R语言【taxa】——从taxa 定义的类中获取组分信息
Package taxa version 0.4.2
tax_auth(x)
在拥有对应信息的对象中设置和获取类群所有权信息。
> x <- taxon(name = c('Homo sapiens', 'Bacillus', 'Ascomycota', 'Ericaceae'),
+ rank = c('species', 'genus', 'phylum', 'family'),
+ id = taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi'),
+ auth = c('Linnaeus, 1758', 'Cohn 1872', NA, 'Juss., 1789'))
> tax_auth(x)
[1] Linnaeus 1758 Cohn 1872 NA Juss. 1789
> tax_auth(x) <- tolower(tax_auth(x))
> tax_auth(x)[1] <- 'Billy'
> x
[1] 9606|Homo sapiens Billy |species 1386|Bacillus cohn 1872|genus
[3] 4890|Ascomycota na |phylum 4345|Ericaceae juss. 1789|family
Rank levels: phylum < family < genus < species
tax_author(x)
设置和获取分类群的作者信息。
> x <- taxon_authority(c('Cham. & Schldl.', 'L.'),
+ date = c('1827', '1753'))
> tax_author(x)
[1] "Cham. & Schldl." "L."
> tax_author(x)[1] <- "Billy"
> tax_author(x) <- tolower(tax_author(x))
> tax_author(x)
[1] "billy" "l."
tax_cite(x)
设置和获取分类群的引用信息。
> x <- taxon_authority(c('Cham. & Schldl.', 'L.'),
+ date = c('1827', '1753'),
+ citation = c(NA, 'Species Plantarum'))
> tax_cite(x)
[1] NA "Species Plantarum"
> tax_cite(x)[1] <- "Cham. et al 1984"
> tax_cite(x)
[1] "Cham. et al 1984" "Species Plantarum"
tax_date(x)
设置和获取分类群的日期信息。
> x <- taxon_authority(c('Cham. & Schldl.', 'L.'),
+ date = c('1827', '1753'))
> tax_date(x)
[1] "1827" "1753"
> tax_date(x)[1] <- "1984"
> tax_date(x) <- c(NA, '1800')
> tax_date(x)
[1] NA "1800"
tax_db(x)
设置和获取分类群的数据库信息。
> x <- taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi')
> tax_db(x)
[1] ncbi ncbi ncbi ncbi
> tax_db(x) <- 'nbn'
> tax_db(x)[2] <- 'itis'
> tax_db(x)
[1] nbn itis nbn nbn
tax_id(x)
设置和获取类群的ID。
> x <- taxon(name = c('Homo sapiens', 'Bacillus', 'Ascomycota', 'Ericaceae'),
+ rank = c('species', 'genus', 'phylum', 'family'),
+ id = taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi'),
+ auth = c('Linnaeus, 1758', 'Cohn 1872', NA, 'Juss., 1789'))
> tax_id(x)
[1] 9606 (ncbi) 1386 (ncbi) 4890 (ncbi) 4345 (ncbi)
> tax_id(x) <- paste0('00', tax_id(x))
> tax_id(x)[1] <- '00000'
> tax_id(x)
[1] 00000 001386 004890 004345
tax_name(x)
设置和获取分类群名称。
> x <- taxon(name = c('Homo sapiens', 'Bacillus', 'Ascomycota', 'Ericaceae'),
+ rank = c('species', 'genus', 'phylum', 'family'),
+ id = taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi'),
+ auth = c('Linnaeus, 1758', 'Cohn 1872', NA, 'Juss., 1789'))
> tax_name(x)
[1] "Homo sapiens" "Bacillus" "Ascomycota" "Ericaceae"
> tax_name(x) <- tolower(tax_name(x))
> tax_name(x)[1] <- 'Billy'
> tax_name(x)
[1] "Billy" "bacillus" "ascomycota" "ericaceae"
tax_rank(x)
设置和获取类群等级。
> x <- taxon(name = c('Homo sapiens', 'Bacillus', 'Ascomycota', 'Ericaceae'),
+ rank = c('species', 'genus', 'phylum', 'family'),
+ id = taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi'),
+ auth = c('Linnaeus, 1758', 'Cohn 1872', NA, 'Juss., 1789'))
> tax_rank(x)
[1] species genus phylum family
Rank levels: phylum < family < genus < species
> tax_rank(x) <- 'species'
> tax_rank(x)[1] <- taxon_rank('family')
> tax_rank(x)
[1] family species species species
Rank levels: family < species