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) <taxon_authority[4]> [1] Linnaeus 1758 Cohn 1872 NA Juss. 1789 > tax_auth(x) <- tolower(tax_auth(x)) > tax_auth(x)[1] <- 'Billy' > x <taxon[4]> [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) <taxon_db[4]> [1] ncbi ncbi ncbi ncbi > tax_db(x) <- 'nbn' > tax_db(x)[2] <- 'itis' > tax_db(x) <taxon_db[4]> [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) <taxon_id[4]> [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) <taxon_id[4]> [1] 00000 001386 004890 004345
tax_name(x)
设置和获取分类群名称。文章来源:https://www.toymoban.com/news/detail-820536.html
> 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。文章来源地址https://www.toymoban.com/news/detail-820536.html
> 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) <taxon_rank[4]> [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) <taxon_rank[4]> [1] family species species species Rank levels: family < species
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