Handling Metadata in RNeXML
Carl Boettiger
Scott Chamberlain
Rutger Vos
Hilmar Lapp
Source:vignettes/metadata.Rmd
metadata.RmdWriting NeXML metadata
The add_basic_meta() function takes as input an existing
nexml object (like the other add_ functions,
if none is provided it will create one), and at the time of this writing
any of the following parameters: title,
description, creator, pubdate,
rights, publisher, citation.
Other metadata elements and corresponding parameters may be added in the
future.
Load the packages and data:
Create an nexml object for the phylogeny
bird.orders and add appropriate metadata:
birds <- add_trees(bird.orders)
birds <- add_basic_meta(
title = "Phylogeny of the Orders of Birds From Sibley and Ahlquist",
description = "This data set describes the phylogenetic relationships of the
orders of birds as reported by Sibley and Ahlquist (1990). Sibley
and Ahlquist inferred this phylogeny from an extensive number of
DNA/DNA hybridization experiments. The ``tapestry'' reported by
these two authors (more than 1000 species out of the ca. 9000
extant bird species) generated a lot of debates.
The present tree is based on the relationships among orders. The
branch lengths were calculated from the values of Delta T50H as
found in Sibley and Ahlquist (1990, fig. 353).",
citation = "Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and
classification of birds: a study in molecular evolution. New
Haven: Yale University Press.",
creator = "Sibley, C. G. and Ahlquist, J. E.",
nexml=birds)Instead of a literal string, citations can also be provided in R’s
bibentry type, which is the one in which R package
citations are obtained:
birds <- add_basic_meta(citation = citation("ape"), nexml = birds)Taxonomic identifiers
RNeXML now uses taxald for fast look-up of taxonomic
information. If a unique match is found, a metadata annotation is added
to the taxon providing the unique URI to the taxonomic unit.
birds <- taxize_nexml(birds, "NCBI")If no perfect match is found, the user is warned to check for possible typographic errors in the taxonomic labels provided.
Custom metadata extensions
We can get a list of namespaces along with their prefixes from the
nexml object:
prefixes <- get_namespaces(birds)
prefixes["dc"] dc
"http://purl.org/dc/elements/1.1/" We create a meta element containing this annotation
using the meta function:
modified <- meta(property = "prism:modificationDate", content = "2013-10-04")We can add this annotation to our existing birds NeXML
file using the add_meta() function. Because we do not
specify a level, it is added to the root node, referring to the NeXML
file as a whole.
birds <- add_meta(modified, birds) The built-in vocabularies are just the tip of the iceberg of
established vocabularies. Here we add an annotation from the
skos namespace which describes the history of where the
data comes from:
history <- meta(property = "skos:historyNote",
content = "Mapped from the bird.orders data in the ape package using RNeXML")Because skos is not in the current namespace list, we
add it with a url when adding this meta element. We also specify that
this annotation be placed at the level of the trees
sub-node in the NeXML file.
birds <- add_meta(history,
birds,
level = "trees",
namespaces = c(skos = "http://www.w3.org/2004/02/skos/core#"))For finer control of the level at which a meta element
is added, we will manipulate the nexml R object directly
using S4 sub-setting, as shown in the supplement.
Much richer metadata annotation is possible. Later we illustrate how
metadata annotation can be used to extend the base NeXML format to
represent new forms of data while maintaining compatibility with any
NeXML parser. The RNeXML package can be easily extended to
support helper functions such as taxize_nexml to add
additional metadata without imposing a large burden on the user.
Reading NeXML metadata
A call to the nexml object prints some metadata
summarizing the data structure:
birdsA nexml object representing:
1 phylogenetic tree block(s), where:
block 1 contains 1 phylogenetic tree(s)
0 character block(s),
23 taxonomic units in 1 block(s)
Taxa: Struthioniformes, Tinamiformes, Craciformes, Galliformes, Anseriformes, Turniciformes ...
Metadata annotations:
18 at top level
0 in block 1 at otu level
This data set describes the phylogenetic relationships of the
orders of birds as reported by Sibley and Ahlquist (1990). Sibley
and Ahlquist inferred this phylogeny from an extensive number of
DNA/DNA hybridization experiments. The ``tapestry'' reported by
these two authors (more than 1000 species out of the ca. 9000
extant bird species) generated a lot of debates.
The present tree is based on the relationships among orders. The
branch lengths were calculated from the values of Delta T50H as
found in Sibley and Ahlquist (1990, fig. 353).
Author(s): Sibley, C. G. and Ahlquist, J. E., cboettig
License: http://creativecommons.org/publicdomain/zero/1.0/
NeXML generated by RNeXML using schema version: 0.9
Size: 358.3 Kb We can extract all metadata pertaining to the NeXML document as a
whole (annotations of the XML root node, <nexml>)
with the command
meta <- get_metadata(birds) This returns a data.frame of available metadata. We can see the kinds of metadata recorded from the names:
meta property datatype
1 dc:title xsd:string
2 dc:creator xsd:string
3 dc:description xsd:string
4 cc:license <NA>
5 dcterms:bibliographicCitation xsd:string
6 dc:creator xsd:string
7 dcterms:references <NA>
8 prism:modificationDate xsd:string
9 prism:volume xsd:string
10 dc:publisher xsd:string
11 prism:publicationName xsd:string
12 prism:endingPage xsd:string
13 prism:startingPage xsd:string
14 prism:publicationDate xsd:string
15 dc:title xsd:string
16 dc:contributor xsd:string
17 dc:contributor xsd:string
18 dcterms:bibliographicCitation xsd:string
content
1 Phylogeny of the Orders of Birds From Sibley and Ahlquist
2 Sibley, C. G. and Ahlquist, J. E.
3 This data set describes the phylogenetic relationships of the\n orders of birds as reported by Sibley and Ahlquist (1990). Sibley\n and Ahlquist inferred this phylogeny from an extensive number of\n DNA/DNA hybridization experiments. The ``tapestry'' reported by\n these two authors (more than 1000 species out of the ca. 9000\n extant bird species) generated a lot of debates.\n\n The present tree is based on the relationships among orders. The\n branch lengths were calculated from the values of Delta T50H as\n found in Sibley and Ahlquist (1990, fig. 353).
4 <NA>
5 Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and\n classification of birds: a study in molecular evolution. New\n Haven: Yale University Press.
6 cboettig
7 <NA>
8 2013-10-04
9 35
10 Bioinformatics
11 Bioinformatics
12 528
13 526
14 2018
15 ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}
16 E. Paradis
17 K. Schliep
18 Paradis E, Schliep K (2018). "ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R."\n_Bioinformatics_, *35*, 526-528.
xsi.type href Meta meta
1 LiteralMeta <NA> m544 <NA>
2 LiteralMeta <NA> m545 <NA>
3 LiteralMeta <NA> m546 <NA>
4 ResourceMeta http://creativecommons.org/publicdomain/zero/1.0/ m547 <NA>
5 LiteralMeta <NA> m548 <NA>
6 LiteralMeta <NA> m549 <NA>
7 ResourceMeta <NA> m560 <NA>
8 LiteralMeta <NA> m561 <NA>
9 LiteralMeta <NA> <NA> m560
10 LiteralMeta <NA> <NA> m560
11 LiteralMeta <NA> <NA> m560
12 LiteralMeta <NA> <NA> m560
13 LiteralMeta <NA> <NA> m560
14 LiteralMeta <NA> <NA> m560
15 LiteralMeta <NA> <NA> m560
16 LiteralMeta <NA> <NA> m560
17 LiteralMeta <NA> <NA> m560
18 LiteralMeta <NA> <NA> m560We can also access a table of taxonomic metadata:
get_taxa(birds) otu label xsi.type otus
1 ou362 Struthioniformes NA os8
2 ou363 Tinamiformes NA os8
3 ou364 Craciformes NA os8
4 ou365 Galliformes NA os8
5 ou366 Anseriformes NA os8
6 ou367 Turniciformes NA os8
7 ou368 Piciformes NA os8
8 ou369 Galbuliformes NA os8
9 ou370 Bucerotiformes NA os8
10 ou371 Upupiformes NA os8
11 ou372 Trogoniformes NA os8
12 ou373 Coraciiformes NA os8
13 ou374 Coliiformes NA os8
14 ou375 Cuculiformes NA os8
15 ou376 Psittaciformes NA os8
16 ou377 Apodiformes NA os8
17 ou378 Trochiliformes NA os8
18 ou379 Musophagiformes NA os8
19 ou380 Strigiformes NA os8
20 ou381 Columbiformes NA os8
21 ou382 Gruiformes NA os8
22 ou383 Ciconiiformes NA os8
23 ou384 Passeriformes NA os8Which returns text from the otu element labels, typically used to define taxonomic names, rather than text from explicit meta elements.
We can also access metadata at a specific level (or use
level=all to extract all meta elements in a list). Here we
show only the first few results:
otu_meta <- get_metadata(birds, level="otus/otu")
otu_meta# A tibble: 0 x 3
# … with 3 variables: otu <chr>, otus <chr>, Meta <chr>Merging metadata tables
We often want to combine metadata from multiple tables. For instance, in this exercise we want to include the taxonomic identifier and id value for each species returned in the character table. This helps us more precisely identify the species whose traits are described by the table.
To begin, let’s generate a NeXML file using the tree and
trait data from the geiger package’s “primates” data:
data("primates")
add_trees(primates$phy) %>%
add_characters(primates$dat, ., append=TRUE) %>%
taxize_nexml("itis") -> nex (Note that we’ve used dplyr’s cute pipe syntax, but
unfortunately our add_ methods take the nexml
object as the second argument instead of the first, so this
isn’t as elegant since we need the stupid . to show where
the piped output should go…)
We now read in the three tables of interest. Note that we tell
get_characters to give us species labels as there own
column, rather than as rownames. The latter is the default only because
this plays more nicely with the default format for character matrices
that is expected by geiger and other phylogenetics
packages, but is in general a silly choice for data manipulation.
otu_meta <- get_metadata(nex, "otus/otu")
taxa <- get_taxa(nex)
char <- get_characters(nex, rownames_as_col = TRUE)We can take a peek at what the tables look like, just to orient ourselves:
otu_meta property href xsi.type otu otus
1 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572992 ResourceMeta ou385 os9
2 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572857 ResourceMeta ou386 os9
3 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572935 ResourceMeta ou387 os9
4 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572936 ResourceMeta ou388 os9
5 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945168 ResourceMeta ou389 os9
6 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945164 ResourceMeta ou390 os9
7 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572939 ResourceMeta ou391 os9
8 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572940 ResourceMeta ou392 os9
9 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572941 ResourceMeta ou393 os9
10 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572942 ResourceMeta ou394 os9
11 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944172 ResourceMeta ou395 os9
12 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572944 ResourceMeta ou396 os9
13 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572949 ResourceMeta ou397 os9
14 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945149 ResourceMeta ou398 os9
15 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572949 ResourceMeta ou399 os9
16 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572947 ResourceMeta ou400 os9
17 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572945 ResourceMeta ou401 os9
18 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572946 ResourceMeta ou402 os9
19 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572951 ResourceMeta ou403 os9
20 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572952 ResourceMeta ou404 os9
21 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572887 ResourceMeta ou405 os9
22 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572888 ResourceMeta ou406 os9
23 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572954 ResourceMeta ou407 os9
24 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572955 ResourceMeta ou408 os9
25 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572957 ResourceMeta ou409 os9
26 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572958 ResourceMeta ou410 os9
27 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572956 ResourceMeta ou411 os9
28 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572953 ResourceMeta ou412 os9
29 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572881 ResourceMeta ou413 os9
30 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572959 ResourceMeta ou414 os9
31 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572983 ResourceMeta ou415 os9
32 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572984 ResourceMeta ou416 os9
33 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025131 ResourceMeta ou417 os9
34 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025134 ResourceMeta ou418 os9
35 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025122 ResourceMeta ou419 os9
36 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025127 ResourceMeta ou420 os9
37 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025112 ResourceMeta ou421 os9
38 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025134 ResourceMeta ou422 os9
39 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025125 ResourceMeta ou423 os9
40 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025116 ResourceMeta ou424 os9
41 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025119 ResourceMeta ou425 os9
42 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025114 ResourceMeta ou426 os9
43 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025115 ResourceMeta ou427 os9
44 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572962 ResourceMeta ou428 os9
45 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025106 ResourceMeta ou429 os9
46 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572909 ResourceMeta ou430 os9
47 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944125 ResourceMeta ou431 os9
48 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572911 ResourceMeta ou432 os9
49 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572912 ResourceMeta ou433 os9
50 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572913 ResourceMeta ou434 os9
51 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944138 ResourceMeta ou435 os9
52 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572915 ResourceMeta ou436 os9
53 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572916 ResourceMeta ou437 os9
54 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572918 ResourceMeta ou438 os9
55 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944123 ResourceMeta ou439 os9
56 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572975 ResourceMeta ou440 os9
57 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944156 ResourceMeta ou441 os9
58 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572977 ResourceMeta ou442 os9
59 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572978 ResourceMeta ou443 os9
60 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572993 ResourceMeta ou444 os9
61 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572994 ResourceMeta ou445 os9
62 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572995 ResourceMeta ou446 os9
63 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572996 ResourceMeta ou447 os9
64 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572997 ResourceMeta ou448 os9
65 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572998 ResourceMeta ou449 os9
66 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572999 ResourceMeta ou450 os9
67 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573000 ResourceMeta ou451 os9
68 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573001 ResourceMeta ou452 os9
69 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573002 ResourceMeta ou453 os9
70 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573003 ResourceMeta ou454 os9
71 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944219 ResourceMeta ou455 os9
72 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573005 ResourceMeta ou456 os9
73 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573006 ResourceMeta ou457 os9
74 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573007 ResourceMeta ou458 os9
75 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573008 ResourceMeta ou459 os9
76 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573009 ResourceMeta ou460 os9
77 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573010 ResourceMeta ou461 os9
78 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945227 ResourceMeta ou462 os9
79 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573014 ResourceMeta ou463 os9
80 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944221 ResourceMeta ou464 os9
81 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573011 ResourceMeta ou465 os9
82 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572858 ResourceMeta ou466 os9
83 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572859 ResourceMeta ou467 os9
84 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572985 ResourceMeta ou468 os9
85 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572986 ResourceMeta ou469 os9
86 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=552515 ResourceMeta ou470 os9
87 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573035 ResourceMeta ou471 os9
88 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573036 ResourceMeta ou472 os9
89 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573037 ResourceMeta ou473 os9
90 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573038 ResourceMeta ou474 os9
91 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572886 ResourceMeta ou475 os9
92 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573015 ResourceMeta ou476 os9
93 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572865 ResourceMeta ou477 os9
94 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572864 ResourceMeta ou478 os9
95 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572866 ResourceMeta ou479 os9
96 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572867 ResourceMeta ou480 os9
97 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572868 ResourceMeta ou481 os9
98 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572893 ResourceMeta ou482 os9
99 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572894 ResourceMeta ou483 os9
100 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944100 ResourceMeta ou484 os9
101 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572896 ResourceMeta ou485 os9
102 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572897 ResourceMeta ou486 os9
103 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572898 ResourceMeta ou487 os9
104 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572899 ResourceMeta ou488 os9
105 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572900 ResourceMeta ou489 os9
106 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025177 ResourceMeta ou490 os9
107 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573080 ResourceMeta ou491 os9
108 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572869 ResourceMeta ou492 os9
109 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572870 ResourceMeta ou493 os9
110 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944072 ResourceMeta ou494 os9
111 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180092 ResourceMeta ou495 os9
112 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573069 ResourceMeta ou496 os9
113 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944286 ResourceMeta ou497 os9
114 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944292 ResourceMeta ou498 os9
115 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945338 ResourceMeta ou499 os9
116 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573073 ResourceMeta ou500 os9
117 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573074 ResourceMeta ou501 os9
118 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944290 ResourceMeta ou502 os9
119 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573076 ResourceMeta ou503 os9
120 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573077 ResourceMeta ou504 os9
121 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573078 ResourceMeta ou505 os9
122 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944293 ResourceMeta ou506 os9
123 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572882 ResourceMeta ou507 os9
124 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572961 ResourceMeta ou508 os9
125 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944187 ResourceMeta ou509 os9
126 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572872 ResourceMeta ou510 os9
127 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572921 ResourceMeta ou511 os9
128 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572920 ResourceMeta ou513 os9
129 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572922 ResourceMeta ou514 os9
130 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572874 ResourceMeta ou515 os9
131 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572875 ResourceMeta ou516 os9
132 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572876 ResourceMeta ou517 os9
133 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572877 ResourceMeta ou518 os9
134 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572878 ResourceMeta ou519 os9
135 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572879 ResourceMeta ou520 os9
136 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572880 ResourceMeta ou521 os9
137 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573016 ResourceMeta ou522 os9
138 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572889 ResourceMeta ou523 os9
139 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573017 ResourceMeta ou524 os9
140 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573018 ResourceMeta ou525 os9
141 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573019 ResourceMeta ou526 os9
142 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180098 ResourceMeta ou527 os9
143 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=555659 ResourceMeta ou528 os9
144 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573020 ResourceMeta ou529 os9
145 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180099 ResourceMeta ou530 os9
146 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573021 ResourceMeta ou531 os9
147 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573022 ResourceMeta ou532 os9
148 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573023 ResourceMeta ou533 os9
149 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573024 ResourceMeta ou534 os9
150 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573025 ResourceMeta ou535 os9
151 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573026 ResourceMeta ou536 os9
152 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573027 ResourceMeta ou537 os9
153 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573028 ResourceMeta ou538 os9
154 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573029 ResourceMeta ou539 os9
155 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573030 ResourceMeta ou540 os9
156 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573031 ResourceMeta ou541 os9
157 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944041 ResourceMeta ou542 os9
158 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572861 ResourceMeta ou543 os9
159 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572862 ResourceMeta ou544 os9
160 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573032 ResourceMeta ou545 os9
161 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944263 ResourceMeta ou546 os9
162 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573040 ResourceMeta ou547 os9
163 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572890 ResourceMeta ou548 os9
164 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572891 ResourceMeta ou549 os9
165 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572902 ResourceMeta ou550 os9
166 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572903 ResourceMeta ou551 os9
Meta
1 m563
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[ reached 'max' / getOption("max.print") -- omitted 66 rows ]
taxa otu label xsi.type otus
1 ou385 Allenopithecus_nigroviridis NA os9
2 ou386 Allocebus_trichotis NA os9
3 ou387 Alouatta_belzebul NA os9
4 ou388 Alouatta_caraya NA os9
5 ou389 Alouatta_coibensis NA os9
6 ou390 Alouatta_fusca NA os9
7 ou391 Alouatta_palliata NA os9
8 ou392 Alouatta_pigra NA os9
9 ou393 Alouatta_sara NA os9
10 ou394 Alouatta_seniculus NA os9
11 ou395 Aotus_azarai NA os9
12 ou396 Aotus_brumbacki NA os9
13 ou397 Aotus_hershkovitzi NA os9
14 ou398 Aotus_infulatus NA os9
15 ou399 Aotus_lemurinus NA os9
16 ou400 Aotus_miconax NA os9
17 ou401 Aotus_nancymaae NA os9
18 ou402 Aotus_nigriceps NA os9
19 ou403 Aotus_trivirgatus NA os9
20 ou404 Aotus_vociferans NA os9
21 ou405 Arctocebus_aureus NA os9
22 ou406 Arctocebus_calabarensis NA os9
23 ou407 Ateles_belzebuth NA os9
24 ou408 Ateles_chamek NA os9
25 ou409 Ateles_fusciceps NA os9
26 ou410 Ateles_geoffroyi NA os9
27 ou411 Ateles_marginatus NA os9
28 ou412 Ateles_paniscus NA os9
29 ou413 Avahi_laniger NA os9
30 ou414 Brachyteles_arachnoides NA os9
31 ou415 Cacajao_calvus NA os9
32 ou416 Cacajao_melanocephalus NA os9
33 ou417 Callicebus_brunneus NA os9
34 ou418 Callicebus_caligatus NA os9
35 ou419 Callicebus_cinerascens NA os9
36 ou420 Callicebus_cupreus NA os9
37 ou421 Callicebus_donacophilus NA os9
38 ou422 Callicebus_dubius NA os9
39 ou423 Callicebus_hoffmannsi NA os9
40 ou424 Callicebus_modestus NA os9
41 ou425 Callicebus_moloch NA os9
42 ou426 Callicebus_oenanthe NA os9
43 ou427 Callicebus_olallae NA os9
44 ou428 Callicebus_personatus NA os9
45 ou429 Callicebus_torquatus NA os9
46 ou430 Callimico_goeldii NA os9
47 ou431 Callithrix_argentata NA os9
48 ou432 Callithrix_aurita NA os9
49 ou433 Callithrix_flaviceps NA os9
50 ou434 Callithrix_geoffroyi NA os9
51 ou435 Callithrix_humeralifera NA os9
52 ou436 Callithrix_jacchus NA os9
53 ou437 Callithrix_kuhlii NA os9
54 ou438 Callithrix_penicillata NA os9
55 ou439 Callithrix_pygmaea NA os9
56 ou440 Cebus_albifrons NA os9
57 ou441 Cebus_apella NA os9
58 ou442 Cebus_capucinus NA os9
59 ou443 Cebus_olivaceus NA os9
60 ou444 Cercocebus_agilis NA os9
61 ou445 Cercocebus_galeritus NA os9
62 ou446 Cercocebus_torquatus NA os9
63 ou447 Cercopithecus_ascanius NA os9
64 ou448 Cercopithecus_campbelli NA os9
65 ou449 Cercopithecus_cephus NA os9
66 ou450 Cercopithecus_diana NA os9
67 ou451 Cercopithecus_dryas NA os9
68 ou452 Cercopithecus_erythrogaster NA os9
69 ou453 Cercopithecus_erythrotis NA os9
70 ou454 Cercopithecus_hamlyni NA os9
71 ou455 Cercopithecus_lhoesti NA os9
72 ou456 Cercopithecus_mitis NA os9
73 ou457 Cercopithecus_mona NA os9
74 ou458 Cercopithecus_neglectus NA os9
75 ou459 Cercopithecus_nictitans NA os9
76 ou460 Cercopithecus_petaurista NA os9
77 ou461 Cercopithecus_pogonias NA os9
78 ou462 Cercopithecus_preussi NA os9
79 ou463 Cercopithecus_sclateri NA os9
80 ou464 Cercopithecus_solatus NA os9
81 ou465 Cercopithecus_wolfi NA os9
82 ou466 Cheirogaleus_major NA os9
83 ou467 Cheirogaleus_medius NA os9
84 ou468 Chiropotes_albinasus NA os9
85 ou469 Chiropotes_satanas NA os9
86 ou470 Chlorocebus_aethiops NA os9
87 ou471 Colobus_angolensis NA os9
88 ou472 Colobus_guereza NA os9
89 ou473 Colobus_polykomos NA os9
90 ou474 Colobus_satanas NA os9
91 ou475 Daubentonia_madagascariensis NA os9
92 ou476 Erythrocebus_patas NA os9
93 ou477 Eulemur_coronatus NA os9
94 ou478 Eulemur_fulvus NA os9
95 ou479 Eulemur_macaco NA os9
96 ou480 Eulemur_mongoz NA os9
97 ou481 Eulemur_rubriventer NA os9
98 ou482 Euoticus_elegantulus NA os9
99 ou483 Euoticus_pallidus NA os9
100 ou484 Galago_alleni NA os9
101 ou485 Galago_gallarum NA os9
102 ou486 Galago_matschiei NA os9
103 ou487 Galago_moholi NA os9
104 ou488 Galago_senegalensis NA os9
105 ou489 Galagoides_demidoff NA os9
106 ou490 Galagoides_zanzibaricus NA os9
107 ou491 Gorilla_gorilla NA os9
108 ou492 Hapalemur_aureus NA os9
109 ou493 Hapalemur_griseus NA os9
110 ou494 Hapalemur_simus NA os9
111 ou495 Homo_sapiens NA os9
112 ou496 Hylobates_agilis NA os9
113 ou497 Hylobates_concolor NA os9
114 ou498 Hylobates_gabriellae NA os9
115 ou499 Hylobates_hoolock NA os9
116 ou500 Hylobates_klossii NA os9
117 ou501 Hylobates_lar NA os9
118 ou502 Hylobates_leucogenys NA os9
119 ou503 Hylobates_moloch NA os9
120 ou504 Hylobates_muelleri NA os9
121 ou505 Hylobates_pileatus NA os9
122 ou506 Hylobates_syndactylus NA os9
123 ou507 Indri_indri NA os9
124 ou508 Lagothrix_flavicauda NA os9
125 ou509 Lagothrix_lagotricha NA os9
126 ou510 Lemur_catta NA os9
127 ou511 Leontopithecus_caissara NA os9
128 ou512 Leontopithecus_chrysomela NA os9
129 ou513 Leontopithecus_chrysopygus NA os9
130 ou514 Leontopithecus_rosalia NA os9
131 ou515 Lepilemur_dorsalis NA os9
132 ou516 Lepilemur_edwardsi NA os9
133 ou517 Lepilemur_leucopus NA os9
134 ou518 Lepilemur_microdon NA os9
135 ou519 Lepilemur_mustelinus NA os9
136 ou520 Lepilemur_ruficaudatus NA os9
137 ou521 Lepilemur_septentrionalis NA os9
138 ou522 Lophocebus_albigena NA os9
139 ou523 Loris_tardigradus NA os9
140 ou524 Macaca_arctoides NA os9
141 ou525 Macaca_assamensis NA os9
142 ou526 Macaca_cyclopis NA os9
143 ou527 Macaca_fascicularis NA os9
144 ou528 Macaca_fuscata NA os9
145 ou529 Macaca_maura NA os9
146 ou530 Macaca_mulatta NA os9
147 ou531 Macaca_nemestrina NA os9
148 ou532 Macaca_nigra NA os9
149 ou533 Macaca_ochreata NA os9
150 ou534 Macaca_radiata NA os9
151 ou535 Macaca_silenus NA os9
152 ou536 Macaca_sinica NA os9
153 ou537 Macaca_sylvanus NA os9
154 ou538 Macaca_thibetana NA os9
155 ou539 Macaca_tonkeana NA os9
156 ou540 Mandrillus_leucophaeus NA os9
157 ou541 Mandrillus_sphinx NA os9
158 ou542 Microcebus_coquereli NA os9
159 ou543 Microcebus_murinus NA os9
160 ou544 Microcebus_rufus NA os9
161 ou545 Miopithecus_talapoin NA os9
162 ou546 Nasalis_concolor NA os9
163 ou547 Nasalis_larvatus NA os9
164 ou548 Nycticebus_coucang NA os9
165 ou549 Nycticebus_pygmaeus NA os9
166 ou550 Otolemur_crassicaudatus NA os9
167 ou551 Otolemur_garnettii NA os9
168 ou552 Pan_paniscus NA os9
169 ou553 Pan_troglodytes NA os9
170 ou554 Papio_hamadryas NA os9
171 ou555 Perodicticus_potto NA os9
172 ou556 Phaner_furcifer NA os9
173 ou557 Pithecia_aequatorialis NA os9
174 ou558 Pithecia_albicans NA os9
175 ou559 Pithecia_irrorata NA os9
176 ou560 Pithecia_monachus NA os9
177 ou561 Pithecia_pithecia NA os9
178 ou562 Pongo_pygmaeus NA os9
179 ou563 Presbytis_comata NA os9
180 ou564 Presbytis_femoralis NA os9
181 ou565 Presbytis_frontata NA os9
182 ou566 Presbytis_hosei NA os9
183 ou567 Presbytis_melalophos NA os9
184 ou568 Presbytis_potenziani NA os9
185 ou569 Presbytis_rubicunda NA os9
186 ou570 Presbytis_thomasi NA os9
187 ou571 Procolobus_badius NA os9
188 ou572 Procolobus_pennantii NA os9
189 ou573 Procolobus_preussi NA os9
190 ou574 Procolobus_rufomitratus NA os9
191 ou575 Procolobus_verus NA os9
192 ou576 Propithecus_diadema NA os9
193 ou577 Propithecus_tattersalli NA os9
194 ou578 Propithecus_verreauxi NA os9
195 ou579 Pygathrix_avunculus NA os9
196 ou580 Pygathrix_bieti NA os9
197 ou581 Pygathrix_brelichi NA os9
198 ou582 Pygathrix_nemaeus NA os9
199 ou583 Pygathrix_roxellana NA os9
200 ou584 Saguinus_bicolor NA os9
201 ou585 Saguinus_fuscicollis NA os9
202 ou586 Saguinus_geoffroyi NA os9
203 ou587 Saguinus_imperator NA os9
204 ou588 Saguinus_inustus NA os9
205 ou589 Saguinus_labiatus NA os9
206 ou590 Saguinus_leucopus NA os9
207 ou591 Saguinus_midas NA os9
208 ou592 Saguinus_mystax NA os9
209 ou593 Saguinus_nigricollis NA os9
210 ou594 Saguinus_oedipus NA os9
211 ou595 Saguinus_tripartitus NA os9
212 ou596 Saimiri_boliviensis NA os9
213 ou597 Saimiri_oerstedii NA os9
214 ou598 Saimiri_sciureus NA os9
215 ou599 Saimiri_ustus NA os9
216 ou600 Saimiri_vanzolinii NA os9
217 ou601 Semnopithecus_entellus NA os9
218 ou602 Tarsius_bancanus NA os9
219 ou603 Tarsius_dianae NA os9
220 ou604 Tarsius_pumilus NA os9
221 ou605 Tarsius_spectrum NA os9
222 ou606 Tarsius_syrichta NA os9
223 ou607 Theropithecus_gelada NA os9
224 ou608 Trachypithecus_auratus NA os9
225 ou609 Trachypithecus_cristatus NA os9
226 ou610 Trachypithecus_francoisi NA os9
227 ou611 Trachypithecus_geei NA os9
228 ou612 Trachypithecus_johnii NA os9
229 ou613 Trachypithecus_obscurus NA os9
230 ou614 Trachypithecus_phayrei NA os9
231 ou615 Trachypithecus_pileatus NA os9
232 ou616 Trachypithecus_vetulus NA os9
233 ou617 Varecia_variegata NA os9
head(char) taxa x
1 Allenopithecus_nigroviridis 8.465900
2 Allocebus_trichotis 4.368181
3 Alouatta_belzebul 8.729074
4 Alouatta_caraya 8.628735
5 Alouatta_coibensis 8.764053
6 Alouatta_fusca 8.554489Now that we have nice data.frame objects for all our
data, it’s easy to join them into the desired table with a few obvious
dplyr commands:
taxa %>%
left_join(char, by = c("label" = "taxa")) %>%
left_join(otu_meta, by = "otu") %>%
select(otu, label, x, href) otu label x
1 ou385 Allenopithecus_nigroviridis 8.465900
2 ou386 Allocebus_trichotis 4.368181
3 ou387 Alouatta_belzebul 8.729074
4 ou388 Alouatta_caraya 8.628735
5 ou389 Alouatta_coibensis 8.764053
6 ou390 Alouatta_fusca 8.554489
7 ou391 Alouatta_palliata 8.791790
8 ou392 Alouatta_pigra 8.881836
9 ou393 Alouatta_sara 8.796339
10 ou394 Alouatta_seniculus 8.767173
11 ou395 Aotus_azarai 7.127694
12 ou396 Aotus_brumbacki 6.401917
13 ou397 Aotus_hershkovitzi 6.684612
14 ou398 Aotus_infulatus 7.122867
15 ou399 Aotus_lemurinus 6.781058
16 ou400 Aotus_miconax 6.684612
17 ou401 Aotus_nancymaae 6.678342
18 ou402 Aotus_nigriceps 6.966024
19 ou403 Aotus_trivirgatus 6.815640
20 ou404 Aotus_vociferans 6.771936
21 ou405 Arctocebus_aureus 5.459586
22 ou406 Arctocebus_calabarensis 5.552960
23 ou407 Ateles_belzebuth 8.812843
24 ou408 Ateles_chamek 8.872067
25 ou409 Ateles_fusciceps 9.112728
26 ou410 Ateles_geoffroyi 8.937218
27 ou411 Ateles_marginatus 8.738735
28 ou412 Ateles_paniscus 9.072227
29 ou413 Avahi_laniger 6.927558
30 ou414 Brachyteles_arachnoides 9.268609
31 ou415 Cacajao_calvus 8.137396
32 ou416 Cacajao_melanocephalus 8.051978
33 ou417 Callicebus_brunneus 6.747587
34 ou418 Callicebus_caligatus 6.899723
35 ou419 Callicebus_cinerascens 6.899723
36 ou420 Callicebus_cupreus 7.021084
37 ou421 Callicebus_donacophilus 6.801283
38 ou422 Callicebus_dubius 6.899723
39 ou423 Callicebus_hoffmannsi 6.975414
40 ou424 Callicebus_modestus 6.899723
41 ou425 Callicebus_moloch 6.872128
42 ou426 Callicebus_oenanthe 6.899723
43 ou427 Callicebus_olallae 6.899723
44 ou428 Callicebus_personatus 7.237059
45 ou429 Callicebus_torquatus 7.106606
46 ou430 Callimico_goeldii 6.324359
47 ou431 Callithrix_argentata 5.910797
48 ou432 Callithrix_aurita 5.961005
49 ou433 Callithrix_flaviceps 5.926926
50 ou434 Callithrix_geoffroyi 5.834811
51 ou435 Callithrix_humeralifera 5.926926
52 ou436 Callithrix_jacchus 5.673323
53 ou437 Callithrix_kuhlii 5.926926
54 ou438 Callithrix_penicillata 5.828946
55 ou439 Callithrix_pygmaea 4.828314
56 ou440 Cebus_albifrons 7.832014
57 ou441 Cebus_apella 7.922986
58 ou442 Cebus_capucinus 8.009695
59 ou443 Cebus_olivaceus 7.937375
60 ou444 Cercocebus_agilis 8.870663
61 ou445 Cercocebus_galeritus 8.865029
62 ou446 Cercocebus_torquatus 8.894259
63 ou447 Cercopithecus_ascanius 8.171882
64 ou448 Cercopithecus_campbelli 8.199739
65 ou449 Cercopithecus_cephus 8.143227
66 ou450 Cercopithecus_diana 8.382518
67 ou451 Cercopithecus_dryas 7.930206
68 ou452 Cercopithecus_erythrogaster 8.143227
69 ou453 Cercopithecus_erythrotis 8.086410
70 ou454 Cercopithecus_hamlyni 8.438150
71 ou455 Cercopithecus_lhoesti 8.579229
72 ou456 Cercopithecus_mitis 8.525161
73 ou457 Cercopithecus_mona 8.289037
74 ou458 Cercopithecus_neglectus 8.579229
75 ou459 Cercopithecus_nictitans 8.567886
76 ou460 Cercopithecus_petaurista 8.083329
77 ou461 Cercopithecus_pogonias 8.183118
78 ou462 Cercopithecus_preussi 8.544808
79 ou463 Cercopithecus_sclateri 8.029433
80 ou464 Cercopithecus_solatus 8.567886
81 ou465 Cercopithecus_wolfi 8.089482
82 ou466 Cheirogaleus_major 6.104793
83 ou467 Cheirogaleus_medius 5.283204
84 ou468 Chiropotes_albinasus 7.937375
85 ou469 Chiropotes_satanas 7.996317
86 ou470 Chlorocebus_aethiops 8.301522
87 ou471 Colobus_angolensis 9.103868
88 ou472 Colobus_guereza 9.210340
89 ou473 Colobus_polykomos 9.060680
90 ou474 Colobus_satanas 9.121509
91 ou475 Daubentonia_madagascariensis 7.919356
92 ou476 Erythrocebus_patas 8.988446
93 ou477 Eulemur_coronatus 7.438384
94 ou478 Eulemur_fulvus 7.779049
95 ou479 Eulemur_macaco 7.816014
96 ou480 Eulemur_mongoz 7.478735
97 ou481 Eulemur_rubriventer 7.620705
98 ou482 Euoticus_elegantulus 5.690359
99 ou483 Euoticus_pallidus 5.627621
100 ou484 Galago_alleni 5.521461
101 ou485 Galago_gallarum 5.365976
102 ou486 Galago_matschiei 5.267858
103 ou487 Galago_moholi 5.375278
104 ou488 Galago_senegalensis 5.594711
105 ou489 Galagoides_demidoff 4.206184
106 ou490 Galagoides_zanzibaricus 4.997212
107 ou491 Gorilla_gorilla 11.643954
108 ou492 Hapalemur_aureus 7.358831
109 ou493 Hapalemur_griseus 6.862758
110 ou494 Hapalemur_simus 7.620705
111 ou495 Homo_sapiens 10.980195
112 ou496 Hylobates_agilis 8.675905
113 ou497 Hylobates_concolor 8.768730
114 ou498 Hylobates_gabriellae 9.047821
115 ou499 Hylobates_hoolock 8.809863
116 ou500 Hylobates_klossii 8.674197
117 ou501 Hylobates_lar 8.635865
118 ou502 Hylobates_leucogenys 8.898366
119 ou503 Hylobates_moloch 8.677610
120 ou504 Hylobates_muelleri 8.687779
121 ou505 Hylobates_pileatus 8.630522
122 ou506 Hylobates_syndactylus 9.296518
123 ou507 Indri_indri 9.065315
124 ou508 Lagothrix_flavicauda 9.020390
125 ou509 Lagothrix_lagotricha 8.743532
126 ou510 Lemur_catta 7.878534
127 ou511 Leontopithecus_caissara 6.405228
128 ou512 Leontopithecus_chrysomela 6.352629
129 ou513 Leontopithecus_chrysopygus 6.486161
130 ou514 Leontopithecus_rosalia 6.385194
131 ou515 Lepilemur_dorsalis 6.232448
132 ou516 Lepilemur_edwardsi 6.711740
133 ou517 Lepilemur_leucopus 6.396930
134 ou518 Lepilemur_microdon 6.863803
135 ou519 Lepilemur_mustelinus 6.508769
136 ou520 Lepilemur_ruficaudatus 6.637258
137 ou521 Lepilemur_septentrionalis 6.638568
138 ou522 Lophocebus_albigena 8.903815
139 ou523 Loris_tardigradus 5.517453
140 ou524 Macaca_arctoides 9.148465
141 ou525 Macaca_assamensis 9.054855
142 ou526 Macaca_cyclopis 8.658693
143 ou527 Macaca_fascicularis 8.431635
144 ou528 Macaca_fuscata 9.220291
145 ou529 Macaca_maura 8.894259
146 ou530 Macaca_mulatta 8.771835
147 ou531 Macaca_nemestrina 8.970813
148 ou532 Macaca_nigra 8.906529
149 ou533 Macaca_ochreata 7.919356
150 ou534 Macaca_radiata 8.517193
151 ou535 Macaca_silenus 8.699515
152 ou536 Macaca_sinica 8.446771
153 ou537 Macaca_sylvanus 9.350102
154 ou538 Macaca_thibetana 9.268609
155 ou539 Macaca_tonkeana 9.220291
156 ou540 Mandrillus_leucophaeus 9.560997
157 ou541 Mandrillus_sphinx 9.729134
158 ou542 Microcebus_coquereli 5.793014
159 ou543 Microcebus_murinus 4.198705
160 ou544 Microcebus_rufus 3.881564
161 ou545 Miopithecus_talapoin 7.130899
162 ou546 Nasalis_concolor 8.979354
163 ou547 Nasalis_larvatus 9.417355
164 ou548 Nycticebus_coucang 6.878326
165 ou549 Nycticebus_pygmaeus 5.840642
166 ou550 Otolemur_crassicaudatus 7.130899
167 ou551 Otolemur_garnettii 6.701960
168 ou552 Pan_paniscus 10.468801
169 ou553 Pan_troglodytes 10.716638
170 ou554 Papio_hamadryas 9.735069
171 ou555 Perodicticus_potto 6.984716
172 ou556 Phaner_furcifer 6.016157
173 ou557 Pithecia_aequatorialis 7.774856
174 ou558 Pithecia_albicans 7.937375
175 ou559 Pithecia_irrorata 7.749322
176 ou560 Pithecia_monachus 7.654443
177 ou561 Pithecia_pithecia 7.420579
178 ou562 Pongo_pygmaeus 10.860920
179 ou563 Presbytis_comata 9.039552
180 ou564 Presbytis_femoralis 8.797851
181 ou565 Presbytis_frontata 8.853665
182 ou566 Presbytis_hosei 8.725832
183 ou567 Presbytis_melalophos 8.748305
184 ou568 Presbytis_potenziani 8.774931
185 ou569 Presbytis_rubicunda 8.773385
186 ou570 Presbytis_thomasi 8.765615
187 ou571 Procolobus_badius 8.808369
188 ou572 Procolobus_pennantii 9.122601
189 ou573 Procolobus_preussi 9.094930
190 ou574 Procolobus_rufomitratus 8.995909
191 ou575 Procolobus_verus 8.289037
192 ou576 Propithecus_diadema 8.794825
193 ou577 Propithecus_tattersalli 8.171882
194 ou578 Propithecus_verreauxi 8.202482
195 ou579 Pygathrix_avunculus 9.164296
196 ou580 Pygathrix_bieti 9.118225
197 ou581 Pygathrix_brelichi 9.305651
198 ou582 Pygathrix_nemaeus 9.417355
199 ou583 Pygathrix_roxellana 9.510445
200 ou584 Saguinus_bicolor 6.142037
201 ou585 Saguinus_fuscicollis 5.976351
202 ou586 Saguinus_geoffroyi 6.200509
203 ou587 Saguinus_imperator 6.016157
204 ou588 Saguinus_inustus 6.688355
205 ou589 Saguinus_labiatus 6.234411
206 ou590 Saguinus_leucopus 6.124683
207 ou591 Saguinus_midas 6.293419
208 ou592 Saguinus_mystax 6.326149
209 ou593 Saguinus_nigricollis 6.109248
210 ou594 Saguinus_oedipus 6.139885
211 ou595 Saguinus_tripartitus 5.953243
212 ou596 Saimiri_boliviensis 6.690842
213 ou597 Saimiri_oerstedii 6.570883
214 ou598 Saimiri_sciureus 6.620073
215 ou599 Saimiri_ustus 6.791221
216 ou600 Saimiri_vanzolinii 6.664409
217 ou601 Semnopithecus_entellus 9.441452
218 ou602 Tarsius_bancanus 4.736198
219 ou603 Tarsius_dianae 4.709530
220 ou604 Tarsius_pumilus 4.808111
221 ou605 Tarsius_spectrum 5.111988
222 ou606 Tarsius_syrichta 4.753590
223 ou607 Theropithecus_gelada 9.680344
224 ou608 Trachypithecus_auratus 9.181941
225 ou609 Trachypithecus_cristatus 8.872067
226 ou610 Trachypithecus_francoisi 9.008224
227 ou611 Trachypithecus_geei 9.031214
228 ou612 Trachypithecus_johnii 9.268609
229 ou613 Trachypithecus_obscurus 8.870663
230 ou614 Trachypithecus_phayrei 8.948976
231 ou615 Trachypithecus_pileatus 9.323669
232 ou616 Trachypithecus_vetulus 8.969542
233 ou617 Varecia_variegata 8.261010
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139 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572889
140 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573017
141 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573018
142 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573019
143 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180098
144 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=555659
145 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573020
146 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180099
147 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573021
148 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573022
149 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573023
150 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573024
151 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573025
152 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573026
153 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573027
154 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573028
155 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573029
156 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573030
157 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573031
158 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944041
159 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572861
160 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572862
161 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573032
162 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944263
163 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573040
164 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572890
165 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572891
166 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572902
167 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572903
168 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573081
169 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573082
170 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573033
171 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572892
172 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572863
173 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572987
174 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572988
175 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572989
176 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572990
177 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572991
178 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573083
179 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573041
180 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573042
181 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573043
182 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573044
183 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573045
184 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573046
185 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573047
186 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573048
187 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944230
188 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944235
189 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944238
190 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944239
191 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573053
192 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572883
193 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572884
194 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572885
195 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944258
196 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944259
197 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944260
198 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573057
199 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945308
200 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572923
201 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=998616
202 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572925
203 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572926
204 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572927
205 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572928
206 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572929
207 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572930
208 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572931
209 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=998617
210 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572933
211 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025098
212 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572979
213 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572980
214 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180095
215 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572981
216 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572982
217 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573059
218 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945103
219 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944117
220 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572906
221 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944115
222 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945107
223 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573034
224 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573060
225 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573061
226 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573062
227 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573063
228 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944270
229 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573065
230 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573066
231 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573067
232 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944269
233 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572873Because these are all from the same otus block anyway, we haven’t selected that column, but were it of interest it is also available in the taxa table.