliation_strings":["Department of Biological Sciences, Macquarie University, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042225879","display_name":"Anne Fuchs","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100608","display_name":"Centre for Australian National Biodiversity Research","ror":"https://ror.org/00n82gt57","country_code":"AU","type":"government","lineage":["https://openalex.org/I1292875679","https://openalex.org/I4210100608"]},{"id":"https://openalex.org/I1292875679","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07","country_code":"AU","type":"government","lineage":["https://openalex.org/I1292875679","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Anne Fuchs","raw_affiliation_string":"Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, Australia","raw_affiliation_strings":["Centre for Australian National Biodiversity Research (a joint venture between Parks Australia and CSIRO), Canberra, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064545403","display_name":"Anna M. 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Atkin","orcid":"https://orcid.org/0000-0003-1041-5202"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Owen K. Atkin","raw_affiliation_string":"The Australian National University, Canberra, Australia","raw_affiliation_strings":["The Australian National University, Canberra, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067508942","display_name":"Joe Atkinson","orcid":"https://orcid.org/0000-0001-9232-4421"},"institutions":[{"id":"https://openalex.org/I4210163172","display_name":"Environmental Earth Sciences","ror":"https://ror.org/04rnwed46","country_code":"AU","type":"other","lineage":["https://openalex.org/I4210163172"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Joe Atkinson","raw_affiliation_string":"Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia","raw_affiliation_strings":["Evolution \u0026 Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, Australia"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021980747","display_name":"Tony D. 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