Package taxa version 0.4.2
Description
定义可以被 taxon_db 对象使用或使用 taxon_db 对象的有效分类数据库，例如 taxon_id 和 taxon。
使用 db_ref$get 查看数据库的详细信息。
用户可以使用 db_ref$set 创建自定义的数据库，并添加到数据库列表中。
每个数据库都必须包含下列信息：
- 数据库对应的网站的URL
- 一段简短的描述
- 定义有效的类群ID的正则表达式
- 数据库中有效的分类等级
Usage
R
db_refFormat
一个长度为3的列表对象。
Attribution
此代码基于knitr包中的代码处理选项。
Examples
查看所有的数据库定义：
R
db_ref$get()
R
<taxon_db_def[8]>
_____________________ ncbi ______________________
url: http://www.ncbi.nlm.nih.gov/taxonomy
desc: NCBI Taxonomy Database
id_regex: [0-9]+
rank_levels:
_____________________________ gbif _____________________________
url: http://www.gbif.org/developer/species
desc: GBIF Taxonomic Backbone
id_regex: [0-9]+
rank_levels: kingdom < phylum < order < family < genus < species
_____________________________________ bold _____________________________________
url: http://www.boldsystems.org
desc: Barcode of Life
id_regex: [0-9]+
rank_levels: phylum < class < order < family < subfamily < genus < species < su...
___________________ col ___________________
url: http://www.catalogueoflife.org
desc: Catalogue of Life
id_regex: [a-z0-9]{32}
rank_levels:
______________ eol ______________
url: http://eol.org
desc: Encyclopedia of Life
id_regex: [0-9]+
rank_levels:
____________________ nbn ____________________
url: https://nbn.org.uk
desc: UK National Biodiversity Network
id_regex: [A-Z]{5}[0-9]{10}
rank_levels:
________________ tps ________________
url: http://www.tropicos.org/
desc: Tropicos
id_regex: [0-9]+
rank_levels:
_______________________ itis _______________________
url: http://www.itis.gov
desc: Integrated Taxonomic Information System
id_regex: [0-9]+
rank_levels: 自定义数据库：
R
db_ref$set(
name = "my_new_database",
url = "http://www.my_tax_database.com",
desc = "I just made this up",
id_regex = ".*"
)
db_ref$get()
R
<taxon_db_def[9]>
_____________________ ncbi ______________________
url: http://www.ncbi.nlm.nih.gov/taxonomy
desc: NCBI Taxonomy Database
id_regex: [0-9]+
rank_levels:
_____________________________ gbif _____________________________
url: http://www.gbif.org/developer/species
desc: GBIF Taxonomic Backbone
id_regex: [0-9]+
rank_levels: kingdom < phylum < order < family < genus < species
________________________________________ bold _________________________________________
url: http://www.boldsystems.org
desc: Barcode of Life
id_regex: [0-9]+
rank_levels: phylum < class < order < family < subfamily < genus < species < subspecies
___________________ col ___________________ ______________ eol ______________
url: http://www.catalogueoflife.org url: http://eol.org
desc: Catalogue of Life desc: Encyclopedia of Life
id_regex: [a-z0-9]{32} id_regex: [0-9]+
rank_levels: rank_levels:
____________________ nbn ____________________ ________________ tps ________________
url: https://nbn.org.uk url: http://www.tropicos.org/
desc: UK National Biodiversity Network desc: Tropicos
id_regex: [A-Z]{5}[0-9]{10} id_regex: [0-9]+
rank_levels: rank_levels:
_______________________ itis _______________________ _____________ my_new_database _____________
url: http://www.itis.gov url: http://www.my_tax_database.com
desc: Integrated Taxonomic Information System desc: I just made this up
id_regex: [0-9]+ id_regex: .*
rank_levels: rank_levels: 恢复默认设置：
R
db_ref$reset()
db_ref$get()
R
<taxon_db_def[8]>
_____________________ ncbi ______________________
url: http://www.ncbi.nlm.nih.gov/taxonomy
desc: NCBI Taxonomy Database
id_regex: [0-9]+
rank_levels:
_____________________________ gbif _____________________________
url: http://www.gbif.org/developer/species
desc: GBIF Taxonomic Backbone
id_regex: [0-9]+
rank_levels: kingdom < phylum < order < family < genus < species
________________________________________ bold _________________________________________
url: http://www.boldsystems.org
desc: Barcode of Life
id_regex: [0-9]+
rank_levels: phylum < class < order < family < subfamily < genus < species < subspecies
___________________ col ___________________ ______________ eol ______________
url: http://www.catalogueoflife.org url: http://eol.org
desc: Catalogue of Life desc: Encyclopedia of Life
id_regex: [a-z0-9]{32} id_regex: [0-9]+
rank_levels: rank_levels:
____________________ nbn ____________________ ________________ tps ________________
url: https://nbn.org.uk url: http://www.tropicos.org/
desc: UK National Biodiversity Network desc: Tropicos
id_regex: [A-Z]{5}[0-9]{10} id_regex: [0-9]+
rank_levels: rank_levels:
_______________________ itis _______________________
url: http://www.itis.gov
desc: Integrated Taxonomic Information System
id_regex: [0-9]+
rank_levels: