knitr::opts_chunk$set( warning = FALSE, message = FALSE, collapse = TRUE, comment = "#>" )
taxizedb
- Tools for Working with Taxonomic Databases on your machine
Docs: https://docs.ropensci.org/taxizedb/
taxize is a heavily used taxonomic toolbelt package in R - However, it makes web requests for nearly all methods. That is fine for most cases, but when the user has many, many names it is much more efficient to do requests to a local SQL database.
Not all taxonomic databases are publicly available, or possible to mash into a SQLized version. Taxonomic DB's supported:
Update schedule for databases:
db_download_ncbi
creates the database when the function
is called, it's updated whenever you run the functiondb_download_itis
to get a new dump;
they I think update the dumps every month or sodb_download_wfo
creates the database when
the function is called, it's updated whenever you run the functionLinks:
Get in touch in the issues with any ideas on new data sources.
All databases are SQLite.
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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