Handling Metadata in RNeXML

Carl Boettiger

Scott Chamberlain

Rutger Vos

Hilmar Lapp

Writing 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:

library('RNeXML')
data(bird.orders)

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:

birds
A nexml object representing:
     1 phylogenetic tree blocks, where: 
     block 1 contains 1 phylogenetic trees 
     20 meta elements 
     0 character matrices 
     23 taxonomic units 
 Taxa:   Struthioniformes, Tinamiformes, Craciformes, Galliformes, Anseriformes, Turniciformes ... 

 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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 xx
10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Bioinformatics
11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Bioinformatics
12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               xxx
13                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               xxx
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\nphylogenetics and evolutionary analyses in R." _Bioinformatics_,\n*xx*, xxx-xxx.
       xsi.type                                              href Meta
1   LiteralMeta                                              <NA>  m16
2   LiteralMeta                                              <NA>  m17
3   LiteralMeta                                              <NA>  m18
4  ResourceMeta http://creativecommons.org/publicdomain/zero/1.0/  m19
5   LiteralMeta                                              <NA>  m20
6   LiteralMeta                                              <NA>  m21
7  ResourceMeta                                              <NA>  m32
8   LiteralMeta                                              <NA>  m33
9   LiteralMeta                                              <NA> <NA>
10  LiteralMeta                                              <NA> <NA>
11  LiteralMeta                                              <NA> <NA>
12  LiteralMeta                                              <NA> <NA>
13  LiteralMeta                                              <NA> <NA>
14  LiteralMeta                                              <NA> <NA>
15  LiteralMeta                                              <NA> <NA>
16  LiteralMeta                                              <NA> <NA>
17  LiteralMeta                                              <NA> <NA>
18  LiteralMeta                                              <NA> <NA>
   meta
1  <NA>
2  <NA>
3  <NA>
4  <NA>
5  <NA>
6  <NA>
7  <NA>
8  <NA>
9   m32
10  m32
11  m32
12  m32
13  m32
14  m32
15  m32
16  m32
17  m32
18  m32

We can also access a table of taxonomic metadata:

get_taxa(birds)
    otu            label xsi.type otus
1  ou70 Struthioniformes       NA  os4
2  ou71     Tinamiformes       NA  os4
3  ou72      Craciformes       NA  os4
4  ou73      Galliformes       NA  os4
5  ou74     Anseriformes       NA  os4
6  ou75    Turniciformes       NA  os4
7  ou76       Piciformes       NA  os4
8  ou77    Galbuliformes       NA  os4
9  ou78   Bucerotiformes       NA  os4
10 ou79      Upupiformes       NA  os4
11 ou80    Trogoniformes       NA  os4
12 ou81    Coraciiformes       NA  os4
13 ou82      Coliiformes       NA  os4
14 ou83     Cuculiformes       NA  os4
15 ou84   Psittaciformes       NA  os4
16 ou85      Apodiformes       NA  os4
17 ou86   Trochiliformes       NA  os4
18 ou87  Musophagiformes       NA  os4
19 ou88     Strigiformes       NA  os4
20 ou89    Columbiformes       NA  os4
21 ou90       Gruiformes       NA  os4
22 ou91    Ciconiiformes       NA  os4
23 ou92    Passeriformes       NA  os4

Which 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.

library("RNeXML")
library("dplyr")
library("geiger")

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
1   tc:toTaxon
2   tc:toTaxon
3   tc:toTaxon
4   tc:toTaxon
5   tc:toTaxon
6   tc:toTaxon
7   tc:toTaxon
8   tc:toTaxon
9   tc:toTaxon
10  tc:toTaxon
11  tc:toTaxon
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25  tc:toTaxon
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28  tc:toTaxon
29  tc:toTaxon
30  tc:toTaxon
31  tc:toTaxon
32  tc:toTaxon
33  tc:toTaxon
34  tc:toTaxon
35  tc:toTaxon
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180 ResourceMeta ou273  os5 m215
181 ResourceMeta ou274  os5 m216
182 ResourceMeta ou275  os5 m217
183 ResourceMeta ou276  os5 m218
184 ResourceMeta ou277  os5 m219
185 ResourceMeta ou278  os5 m220
186 ResourceMeta ou279  os5 m221
187 ResourceMeta ou280  os5 m222
188 ResourceMeta ou281  os5 m223
189 ResourceMeta ou282  os5 m224
190 ResourceMeta ou283  os5 m225
191 ResourceMeta ou284  os5 m226
192 ResourceMeta ou285  os5 m227
193 ResourceMeta ou286  os5 m228
194 ResourceMeta ou287  os5 m229
195 ResourceMeta ou288  os5 m230
196 ResourceMeta ou289  os5 m231
197 ResourceMeta ou290  os5 m232
198 ResourceMeta ou291  os5 m233
199 ResourceMeta ou292  os5 m234
200 ResourceMeta ou294  os5 m235
201 ResourceMeta ou295  os5 m236
202 ResourceMeta ou296  os5 m237
203 ResourceMeta ou297  os5 m238
204 ResourceMeta ou298  os5 m239
205 ResourceMeta ou299  os5 m240
206 ResourceMeta ou300  os5 m241
207 ResourceMeta ou302  os5 m242
208 ResourceMeta ou303  os5 m243
209 ResourceMeta ou304  os5 m244
210 ResourceMeta ou305  os5 m245
211 ResourceMeta ou306  os5 m246
212 ResourceMeta ou307  os5 m247
213 ResourceMeta ou308  os5 m248
214 ResourceMeta ou309  os5 m249
215 ResourceMeta ou310  os5 m250
216 ResourceMeta ou311  os5 m251
217 ResourceMeta ou312  os5 m252
218 ResourceMeta ou313  os5 m253
219 ResourceMeta ou314  os5 m254
220 ResourceMeta ou315  os5 m255
221 ResourceMeta ou316  os5 m256
222 ResourceMeta ou317  os5 m257
223 ResourceMeta ou318  os5 m258
224 ResourceMeta ou319  os5 m259
225 ResourceMeta ou320  os5 m260
226 ResourceMeta ou321  os5 m261
227 ResourceMeta ou322  os5 m262
228 ResourceMeta ou323  os5 m263
229 ResourceMeta ou324  os5 m264
230 ResourceMeta ou325  os5 m265
taxa
      otu                        label xsi.type otus
1    ou93  Allenopithecus_nigroviridis       NA  os5
2    ou94          Allocebus_trichotis       NA  os5
3    ou95            Alouatta_belzebul       NA  os5
4    ou96              Alouatta_caraya       NA  os5
5    ou97           Alouatta_coibensis       NA  os5
6    ou98               Alouatta_fusca       NA  os5
7    ou99            Alouatta_palliata       NA  os5
8   ou100               Alouatta_pigra       NA  os5
9   ou101                Alouatta_sara       NA  os5
10  ou102           Alouatta_seniculus       NA  os5
11  ou103                 Aotus_azarai       NA  os5
12  ou104              Aotus_brumbacki       NA  os5
13  ou105           Aotus_hershkovitzi       NA  os5
14  ou106              Aotus_infulatus       NA  os5
15  ou107              Aotus_lemurinus       NA  os5
16  ou108                Aotus_miconax       NA  os5
17  ou109              Aotus_nancymaae       NA  os5
18  ou110              Aotus_nigriceps       NA  os5
19  ou111            Aotus_trivirgatus       NA  os5
20  ou112             Aotus_vociferans       NA  os5
21  ou113            Arctocebus_aureus       NA  os5
22  ou114      Arctocebus_calabarensis       NA  os5
23  ou115             Ateles_belzebuth       NA  os5
24  ou116                Ateles_chamek       NA  os5
25  ou117             Ateles_fusciceps       NA  os5
26  ou118             Ateles_geoffroyi       NA  os5
27  ou119            Ateles_marginatus       NA  os5
28  ou120              Ateles_paniscus       NA  os5
29  ou121                Avahi_laniger       NA  os5
30  ou122      Brachyteles_arachnoides       NA  os5
31  ou123               Cacajao_calvus       NA  os5
32  ou124       Cacajao_melanocephalus       NA  os5
33  ou125          Callicebus_brunneus       NA  os5
34  ou126         Callicebus_caligatus       NA  os5
35  ou127       Callicebus_cinerascens       NA  os5
36  ou128           Callicebus_cupreus       NA  os5
37  ou129      Callicebus_donacophilus       NA  os5
38  ou130            Callicebus_dubius       NA  os5
39  ou131        Callicebus_hoffmannsi       NA  os5
40  ou132          Callicebus_modestus       NA  os5
41  ou133            Callicebus_moloch       NA  os5
42  ou134          Callicebus_oenanthe       NA  os5
43  ou135           Callicebus_olallae       NA  os5
44  ou136        Callicebus_personatus       NA  os5
45  ou137         Callicebus_torquatus       NA  os5
46  ou138            Callimico_goeldii       NA  os5
47  ou139         Callithrix_argentata       NA  os5
48  ou140            Callithrix_aurita       NA  os5
49  ou141         Callithrix_flaviceps       NA  os5
50  ou142         Callithrix_geoffroyi       NA  os5
51  ou143      Callithrix_humeralifera       NA  os5
52  ou144           Callithrix_jacchus       NA  os5
53  ou145            Callithrix_kuhlii       NA  os5
54  ou146       Callithrix_penicillata       NA  os5
55  ou147           Callithrix_pygmaea       NA  os5
56  ou148              Cebus_albifrons       NA  os5
57  ou149                 Cebus_apella       NA  os5
58  ou150              Cebus_capucinus       NA  os5
59  ou151              Cebus_olivaceus       NA  os5
60  ou152            Cercocebus_agilis       NA  os5
61  ou153         Cercocebus_galeritus       NA  os5
62  ou154         Cercocebus_torquatus       NA  os5
63  ou155       Cercopithecus_ascanius       NA  os5
64  ou156      Cercopithecus_campbelli       NA  os5
65  ou157         Cercopithecus_cephus       NA  os5
66  ou158          Cercopithecus_diana       NA  os5
67  ou159          Cercopithecus_dryas       NA  os5
68  ou160  Cercopithecus_erythrogaster       NA  os5
69  ou161     Cercopithecus_erythrotis       NA  os5
70  ou162        Cercopithecus_hamlyni       NA  os5
71  ou163        Cercopithecus_lhoesti       NA  os5
72  ou164          Cercopithecus_mitis       NA  os5
73  ou165           Cercopithecus_mona       NA  os5
74  ou166      Cercopithecus_neglectus       NA  os5
75  ou167      Cercopithecus_nictitans       NA  os5
76  ou168     Cercopithecus_petaurista       NA  os5
77  ou169       Cercopithecus_pogonias       NA  os5
78  ou170        Cercopithecus_preussi       NA  os5
79  ou171       Cercopithecus_sclateri       NA  os5
80  ou172        Cercopithecus_solatus       NA  os5
81  ou173          Cercopithecus_wolfi       NA  os5
82  ou174           Cheirogaleus_major       NA  os5
83  ou175          Cheirogaleus_medius       NA  os5
84  ou176         Chiropotes_albinasus       NA  os5
85  ou177           Chiropotes_satanas       NA  os5
86  ou178         Chlorocebus_aethiops       NA  os5
87  ou179           Colobus_angolensis       NA  os5
88  ou180              Colobus_guereza       NA  os5
89  ou181            Colobus_polykomos       NA  os5
90  ou182              Colobus_satanas       NA  os5
91  ou183 Daubentonia_madagascariensis       NA  os5
92  ou184           Erythrocebus_patas       NA  os5
93  ou185            Eulemur_coronatus       NA  os5
94  ou186               Eulemur_fulvus       NA  os5
95  ou187               Eulemur_macaco       NA  os5
96  ou188               Eulemur_mongoz       NA  os5
97  ou189          Eulemur_rubriventer       NA  os5
98  ou190         Euoticus_elegantulus       NA  os5
99  ou191            Euoticus_pallidus       NA  os5
100 ou192                Galago_alleni       NA  os5
101 ou193              Galago_gallarum       NA  os5
102 ou194             Galago_matschiei       NA  os5
103 ou195                Galago_moholi       NA  os5
104 ou196          Galago_senegalensis       NA  os5
105 ou197          Galagoides_demidoff       NA  os5
106 ou198      Galagoides_zanzibaricus       NA  os5
107 ou199              Gorilla_gorilla       NA  os5
108 ou200             Hapalemur_aureus       NA  os5
109 ou201            Hapalemur_griseus       NA  os5
110 ou202              Hapalemur_simus       NA  os5
111 ou203                 Homo_sapiens       NA  os5
112 ou204             Hylobates_agilis       NA  os5
113 ou205           Hylobates_concolor       NA  os5
114 ou206         Hylobates_gabriellae       NA  os5
115 ou207            Hylobates_hoolock       NA  os5
116 ou208            Hylobates_klossii       NA  os5
117 ou209                Hylobates_lar       NA  os5
118 ou210         Hylobates_leucogenys       NA  os5
119 ou211             Hylobates_moloch       NA  os5
120 ou212           Hylobates_muelleri       NA  os5
121 ou213           Hylobates_pileatus       NA  os5
122 ou214        Hylobates_syndactylus       NA  os5
123 ou215                  Indri_indri       NA  os5
124 ou216         Lagothrix_flavicauda       NA  os5
125 ou217         Lagothrix_lagotricha       NA  os5
126 ou218                  Lemur_catta       NA  os5
127 ou219      Leontopithecus_caissara       NA  os5
128 ou220    Leontopithecus_chrysomela       NA  os5
129 ou221   Leontopithecus_chrysopygus       NA  os5
130 ou222       Leontopithecus_rosalia       NA  os5
131 ou223           Lepilemur_dorsalis       NA  os5
132 ou224           Lepilemur_edwardsi       NA  os5
133 ou225           Lepilemur_leucopus       NA  os5
134 ou226           Lepilemur_microdon       NA  os5
135 ou227         Lepilemur_mustelinus       NA  os5
136 ou228       Lepilemur_ruficaudatus       NA  os5
137 ou229    Lepilemur_septentrionalis       NA  os5
138 ou230          Lophocebus_albigena       NA  os5
139 ou231            Loris_tardigradus       NA  os5
140 ou232             Macaca_arctoides       NA  os5
141 ou233            Macaca_assamensis       NA  os5
142 ou234              Macaca_cyclopis       NA  os5
143 ou235          Macaca_fascicularis       NA  os5
144 ou236               Macaca_fuscata       NA  os5
145 ou237                 Macaca_maura       NA  os5
146 ou238               Macaca_mulatta       NA  os5
147 ou239            Macaca_nemestrina       NA  os5
148 ou240                 Macaca_nigra       NA  os5
149 ou241              Macaca_ochreata       NA  os5
150 ou242               Macaca_radiata       NA  os5
151 ou243               Macaca_silenus       NA  os5
152 ou244                Macaca_sinica       NA  os5
153 ou245              Macaca_sylvanus       NA  os5
154 ou246             Macaca_thibetana       NA  os5
155 ou247              Macaca_tonkeana       NA  os5
156 ou248       Mandrillus_leucophaeus       NA  os5
157 ou249            Mandrillus_sphinx       NA  os5
158 ou250         Microcebus_coquereli       NA  os5
159 ou251           Microcebus_murinus       NA  os5
160 ou252             Microcebus_rufus       NA  os5
161 ou253         Miopithecus_talapoin       NA  os5
162 ou254             Nasalis_concolor       NA  os5
163 ou255             Nasalis_larvatus       NA  os5
164 ou256           Nycticebus_coucang       NA  os5
165 ou257          Nycticebus_pygmaeus       NA  os5
166 ou258      Otolemur_crassicaudatus       NA  os5
167 ou259           Otolemur_garnettii       NA  os5
168 ou260                 Pan_paniscus       NA  os5
169 ou261              Pan_troglodytes       NA  os5
170 ou262              Papio_hamadryas       NA  os5
171 ou263           Perodicticus_potto       NA  os5
172 ou264              Phaner_furcifer       NA  os5
173 ou265       Pithecia_aequatorialis       NA  os5
174 ou266            Pithecia_albicans       NA  os5
175 ou267            Pithecia_irrorata       NA  os5
176 ou268            Pithecia_monachus       NA  os5
177 ou269            Pithecia_pithecia       NA  os5
178 ou270               Pongo_pygmaeus       NA  os5
179 ou271             Presbytis_comata       NA  os5
180 ou272          Presbytis_femoralis       NA  os5
181 ou273           Presbytis_frontata       NA  os5
182 ou274              Presbytis_hosei       NA  os5
183 ou275         Presbytis_melalophos       NA  os5
184 ou276         Presbytis_potenziani       NA  os5
185 ou277          Presbytis_rubicunda       NA  os5
186 ou278            Presbytis_thomasi       NA  os5
187 ou279            Procolobus_badius       NA  os5
188 ou280         Procolobus_pennantii       NA  os5
189 ou281           Procolobus_preussi       NA  os5
190 ou282      Procolobus_rufomitratus       NA  os5
191 ou283             Procolobus_verus       NA  os5
192 ou284          Propithecus_diadema       NA  os5
193 ou285      Propithecus_tattersalli       NA  os5
194 ou286        Propithecus_verreauxi       NA  os5
195 ou287          Pygathrix_avunculus       NA  os5
196 ou288              Pygathrix_bieti       NA  os5
197 ou289           Pygathrix_brelichi       NA  os5
198 ou290            Pygathrix_nemaeus       NA  os5
199 ou291          Pygathrix_roxellana       NA  os5
200 ou292             Saguinus_bicolor       NA  os5
201 ou293         Saguinus_fuscicollis       NA  os5
202 ou294           Saguinus_geoffroyi       NA  os5
203 ou295           Saguinus_imperator       NA  os5
204 ou296             Saguinus_inustus       NA  os5
205 ou297            Saguinus_labiatus       NA  os5
206 ou298            Saguinus_leucopus       NA  os5
207 ou299               Saguinus_midas       NA  os5
208 ou300              Saguinus_mystax       NA  os5
209 ou301         Saguinus_nigricollis       NA  os5
210 ou302             Saguinus_oedipus       NA  os5
211 ou303         Saguinus_tripartitus       NA  os5
212 ou304          Saimiri_boliviensis       NA  os5
213 ou305            Saimiri_oerstedii       NA  os5
214 ou306             Saimiri_sciureus       NA  os5
215 ou307                Saimiri_ustus       NA  os5
216 ou308           Saimiri_vanzolinii       NA  os5
217 ou309       Semnopithecus_entellus       NA  os5
218 ou310             Tarsius_bancanus       NA  os5
219 ou311               Tarsius_dianae       NA  os5
220 ou312              Tarsius_pumilus       NA  os5
221 ou313             Tarsius_spectrum       NA  os5
222 ou314             Tarsius_syrichta       NA  os5
223 ou315         Theropithecus_gelada       NA  os5
224 ou316       Trachypithecus_auratus       NA  os5
225 ou317     Trachypithecus_cristatus       NA  os5
226 ou318     Trachypithecus_francoisi       NA  os5
227 ou319          Trachypithecus_geei       NA  os5
228 ou320        Trachypithecus_johnii       NA  os5
229 ou321      Trachypithecus_obscurus       NA  os5
230 ou322       Trachypithecus_phayrei       NA  os5
231 ou323      Trachypithecus_pileatus       NA  os5
232 ou324       Trachypithecus_vetulus       NA  os5
233 ou325            Varecia_variegata       NA  os5
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 8.554489

Now 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    ou93  Allenopithecus_nigroviridis  8.465900
2    ou94          Allocebus_trichotis  4.368181
3    ou95            Alouatta_belzebul  8.729074
4    ou96              Alouatta_caraya  8.628735
5    ou97           Alouatta_coibensis  8.764053
6    ou98               Alouatta_fusca  8.554489
7    ou99            Alouatta_palliata  8.791790
8   ou100               Alouatta_pigra  8.881836
9   ou101                Alouatta_sara  8.796339
10  ou102           Alouatta_seniculus  8.767173
11  ou103                 Aotus_azarai  7.127694
12  ou104              Aotus_brumbacki  6.401917
13  ou105           Aotus_hershkovitzi  6.684612
14  ou106              Aotus_infulatus  7.122867
15  ou107              Aotus_lemurinus  6.781058
16  ou108                Aotus_miconax  6.684612
17  ou109              Aotus_nancymaae  6.678342
18  ou110              Aotus_nigriceps  6.966024
19  ou111            Aotus_trivirgatus  6.815640
20  ou112             Aotus_vociferans  6.771936
21  ou113            Arctocebus_aureus  5.459586
22  ou114      Arctocebus_calabarensis  5.552960
23  ou115             Ateles_belzebuth  8.812843
24  ou116                Ateles_chamek  8.872067
25  ou117             Ateles_fusciceps  9.112728
26  ou118             Ateles_geoffroyi  8.937218
27  ou119            Ateles_marginatus  8.738735
28  ou120              Ateles_paniscus  9.072227
29  ou121                Avahi_laniger  6.927558
30  ou122      Brachyteles_arachnoides  9.268609
31  ou123               Cacajao_calvus  8.137396
32  ou124       Cacajao_melanocephalus  8.051978
33  ou125          Callicebus_brunneus  6.747587
34  ou126         Callicebus_caligatus  6.899723
35  ou127       Callicebus_cinerascens  6.899723
36  ou128           Callicebus_cupreus  7.021084
37  ou129      Callicebus_donacophilus  6.801283
38  ou130            Callicebus_dubius  6.899723
39  ou131        Callicebus_hoffmannsi  6.975414
40  ou132          Callicebus_modestus  6.899723
41  ou133            Callicebus_moloch  6.872128
42  ou134          Callicebus_oenanthe  6.899723
43  ou135           Callicebus_olallae  6.899723
44  ou136        Callicebus_personatus  7.237059
45  ou137         Callicebus_torquatus  7.106606
46  ou138            Callimico_goeldii  6.324359
47  ou139         Callithrix_argentata  5.910797
48  ou140            Callithrix_aurita  5.961005
49  ou141         Callithrix_flaviceps  5.926926
50  ou142         Callithrix_geoffroyi  5.834811
51  ou143      Callithrix_humeralifera  5.926926
52  ou144           Callithrix_jacchus  5.673323
53  ou145            Callithrix_kuhlii  5.926926
54  ou146       Callithrix_penicillata  5.828946
55  ou147           Callithrix_pygmaea  4.828314
56  ou148              Cebus_albifrons  7.832014
57  ou149                 Cebus_apella  7.922986
58  ou150              Cebus_capucinus  8.009695
59  ou151              Cebus_olivaceus  7.937375
60  ou152            Cercocebus_agilis  8.870663
61  ou153         Cercocebus_galeritus  8.865029
62  ou154         Cercocebus_torquatus  8.894259
63  ou155       Cercopithecus_ascanius  8.171882
64  ou156      Cercopithecus_campbelli  8.199739
65  ou157         Cercopithecus_cephus  8.143227
66  ou158          Cercopithecus_diana  8.382518
67  ou159          Cercopithecus_dryas  7.930206
68  ou160  Cercopithecus_erythrogaster  8.143227
69  ou161     Cercopithecus_erythrotis  8.086410
70  ou162        Cercopithecus_hamlyni  8.438150
71  ou163        Cercopithecus_lhoesti  8.579229
72  ou164          Cercopithecus_mitis  8.525161
73  ou165           Cercopithecus_mona  8.289037
74  ou166      Cercopithecus_neglectus  8.579229
75  ou167      Cercopithecus_nictitans  8.567886
76  ou168     Cercopithecus_petaurista  8.083329
77  ou169       Cercopithecus_pogonias  8.183118
78  ou170        Cercopithecus_preussi  8.544808
79  ou171       Cercopithecus_sclateri  8.029433
80  ou172        Cercopithecus_solatus  8.567886
81  ou173          Cercopithecus_wolfi  8.089482
82  ou174           Cheirogaleus_major  6.104793
83  ou175          Cheirogaleus_medius  5.283204
84  ou176         Chiropotes_albinasus  7.937375
85  ou177           Chiropotes_satanas  7.996317
86  ou178         Chlorocebus_aethiops  8.301522
87  ou179           Colobus_angolensis  9.103868
88  ou180              Colobus_guereza  9.210340
89  ou181            Colobus_polykomos  9.060680
90  ou182              Colobus_satanas  9.121509
91  ou183 Daubentonia_madagascariensis  7.919356
92  ou184           Erythrocebus_patas  8.988446
93  ou185            Eulemur_coronatus  7.438384
94  ou186               Eulemur_fulvus  7.779049
95  ou187               Eulemur_macaco  7.816014
96  ou188               Eulemur_mongoz  7.478735
97  ou189          Eulemur_rubriventer  7.620705
98  ou190         Euoticus_elegantulus  5.690359
99  ou191            Euoticus_pallidus  5.627621
100 ou192                Galago_alleni  5.521461
101 ou193              Galago_gallarum  5.365976
102 ou194             Galago_matschiei  5.267858
103 ou195                Galago_moholi  5.375278
104 ou196          Galago_senegalensis  5.594711
105 ou197          Galagoides_demidoff  4.206184
106 ou198      Galagoides_zanzibaricus  4.997212
107 ou199              Gorilla_gorilla 11.643954
108 ou200             Hapalemur_aureus  7.358831
109 ou201            Hapalemur_griseus  6.862758
110 ou202              Hapalemur_simus  7.620705
111 ou203                 Homo_sapiens 10.980195
112 ou204             Hylobates_agilis  8.675905
113 ou205           Hylobates_concolor  8.768730
114 ou206         Hylobates_gabriellae  9.047821
115 ou207            Hylobates_hoolock  8.809863
116 ou208            Hylobates_klossii  8.674197
117 ou209                Hylobates_lar  8.635865
118 ou210         Hylobates_leucogenys  8.898366
119 ou211             Hylobates_moloch  8.677610
120 ou212           Hylobates_muelleri  8.687779
121 ou213           Hylobates_pileatus  8.630522
122 ou214        Hylobates_syndactylus  9.296518
123 ou215                  Indri_indri  9.065315
124 ou216         Lagothrix_flavicauda  9.020390
125 ou217         Lagothrix_lagotricha  8.743532
126 ou218                  Lemur_catta  7.878534
127 ou219      Leontopithecus_caissara  6.405228
128 ou220    Leontopithecus_chrysomela  6.352629
129 ou221   Leontopithecus_chrysopygus  6.486161
130 ou222       Leontopithecus_rosalia  6.385194
131 ou223           Lepilemur_dorsalis  6.232448
132 ou224           Lepilemur_edwardsi  6.711740
133 ou225           Lepilemur_leucopus  6.396930
134 ou226           Lepilemur_microdon  6.863803
135 ou227         Lepilemur_mustelinus  6.508769
136 ou228       Lepilemur_ruficaudatus  6.637258
137 ou229    Lepilemur_septentrionalis  6.638568
138 ou230          Lophocebus_albigena  8.903815
139 ou231            Loris_tardigradus  5.517453
140 ou232             Macaca_arctoides  9.148465
141 ou233            Macaca_assamensis  9.054855
142 ou234              Macaca_cyclopis  8.658693
143 ou235          Macaca_fascicularis  8.431635
144 ou236               Macaca_fuscata  9.220291
145 ou237                 Macaca_maura  8.894259
146 ou238               Macaca_mulatta  8.771835
147 ou239            Macaca_nemestrina  8.970813
148 ou240                 Macaca_nigra  8.906529
149 ou241              Macaca_ochreata  7.919356
150 ou242               Macaca_radiata  8.517193
151 ou243               Macaca_silenus  8.699515
152 ou244                Macaca_sinica  8.446771
153 ou245              Macaca_sylvanus  9.350102
154 ou246             Macaca_thibetana  9.268609
155 ou247              Macaca_tonkeana  9.220291
156 ou248       Mandrillus_leucophaeus  9.560997
157 ou249            Mandrillus_sphinx  9.729134
158 ou250         Microcebus_coquereli  5.793014
159 ou251           Microcebus_murinus  4.198705
160 ou252             Microcebus_rufus  3.881564
161 ou253         Miopithecus_talapoin  7.130899
162 ou254             Nasalis_concolor  8.979354
163 ou255             Nasalis_larvatus  9.417355
164 ou256           Nycticebus_coucang  6.878326
165 ou257          Nycticebus_pygmaeus  5.840642
166 ou258      Otolemur_crassicaudatus  7.130899
167 ou259           Otolemur_garnettii  6.701960
168 ou260                 Pan_paniscus 10.468801
169 ou261              Pan_troglodytes 10.716638
170 ou262              Papio_hamadryas  9.735069
171 ou263           Perodicticus_potto  6.984716
172 ou264              Phaner_furcifer  6.016157
173 ou265       Pithecia_aequatorialis  7.774856
174 ou266            Pithecia_albicans  7.937375
175 ou267            Pithecia_irrorata  7.749322
176 ou268            Pithecia_monachus  7.654443
177 ou269            Pithecia_pithecia  7.420579
178 ou270               Pongo_pygmaeus 10.860920
179 ou271             Presbytis_comata  9.039552
180 ou272          Presbytis_femoralis  8.797851
181 ou273           Presbytis_frontata  8.853665
182 ou274              Presbytis_hosei  8.725832
183 ou275         Presbytis_melalophos  8.748305
184 ou276         Presbytis_potenziani  8.774931
185 ou277          Presbytis_rubicunda  8.773385
186 ou278            Presbytis_thomasi  8.765615
187 ou279            Procolobus_badius  8.808369
188 ou280         Procolobus_pennantii  9.122601
189 ou281           Procolobus_preussi  9.094930
190 ou282      Procolobus_rufomitratus  8.995909
191 ou283             Procolobus_verus  8.289037
192 ou284          Propithecus_diadema  8.794825
193 ou285      Propithecus_tattersalli  8.171882
194 ou286        Propithecus_verreauxi  8.202482
195 ou287          Pygathrix_avunculus  9.164296
196 ou288              Pygathrix_bieti  9.118225
197 ou289           Pygathrix_brelichi  9.305651
198 ou290            Pygathrix_nemaeus  9.417355
199 ou291          Pygathrix_roxellana  9.510445
200 ou292             Saguinus_bicolor  6.142037
201 ou293         Saguinus_fuscicollis  5.976351
202 ou294           Saguinus_geoffroyi  6.200509
203 ou295           Saguinus_imperator  6.016157
204 ou296             Saguinus_inustus  6.688355
205 ou297            Saguinus_labiatus  6.234411
206 ou298            Saguinus_leucopus  6.124683
207 ou299               Saguinus_midas  6.293419
208 ou300              Saguinus_mystax  6.326149
209 ou301         Saguinus_nigricollis  6.109248
210 ou302             Saguinus_oedipus  6.139885
211 ou303         Saguinus_tripartitus  5.953243
212 ou304          Saimiri_boliviensis  6.690842
213 ou305            Saimiri_oerstedii  6.570883
214 ou306             Saimiri_sciureus  6.620073
215 ou307                Saimiri_ustus  6.791221
216 ou308           Saimiri_vanzolinii  6.664409
217 ou309       Semnopithecus_entellus  9.441452
218 ou310             Tarsius_bancanus  4.736198
219 ou311               Tarsius_dianae  4.709530
220 ou312              Tarsius_pumilus  4.808111
221 ou313             Tarsius_spectrum  5.111988
222 ou314             Tarsius_syrichta  4.753590
223 ou315         Theropithecus_gelada  9.680344
224 ou316       Trachypithecus_auratus  9.181941
225 ou317     Trachypithecus_cristatus  8.872067
226 ou318     Trachypithecus_francoisi  9.008224
227 ou319          Trachypithecus_geei  9.031214
228 ou320        Trachypithecus_johnii  9.268609
229 ou321      Trachypithecus_obscurus  8.870663
230 ou322       Trachypithecus_phayrei  8.948976
231 ou323      Trachypithecus_pileatus  9.323669
232 ou324       Trachypithecus_vetulus  8.969542
233 ou325            Varecia_variegata  8.261010
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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                                                                                  <NA>
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                                                                                  <NA>
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=572873

Because 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.