Get data in a taxmap object by name

Source: R/taxonomy--docs.R

Given a vector of names, return a list of data (usually lists/vectors) contained in a taxonomy() or taxmap() object. Each item will be named by taxon ids when possible.

obj$get_data(name = NULL, ...)
get_data(obj, name = NULL, ...)

Arguments

obj

A taxonomy() or taxmap() object
name

(character) Names of data to return. If not supplied, return all data listed in all_names().
...

Passed to all_names(). Used to filter what kind of data is returned (e.g. columns in tables or function output?) if name is not supplied or what kinds are allowed if name is supplied.

Value

list of vectors or lists. Each vector or list will be named by associated taxon ids if possible.

See also

Other NSE helpers: all_names(), data_used, names_used

Examples

# Get specific values
get_data(ex_taxmap, c("reaction", "n_legs", "taxon_ranks"))

#> $reaction
#> [1] "Watch out! That tiger might attack!" "No worries; its just a cat."        
#> [3] "No worries; its just a mole."        "Watch out! That human might attack!"
#> [5] "No worries; its just a tomato."      "No worries; its just a potato."     
#> 
#> $n_legs
#> m n o p q r 
#> 4 4 4 2 0 0 
#> 
#> $taxon_ranks
#>         b         c         d         e         f         g         h         i 
#>   "class" "kingdom"  "family"  "family"  "family"  "family"   "genus"   "genus" 
#>         j         k         l         m         n         o         p         q 
#>   "genus"   "genus"   "genus" "species" "species" "species" "species" "species" 
#>         r 
#> "species" 
#> 

# Get all values
get_data(ex_taxmap)

#> $taxon_names
#>              b              c              d              e              f 
#>     "Mammalia"      "Plantae"      "Felidae" "Notoryctidae"    "Hominidae" 
#>              g              h              i              j              k 
#>   "Solanaceae"     "Panthera"        "Felis"   "Notoryctes"         "homo" 
#>              l              m              n              o              p 
#>      "Solanum"       "tigris"        "catus"     "typhlops"      "sapiens" 
#>              q              r 
#> "lycopersicum"    "tuberosum" 
#> 
#> $taxon_ids
#>   b   c   d   e   f   g   h   i   j   k   l   m   n   o   p   q   r 
#> "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" 
#> 
#> $taxon_indexes
#>  b  c  d  e  f  g  h  i  j  k  l  m  n  o  p  q  r 
#>  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 
#> 
#> $classifications
#>                                           b 
#>                                  "Mammalia" 
#>                                           c 
#>                                   "Plantae" 
#>                                           d 
#>                          "Mammalia;Felidae" 
#>                                           e 
#>                     "Mammalia;Notoryctidae" 
#>                                           f 
#>                        "Mammalia;Hominidae" 
#>                                           g 
#>                        "Plantae;Solanaceae" 
#>                                           h 
#>                 "Mammalia;Felidae;Panthera" 
#>                                           i 
#>                    "Mammalia;Felidae;Felis" 
#>                                           j 
#>          "Mammalia;Notoryctidae;Notoryctes" 
#>                                           k 
#>                   "Mammalia;Hominidae;homo" 
#>                                           l 
#>                "Plantae;Solanaceae;Solanum" 
#>                                           m 
#>          "Mammalia;Felidae;Panthera;tigris" 
#>                                           n 
#>              "Mammalia;Felidae;Felis;catus" 
#>                                           o 
#> "Mammalia;Notoryctidae;Notoryctes;typhlops" 
#>                                           p 
#>           "Mammalia;Hominidae;homo;sapiens" 
#>                                           q 
#>   "Plantae;Solanaceae;Solanum;lycopersicum" 
#>                                           r 
#>      "Plantae;Solanaceae;Solanum;tuberosum" 
#> 
#> $n_supertaxa
#> b c d e f g h i j k l m n o p q r 
#> 0 0 1 1 1 1 2 2 2 2 2 3 3 3 3 3 3 
#> 
#> $n_supertaxa_1
#> b c d e f g h i j k l m n o p q r 
#> 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
#> 
#> $n_subtaxa
#>  b  c  d  e  f  g  h  i  j  k  l  m  n  o  p  q  r 
#> 11  4  4  2  2  3  1  1  1  1  2  0  0  0  0  0  0 
#> 
#> $n_subtaxa_1
#> b c d e f g h i j k l m n o p q r 
#> 3 1 2 1 1 1 1 1 1 1 2 0 0 0 0 0 0 
#> 
#> $n_leaves
#> b c d e f g h i j k l m n o p q r 
#> 4 2 2 1 1 2 1 1 1 1 2 0 0 0 0 0 0 
#> 
#> $n_leaves_1
#> b c d e f g h i j k l m n o p q r 
#> 0 0 0 0 0 0 1 1 1 1 2 0 0 0 0 0 0 
#> 
#> $taxon_ranks
#>         b         c         d         e         f         g         h         i 
#>   "class" "kingdom"  "family"  "family"  "family"  "family"   "genus"   "genus" 
#>         j         k         l         m         n         o         p         q 
#>   "genus"   "genus"   "genus" "species" "species" "species" "species" "species" 
#>         r 
#> "species" 
#> 
#> $is_root
#>     b     c     d     e     f     g     h     i     j     k     l     m     n 
#>  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 
#>     o     p     q     r 
#> FALSE FALSE FALSE FALSE 
#> 
#> $is_stem
#>     b     c     d     e     f     g     h     i     j     k     l     m     n 
#> FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 
#>     o     p     q     r 
#> FALSE FALSE FALSE FALSE 
#> 
#> $is_branch
#>     b     c     d     e     f     g     h     i     j     k     l     m     n 
#> FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE 
#>     o     p     q     r 
#> FALSE FALSE FALSE FALSE 
#> 
#> $is_leaf
#>     b     c     d     e     f     g     h     i     j     k     l     m     n 
#> FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE 
#>     o     p     q     r 
#>  TRUE  TRUE  TRUE  TRUE 
#> 
#> $is_internode
#>     b     c     d     e     f     g     h     i     j     k     l     m     n 
#> FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE 
#>     o     p     q     r 
#> FALSE FALSE FALSE FALSE 
#> 
#> $n_obs
#> b c d e f g h i j k l m n o p q r 
#> 4 2 2 1 1 2 1 1 1 1 2 1 1 1 1 1 1 
#> 
#> $n_obs_1
#> b c d e f g h i j k l m n o p q r 
#> 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 
#> 
#> $name
#>        m        n        o        p        q        r 
#>  "tiger"    "cat"   "mole"  "human" "tomato" "potato" 
#> 
#> $n_legs
#> m n o p q r 
#> 4 4 4 2 0 0 
#> 
#> $dangerous
#>     m     n     o     p     q     r 
#>  TRUE FALSE FALSE  TRUE FALSE FALSE 
#> 
#> $code
#> m n o p m n o p 
#> T C M H T C M H 
#> Levels: C H M T
#> 
#> $sample_id
#> m n o p m n o p 
#> A A B B A A B B 
#> Levels: A B
#> 
#> $count
#> m n o p m n o p 
#> 1 2 5 2 6 2 4 0 
#> 
#> $taxon_index
#> m n o p m n o p 
#> 1 2 3 4 1 2 3 4 
#> 
#> $phylopic_ids
#>                                      m                                      n 
#> "e148eabb-f138-43c6-b1e4-5cda2180485a" "12899ba0-9923-4feb-a7f9-758c3c7d5e13" 
#>                                      o                                      p 
#> "11b783d5-af1c-4f4e-8ab5-a51470652b47" "9fae30cd-fb59-4a81-a39c-e1826a35f612" 
#>                                      q                                      r 
#> "b6400f39-345a-4711-ab4f-92fd4e22cb1a" "63604565-0406-460b-8cb8-1abe954b3f3a" 
#> 
#> $foods
#> $foods$m
#> [1] "mammals" "birds"  
#> 
#> $foods$n
#> [1] "cat food" "mice"    
#> 
#> $foods$o
#> [1] "insects"
#> 
#> $foods$p
#> [1] "Most things, but especially anything rare or expensive"
#> 
#> $foods$q
#> [1] "light" "dirt" 
#> 
#> $foods$r
#> [1] "light" "dirt" 
#> 
#> 
#> $reaction
#> [1] "Watch out! That tiger might attack!" "No worries; its just a cat."        
#> [3] "No worries; its just a mole."        "Watch out! That human might attack!"
#> [5] "No worries; its just a tomato."      "No worries; its just a potato."     
#>