knitr::opts_chunk$set( warning = FALSE, message = FALSE, collapse = TRUE, comment = "#>" )
taxizedb
- Tools for Working with Taxonomic Databases
Docs: https://docs.ropensci.org/taxizedb/
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.
This two step approach is different from tools which interact with web services for each query, and has a number of advantages:
When 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:
Get in touch in the issues with any ideas on new data sources.
This package for each data sources performs the following tasks:
db_download_*
dplyr
SQL backend via dbplyr::src_dbi
- src_*
sql_collect
tdb_cache
children
classification
downstream
name2taxid
taxid2name
taxid2rank
You can use the src
connections with dplyr
, etc. to do operations downstream. Or use the database connection to do raw SQL queries.
CRAN version
install.packages("taxizedb")
dev version
remotes::install_github("ropensci/taxizedb")
To cite taxizedb in publications use:
taxizedb
in R with citation(package = 'taxizedb')
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