taxizedb
Tools for Working with 'Taxonomic' Databases
Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.
taxizedb - Tools for Working with Taxonomic Databases on your Machine
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 thus far:
- ITIS - they provide a SQL dump
- COL - they provide a SQL dump
- Theplantlist - we make a SQL database from CSV files they provide
- GBIF taxonomic backbone - we make a SQL database from darwin core archive
Get in touch in the issues with any ideas on new data sources.
This package for each data sources performs the following tasks:
- Download database -
db_download_* - Load database into SQL -
db_load_* - Create
dplyrSQL backend -src_*
cran version
install.packages("taxizedb")dev version
devtools::install_github("ropensci/taxizedb")library("taxizedb")library("dplyr")start your SQL DBs
Remember to start your PostgreSQL database for ITIS and ThePlantList and your MySQL database for COL
Download and load DBs
ITIS
x <- db_download_itis()db_load_itis(x)The Plant List (TPL)
x <- db_download_tpl()db_load_tpl(x)Catalogue of Life (COL)
x <- db_download_col()db_load_col(x)connect to the DBs
ITIS
src <- src_itis(user = "<user name>", password = "<password>")TPL
src <- src_tpl()COL
src <- src_col()query with SQL syntax
sql_collect(src, "select * from hierarchy limit 5")#> # A tibble: 5 x 5#> hierarchy_string tsn parent_tsn level childrencount#> * <chr> <int> <int> <int> <int>#> 1 202422 202422 0 0 154282#> 2 202422-846491 846491 202422 1 2666#> 3 202422-846491-660046 660046 846491 2 2654#> 4 202422-846491-660046-846497 846497 660046 3 7#> 5 202422-846491-660046-846497-846508 846508 846497 4 6# or pipe the src to sql_collectsrc %>% sql_collect("select * from hierarchy limit 5")#> # A tibble: 5 x 5#> hierarchy_string tsn parent_tsn level childrencount#> * <chr> <int> <int> <int> <int>#> 1 202422 202422 0 0 154282#> 2 202422-846491 846491 202422 1 2666#> 3 202422-846491-660046 660046 846491 2 2654#> 4 202422-846491-660046-846497 846497 660046 3 7#> 5 202422-846491-660046-846497-846508 846508 846497 4 6use dplyr verbs
get a tbl
hiers <- src %>% tbl("hierarchy")#> # Source: table<hierarchy> [?? x 5]#> # Database: postgres 9.6.0 [[email protected]:5432/ITIS]#> hierarchy_string tsn parent_tsn level childrencount#> <chr> <int> <int> <int> <int>#> 1 202422 202422 0 0 154282#> 2 202422-846491 846491 202422 1 2666#> 3 202422-846491-660046 660046 846491 2 2654#> 4 202422-846491-660046-846497 846497 660046 3 7#> 5 202422-846491-660046-846497-846508 846508 846497 4 6#> 6 202422-846491-660046-846497-846508-846553 846553 846508 5 5#> 7 202422-846491-660046-846497-846508-846553-954935 954935 846553 6 3#> 8 202422-846491-660046-846497-846508-846553-954935-5549 5549 954935 7 2#> 9 202422-846491-660046-846497-846508-846553-954935-5549-5550 5550 5549 8 0#> 10 202422-846491-660046-846497-846508-846553-954936 954936 846553 6 0#> # ... with more rowsselect certain fields
hiers %>% select(tsn, level)#> # Source: lazy query [?? x 2]#> # Database: postgres 9.6.0 [[email protected]:5432/ITIS]#> tsn level#> <int> <int>#> 1 202422 0#> 2 846491 1#> 3 660046 2#> 4 846497 3#> 5 846508 4#> 6 846553 5#> 7 954935 6#> 8 5549 7#> 9 5550 8#> 10 954936 6#> # ... with more rowsMeta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
taxizedbin R doingcitation(package = 'taxizedb') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
News
taxizedb 0.1.4
BUG FIXES
- Fixes to SQL database connection functions for changes in
dplyr, which now requiresdbplyrpackage - alsoDBInow imported (#16)
taxizedb 0.1.0
NEW FEATURES
- Released to CRAN