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Please edit that file --\u003e\n\ntaxizedb\n========\n\n```{r echo=FALSE}\nknitr::opts_chunk$set(\n  warning = FALSE,\n  message = FALSE,\n  collapse = TRUE,\n  comment = \"#\u003e\"\n)\n```\n\n[![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![cran checks](https://badges.cranchecks.info/worst/taxizedb.svg)](https://badges.cranchecks.info/worst/taxizedb.svg)\n[![R-check](https://github.com/ropensci/taxizedb/workflows/R-check/badge.svg)](https://github.com/ropensci/taxizedb/actions)\n[![codecov](https://codecov.io/gh/ropensci/taxizedb/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/taxizedb)\n[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/taxizedb)](https://github.com/r-hub/cranlogs.app)\n[![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/taxizedb?color=blue)](https://cran.r-project.org/package=taxizedb)\n[![cran version](https://www.r-pkg.org/badges/version/taxizedb)](https://cran.r-project.org/package=taxizedb)\n[![DOI](https://zenodo.org/badge/53961466.svg)](https://zenodo.org/badge/latestdoi/53961466)\n\n`taxizedb` - Tools for Working with Taxonomic Databases\n\nDocs: \u003chttps://docs.ropensci.org/taxizedb/\u003e\n\n`taxizedb` is an R package for interacting with taxonomic databases. Its functionality can be divided in two parts: 1. You can download the databases to your platform 2. You can query the downloaded databases to retrieve taxonomic information.\n\nThis two step approach is different from tools which interact with web services for each query, and has a number of advantages:\n\n* Once you download a database you can work with it offline\n* Once you download a database querying it is super fast\n* As long as you store your database files all the queries in your analysis will be fully reproducible\n\n## Data sources\n\nWhen you download a database with `taxizedb` it will automatically convert it to SQLite and then all query functions will interact with this SQLite database. However, not all taxonomic databases are publicly available, or can be converted to SQLite. The following databases are supported:\n\n- [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy)\n- [ITIS](https://itis.gov/)\n- [World Flora Online (WFO)](https://www.worldfloraonline.org/)\n- [Catalogue of Life (COL)](https://www.catalogueoflife.org/)\n- [Global Biodiversity Information Facility (GBIF)](https://www.gbif.org/)\n- [Wikidata](https://zenodo.org/records/1213477)\n\nGet in touch [in the issues](https://github.com/ropensci/taxizedb/issues) with\nany ideas on new data sources.\n\n## Data sources - legacy support\n\n[The Plant List (TPL)](https://en.wikipedia.org/wiki/The_Plant_List) has been replaced by World Flora Online. The website seems to be down so `taxizedb` can no longer facilitate new downloads. However, already downloaded database files can still be queried using `taxizedb` functions, for reproducibility.\n\n## Package API\n\nThis package for each data sources performs the following tasks:\n\n* Downloaded taxonomic databases `db_download_*`\n* Create `dplyr` SQL backend via `dbplyr::src_dbi` - `src_*` \n* Query and get data back into a data.frame - `sql_collect`\n* Manage cached database files - `tdb_cache`\n* Retrieve immediate descendents of a taxon - `children`\n* Retrieve the taxonomic hierarchies from local database - `classification`\n* Retrieve all taxa descending from a vector of taxa - `downstream`\n* Convert species names to taxon IDs - `name2taxid`\n* Convert taxon IDs to species names - `taxid2name`\n* Convert taxon IDs to ranks - `taxid2rank`\n\nYou can use the `src` connections with `dplyr`, etc. to do operations downstream. 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