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:

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:

                                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:

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:

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

This returns a data.frame of available metadata. We can see the kinds of metadata recorded from the names:

                        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>   m1
2   LiteralMeta                                              <NA>   m2
3   LiteralMeta                                              <NA>   m3
4  ResourceMeta http://creativecommons.org/publicdomain/zero/1.0/   m4
5   LiteralMeta                                              <NA>   m5
6   LiteralMeta                                              <NA>   m6
7  ResourceMeta                                              <NA>  m17
8   LiteralMeta                                              <NA>  m18
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   m17
10  m17
11  m17
12  m17
13  m17
14  m17
15  m17
16  m17
17  m17
18  m17

We can also access a table of taxonomic metadata:

get_taxa(birds)
    otu            label xsi.type otus
1   ou1 Struthioniformes       NA  os1
2   ou2     Tinamiformes       NA  os1
3   ou3      Craciformes       NA  os1
4   ou4      Galliformes       NA  os1
5   ou5     Anseriformes       NA  os1
6   ou6    Turniciformes       NA  os1
7   ou7       Piciformes       NA  os1
8   ou8    Galbuliformes       NA  os1
9   ou9   Bucerotiformes       NA  os1
10 ou10      Upupiformes       NA  os1
11 ou11    Trogoniformes       NA  os1
12 ou12    Coraciiformes       NA  os1
13 ou13      Coliiformes       NA  os1
14 ou14     Cuculiformes       NA  os1
15 ou15   Psittaciformes       NA  os1
16 ou16      Apodiformes       NA  os1
17 ou17   Trochiliformes       NA  os1
18 ou18  Musophagiformes       NA  os1
19 ou19     Strigiformes       NA  os1
20 ou20    Columbiformes       NA  os1
21 ou21       Gruiformes       NA  os1
22 ou22    Ciconiiformes       NA  os1
23 ou23    Passeriformes       NA  os1

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:

      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
12  tc:toTaxon
13  tc:toTaxon
14  tc:toTaxon
15  tc:toTaxon
16  tc:toTaxon
17  tc:toTaxon
18  tc:toTaxon
19  tc:toTaxon
20  tc:toTaxon
21  tc:toTaxon
22  tc:toTaxon
23  tc:toTaxon
24  tc:toTaxon
25  tc:toTaxon
26  tc:toTaxon
27  tc:toTaxon
28  tc:toTaxon
29  tc:toTaxon
30  tc:toTaxon
31  tc:toTaxon
32  tc:toTaxon
33  tc:toTaxon
34  tc:toTaxon
35  tc:toTaxon
36  tc:toTaxon
37  tc:toTaxon
38  tc:toTaxon
39  tc:toTaxon
40  tc:toTaxon
41  tc:toTaxon
42  tc:toTaxon
43  tc:toTaxon
44  tc:toTaxon
45  tc:toTaxon
46  tc:toTaxon
47  tc:toTaxon
48  tc:toTaxon
49  tc:toTaxon
50  tc:toTaxon
51  tc:toTaxon
52  tc:toTaxon
53  tc:toTaxon
54  tc:toTaxon
55  tc:toTaxon
56  tc:toTaxon
57  tc:toTaxon
58  tc:toTaxon
59  tc:toTaxon
60  tc:toTaxon
61  tc:toTaxon
62  tc:toTaxon
63  tc:toTaxon
64  tc:toTaxon
65  tc:toTaxon
66  tc:toTaxon
67  tc:toTaxon
68  tc:toTaxon
69  tc:toTaxon
70  tc:toTaxon
71  tc:toTaxon
72  tc:toTaxon
73  tc:toTaxon
74  tc:toTaxon
75  tc:toTaxon
76  tc:toTaxon
77  tc:toTaxon
78  tc:toTaxon
79  tc:toTaxon
80  tc:toTaxon
81  tc:toTaxon
82  tc:toTaxon
83  tc:toTaxon
84  tc:toTaxon
85  tc:toTaxon
86  tc:toTaxon
87  tc:toTaxon
88  tc:toTaxon
89  tc:toTaxon
90  tc:toTaxon
91  tc:toTaxon
92  tc:toTaxon
93  tc:toTaxon
94  tc:toTaxon
95  tc:toTaxon
96  tc:toTaxon
97  tc:toTaxon
98  tc:toTaxon
99  tc:toTaxon
100 tc:toTaxon
101 tc:toTaxon
102 tc:toTaxon
103 tc:toTaxon
104 tc:toTaxon
105 tc:toTaxon
106 tc:toTaxon
107 tc:toTaxon
108 tc:toTaxon
109 tc:toTaxon
110 tc:toTaxon
111 tc:toTaxon
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113 tc:toTaxon
114 tc:toTaxon
115 tc:toTaxon
116 tc:toTaxon
117 tc:toTaxon
118 tc:toTaxon
119 tc:toTaxon
120 tc:toTaxon
121 tc:toTaxon
122 tc:toTaxon
123 tc:toTaxon
124 tc:toTaxon
125 tc:toTaxon
126 tc:toTaxon
127 tc:toTaxon
128 tc:toTaxon
129 tc:toTaxon
130 tc:toTaxon
131 tc:toTaxon
132 tc:toTaxon
133 tc:toTaxon
134 tc:toTaxon
135 tc:toTaxon
136 tc:toTaxon
137 tc:toTaxon
138 tc:toTaxon
139 tc:toTaxon
140 tc:toTaxon
141 tc:toTaxon
142 tc:toTaxon
143 tc:toTaxon
144 tc:toTaxon
145 tc:toTaxon
146 tc:toTaxon
147 tc:toTaxon
148 tc:toTaxon
149 tc:toTaxon
150 tc:toTaxon
151 tc:toTaxon
152 tc:toTaxon
153 tc:toTaxon
154 tc:toTaxon
155 tc:toTaxon
156 tc:toTaxon
157 tc:toTaxon
158 tc:toTaxon
159 tc:toTaxon
160 tc:toTaxon
161 tc:toTaxon
162 tc:toTaxon
163 tc:toTaxon
164 tc:toTaxon
165 tc:toTaxon
166 tc:toTaxon
167 tc:toTaxon
168 tc:toTaxon
169 tc:toTaxon
170 tc:toTaxon
171 tc:toTaxon
172 tc:toTaxon
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174 tc:toTaxon
175 tc:toTaxon
176 tc:toTaxon
177 tc:toTaxon
178 tc:toTaxon
179 tc:toTaxon
180 tc:toTaxon
181 tc:toTaxon
182 tc:toTaxon
183 tc:toTaxon
184 tc:toTaxon
185 tc:toTaxon
186 tc:toTaxon
187 tc:toTaxon
188 tc:toTaxon
189 tc:toTaxon
190 tc:toTaxon
191 tc:toTaxon
192 tc:toTaxon
193 tc:toTaxon
194 tc:toTaxon
195 tc:toTaxon
196 tc:toTaxon
197 tc:toTaxon
198 tc:toTaxon
199 tc:toTaxon
200 tc:toTaxon
201 tc:toTaxon
202 tc:toTaxon
203 tc:toTaxon
204 tc:toTaxon
205 tc:toTaxon
206 tc:toTaxon
207 tc:toTaxon
208 tc:toTaxon
209 tc:toTaxon
210 tc:toTaxon
211 tc:toTaxon
212 tc:toTaxon
213 tc:toTaxon
214 tc:toTaxon
215 tc:toTaxon
216 tc:toTaxon
217 tc:toTaxon
218 tc:toTaxon
219 tc:toTaxon
220 tc:toTaxon
221 tc:toTaxon
222 tc:toTaxon
223 tc:toTaxon
224 tc:toTaxon
225 tc:toTaxon
226 tc:toTaxon
227 tc:toTaxon
228 tc:toTaxon
229 tc:toTaxon
230 tc:toTaxon
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204 ResourceMeta ou229  os2 m224
205 ResourceMeta ou230  os2 m225
206 ResourceMeta ou231  os2 m226
207 ResourceMeta ou233  os2 m227
208 ResourceMeta ou234  os2 m228
209 ResourceMeta ou235  os2 m229
210 ResourceMeta ou236  os2 m230
211 ResourceMeta ou237  os2 m231
212 ResourceMeta ou238  os2 m232
213 ResourceMeta ou239  os2 m233
214 ResourceMeta ou240  os2 m234
215 ResourceMeta ou241  os2 m235
216 ResourceMeta ou242  os2 m236
217 ResourceMeta ou243  os2 m237
218 ResourceMeta ou244  os2 m238
219 ResourceMeta ou245  os2 m239
220 ResourceMeta ou246  os2 m240
221 ResourceMeta ou247  os2 m241
222 ResourceMeta ou248  os2 m242
223 ResourceMeta ou249  os2 m243
224 ResourceMeta ou250  os2 m244
225 ResourceMeta ou251  os2 m245
226 ResourceMeta ou252  os2 m246
227 ResourceMeta ou253  os2 m247
228 ResourceMeta ou254  os2 m248
229 ResourceMeta ou255  os2 m249
230 ResourceMeta ou256  os2 m250
      otu                        label xsi.type otus
1    ou24  Allenopithecus_nigroviridis       NA  os2
2    ou25          Allocebus_trichotis       NA  os2
3    ou26            Alouatta_belzebul       NA  os2
4    ou27              Alouatta_caraya       NA  os2
5    ou28           Alouatta_coibensis       NA  os2
6    ou29               Alouatta_fusca       NA  os2
7    ou30            Alouatta_palliata       NA  os2
8    ou31               Alouatta_pigra       NA  os2
9    ou32                Alouatta_sara       NA  os2
10   ou33           Alouatta_seniculus       NA  os2
11   ou34                 Aotus_azarai       NA  os2
12   ou35              Aotus_brumbacki       NA  os2
13   ou36           Aotus_hershkovitzi       NA  os2
14   ou37              Aotus_infulatus       NA  os2
15   ou38              Aotus_lemurinus       NA  os2
16   ou39                Aotus_miconax       NA  os2
17   ou40              Aotus_nancymaae       NA  os2
18   ou41              Aotus_nigriceps       NA  os2
19   ou42            Aotus_trivirgatus       NA  os2
20   ou43             Aotus_vociferans       NA  os2
21   ou44            Arctocebus_aureus       NA  os2
22   ou45      Arctocebus_calabarensis       NA  os2
23   ou46             Ateles_belzebuth       NA  os2
24   ou47                Ateles_chamek       NA  os2
25   ou48             Ateles_fusciceps       NA  os2
26   ou49             Ateles_geoffroyi       NA  os2
27   ou50            Ateles_marginatus       NA  os2
28   ou51              Ateles_paniscus       NA  os2
29   ou52                Avahi_laniger       NA  os2
30   ou53      Brachyteles_arachnoides       NA  os2
31   ou54               Cacajao_calvus       NA  os2
32   ou55       Cacajao_melanocephalus       NA  os2
33   ou56          Callicebus_brunneus       NA  os2
34   ou57         Callicebus_caligatus       NA  os2
35   ou58       Callicebus_cinerascens       NA  os2
36   ou59           Callicebus_cupreus       NA  os2
37   ou60      Callicebus_donacophilus       NA  os2
38   ou61            Callicebus_dubius       NA  os2
39   ou62        Callicebus_hoffmannsi       NA  os2
40   ou63          Callicebus_modestus       NA  os2
41   ou64            Callicebus_moloch       NA  os2
42   ou65          Callicebus_oenanthe       NA  os2
43   ou66           Callicebus_olallae       NA  os2
44   ou67        Callicebus_personatus       NA  os2
45   ou68         Callicebus_torquatus       NA  os2
46   ou69            Callimico_goeldii       NA  os2
47   ou70         Callithrix_argentata       NA  os2
48   ou71            Callithrix_aurita       NA  os2
49   ou72         Callithrix_flaviceps       NA  os2
50   ou73         Callithrix_geoffroyi       NA  os2
51   ou74      Callithrix_humeralifera       NA  os2
52   ou75           Callithrix_jacchus       NA  os2
53   ou76            Callithrix_kuhlii       NA  os2
54   ou77       Callithrix_penicillata       NA  os2
55   ou78           Callithrix_pygmaea       NA  os2
56   ou79              Cebus_albifrons       NA  os2
57   ou80                 Cebus_apella       NA  os2
58   ou81              Cebus_capucinus       NA  os2
59   ou82              Cebus_olivaceus       NA  os2
60   ou83            Cercocebus_agilis       NA  os2
61   ou84         Cercocebus_galeritus       NA  os2
62   ou85         Cercocebus_torquatus       NA  os2
63   ou86       Cercopithecus_ascanius       NA  os2
64   ou87      Cercopithecus_campbelli       NA  os2
65   ou88         Cercopithecus_cephus       NA  os2
66   ou89          Cercopithecus_diana       NA  os2
67   ou90          Cercopithecus_dryas       NA  os2
68   ou91  Cercopithecus_erythrogaster       NA  os2
69   ou92     Cercopithecus_erythrotis       NA  os2
70   ou93        Cercopithecus_hamlyni       NA  os2
71   ou94        Cercopithecus_lhoesti       NA  os2
72   ou95          Cercopithecus_mitis       NA  os2
73   ou96           Cercopithecus_mona       NA  os2
74   ou97      Cercopithecus_neglectus       NA  os2
75   ou98      Cercopithecus_nictitans       NA  os2
76   ou99     Cercopithecus_petaurista       NA  os2
77  ou100       Cercopithecus_pogonias       NA  os2
78  ou101        Cercopithecus_preussi       NA  os2
79  ou102       Cercopithecus_sclateri       NA  os2
80  ou103        Cercopithecus_solatus       NA  os2
81  ou104          Cercopithecus_wolfi       NA  os2
82  ou105           Cheirogaleus_major       NA  os2
83  ou106          Cheirogaleus_medius       NA  os2
84  ou107         Chiropotes_albinasus       NA  os2
85  ou108           Chiropotes_satanas       NA  os2
86  ou109         Chlorocebus_aethiops       NA  os2
87  ou110           Colobus_angolensis       NA  os2
88  ou111              Colobus_guereza       NA  os2
89  ou112            Colobus_polykomos       NA  os2
90  ou113              Colobus_satanas       NA  os2
91  ou114 Daubentonia_madagascariensis       NA  os2
92  ou115           Erythrocebus_patas       NA  os2
93  ou116            Eulemur_coronatus       NA  os2
94  ou117               Eulemur_fulvus       NA  os2
95  ou118               Eulemur_macaco       NA  os2
96  ou119               Eulemur_mongoz       NA  os2
97  ou120          Eulemur_rubriventer       NA  os2
98  ou121         Euoticus_elegantulus       NA  os2
99  ou122            Euoticus_pallidus       NA  os2
100 ou123                Galago_alleni       NA  os2
101 ou124              Galago_gallarum       NA  os2
102 ou125             Galago_matschiei       NA  os2
103 ou126                Galago_moholi       NA  os2
104 ou127          Galago_senegalensis       NA  os2
105 ou128          Galagoides_demidoff       NA  os2
106 ou129      Galagoides_zanzibaricus       NA  os2
107 ou130              Gorilla_gorilla       NA  os2
108 ou131             Hapalemur_aureus       NA  os2
109 ou132            Hapalemur_griseus       NA  os2
110 ou133              Hapalemur_simus       NA  os2
111 ou134                 Homo_sapiens       NA  os2
112 ou135             Hylobates_agilis       NA  os2
113 ou136           Hylobates_concolor       NA  os2
114 ou137         Hylobates_gabriellae       NA  os2
115 ou138            Hylobates_hoolock       NA  os2
116 ou139            Hylobates_klossii       NA  os2
117 ou140                Hylobates_lar       NA  os2
118 ou141         Hylobates_leucogenys       NA  os2
119 ou142             Hylobates_moloch       NA  os2
120 ou143           Hylobates_muelleri       NA  os2
121 ou144           Hylobates_pileatus       NA  os2
122 ou145        Hylobates_syndactylus       NA  os2
123 ou146                  Indri_indri       NA  os2
124 ou147         Lagothrix_flavicauda       NA  os2
125 ou148         Lagothrix_lagotricha       NA  os2
126 ou149                  Lemur_catta       NA  os2
127 ou150      Leontopithecus_caissara       NA  os2
128 ou151    Leontopithecus_chrysomela       NA  os2
129 ou152   Leontopithecus_chrysopygus       NA  os2
130 ou153       Leontopithecus_rosalia       NA  os2
131 ou154           Lepilemur_dorsalis       NA  os2
132 ou155           Lepilemur_edwardsi       NA  os2
133 ou156           Lepilemur_leucopus       NA  os2
134 ou157           Lepilemur_microdon       NA  os2
135 ou158         Lepilemur_mustelinus       NA  os2
136 ou159       Lepilemur_ruficaudatus       NA  os2
137 ou160    Lepilemur_septentrionalis       NA  os2
138 ou161          Lophocebus_albigena       NA  os2
139 ou162            Loris_tardigradus       NA  os2
140 ou163             Macaca_arctoides       NA  os2
141 ou164            Macaca_assamensis       NA  os2
142 ou165              Macaca_cyclopis       NA  os2
143 ou166          Macaca_fascicularis       NA  os2
144 ou167               Macaca_fuscata       NA  os2
145 ou168                 Macaca_maura       NA  os2
146 ou169               Macaca_mulatta       NA  os2
147 ou170            Macaca_nemestrina       NA  os2
148 ou171                 Macaca_nigra       NA  os2
149 ou172              Macaca_ochreata       NA  os2
150 ou173               Macaca_radiata       NA  os2
151 ou174               Macaca_silenus       NA  os2
152 ou175                Macaca_sinica       NA  os2
153 ou176              Macaca_sylvanus       NA  os2
154 ou177             Macaca_thibetana       NA  os2
155 ou178              Macaca_tonkeana       NA  os2
156 ou179       Mandrillus_leucophaeus       NA  os2
157 ou180            Mandrillus_sphinx       NA  os2
158 ou181         Microcebus_coquereli       NA  os2
159 ou182           Microcebus_murinus       NA  os2
160 ou183             Microcebus_rufus       NA  os2
161 ou184         Miopithecus_talapoin       NA  os2
162 ou185             Nasalis_concolor       NA  os2
163 ou186             Nasalis_larvatus       NA  os2
164 ou187           Nycticebus_coucang       NA  os2
165 ou188          Nycticebus_pygmaeus       NA  os2
166 ou189      Otolemur_crassicaudatus       NA  os2
167 ou190           Otolemur_garnettii       NA  os2
168 ou191                 Pan_paniscus       NA  os2
169 ou192              Pan_troglodytes       NA  os2
170 ou193              Papio_hamadryas       NA  os2
171 ou194           Perodicticus_potto       NA  os2
172 ou195              Phaner_furcifer       NA  os2
173 ou196       Pithecia_aequatorialis       NA  os2
174 ou197            Pithecia_albicans       NA  os2
175 ou198            Pithecia_irrorata       NA  os2
176 ou199            Pithecia_monachus       NA  os2
177 ou200            Pithecia_pithecia       NA  os2
178 ou201               Pongo_pygmaeus       NA  os2
179 ou202             Presbytis_comata       NA  os2
180 ou203          Presbytis_femoralis       NA  os2
181 ou204           Presbytis_frontata       NA  os2
182 ou205              Presbytis_hosei       NA  os2
183 ou206         Presbytis_melalophos       NA  os2
184 ou207         Presbytis_potenziani       NA  os2
185 ou208          Presbytis_rubicunda       NA  os2
186 ou209            Presbytis_thomasi       NA  os2
187 ou210            Procolobus_badius       NA  os2
188 ou211         Procolobus_pennantii       NA  os2
189 ou212           Procolobus_preussi       NA  os2
190 ou213      Procolobus_rufomitratus       NA  os2
191 ou214             Procolobus_verus       NA  os2
192 ou215          Propithecus_diadema       NA  os2
193 ou216      Propithecus_tattersalli       NA  os2
194 ou217        Propithecus_verreauxi       NA  os2
195 ou218          Pygathrix_avunculus       NA  os2
196 ou219              Pygathrix_bieti       NA  os2
197 ou220           Pygathrix_brelichi       NA  os2
198 ou221            Pygathrix_nemaeus       NA  os2
199 ou222          Pygathrix_roxellana       NA  os2
200 ou223             Saguinus_bicolor       NA  os2
201 ou224         Saguinus_fuscicollis       NA  os2
202 ou225           Saguinus_geoffroyi       NA  os2
203 ou226           Saguinus_imperator       NA  os2
204 ou227             Saguinus_inustus       NA  os2
205 ou228            Saguinus_labiatus       NA  os2
206 ou229            Saguinus_leucopus       NA  os2
207 ou230               Saguinus_midas       NA  os2
208 ou231              Saguinus_mystax       NA  os2
209 ou232         Saguinus_nigricollis       NA  os2
210 ou233             Saguinus_oedipus       NA  os2
211 ou234         Saguinus_tripartitus       NA  os2
212 ou235          Saimiri_boliviensis       NA  os2
213 ou236            Saimiri_oerstedii       NA  os2
214 ou237             Saimiri_sciureus       NA  os2
215 ou238                Saimiri_ustus       NA  os2
216 ou239           Saimiri_vanzolinii       NA  os2
217 ou240       Semnopithecus_entellus       NA  os2
218 ou241             Tarsius_bancanus       NA  os2
219 ou242               Tarsius_dianae       NA  os2
220 ou243              Tarsius_pumilus       NA  os2
221 ou244             Tarsius_spectrum       NA  os2
222 ou245             Tarsius_syrichta       NA  os2
223 ou246         Theropithecus_gelada       NA  os2
224 ou247       Trachypithecus_auratus       NA  os2
225 ou248     Trachypithecus_cristatus       NA  os2
226 ou249     Trachypithecus_francoisi       NA  os2
227 ou250          Trachypithecus_geei       NA  os2
228 ou251        Trachypithecus_johnii       NA  os2
229 ou252      Trachypithecus_obscurus       NA  os2
230 ou253       Trachypithecus_phayrei       NA  os2
231 ou254      Trachypithecus_pileatus       NA  os2
232 ou255       Trachypithecus_vetulus       NA  os2
233 ou256            Varecia_variegata       NA  os2
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    ou24  Allenopithecus_nigroviridis  8.465900
2    ou25          Allocebus_trichotis  4.368181
3    ou26            Alouatta_belzebul  8.729074
4    ou27              Alouatta_caraya  8.628735
5    ou28           Alouatta_coibensis  8.764053
6    ou29               Alouatta_fusca  8.554489
7    ou30            Alouatta_palliata  8.791790
8    ou31               Alouatta_pigra  8.881836
9    ou32                Alouatta_sara  8.796339
10   ou33           Alouatta_seniculus  8.767173
11   ou34                 Aotus_azarai  7.127694
12   ou35              Aotus_brumbacki  6.401917
13   ou36           Aotus_hershkovitzi  6.684612
14   ou37              Aotus_infulatus  7.122867
15   ou38              Aotus_lemurinus  6.781058
16   ou39                Aotus_miconax  6.684612
17   ou40              Aotus_nancymaae  6.678342
18   ou41              Aotus_nigriceps  6.966024
19   ou42            Aotus_trivirgatus  6.815640
20   ou43             Aotus_vociferans  6.771936
21   ou44            Arctocebus_aureus  5.459586
22   ou45      Arctocebus_calabarensis  5.552960
23   ou46             Ateles_belzebuth  8.812843
24   ou47                Ateles_chamek  8.872067
25   ou48             Ateles_fusciceps  9.112728
26   ou49             Ateles_geoffroyi  8.937218
27   ou50            Ateles_marginatus  8.738735
28   ou51              Ateles_paniscus  9.072227
29   ou52                Avahi_laniger  6.927558
30   ou53      Brachyteles_arachnoides  9.268609
31   ou54               Cacajao_calvus  8.137396
32   ou55       Cacajao_melanocephalus  8.051978
33   ou56          Callicebus_brunneus  6.747587
34   ou57         Callicebus_caligatus  6.899723
35   ou58       Callicebus_cinerascens  6.899723
36   ou59           Callicebus_cupreus  7.021084
37   ou60      Callicebus_donacophilus  6.801283
38   ou61            Callicebus_dubius  6.899723
39   ou62        Callicebus_hoffmannsi  6.975414
40   ou63          Callicebus_modestus  6.899723
41   ou64            Callicebus_moloch  6.872128
42   ou65          Callicebus_oenanthe  6.899723
43   ou66           Callicebus_olallae  6.899723
44   ou67        Callicebus_personatus  7.237059
45   ou68         Callicebus_torquatus  7.106606
46   ou69            Callimico_goeldii  6.324359
47   ou70         Callithrix_argentata  5.910797
48   ou71            Callithrix_aurita  5.961005
49   ou72         Callithrix_flaviceps  5.926926
50   ou73         Callithrix_geoffroyi  5.834811
51   ou74      Callithrix_humeralifera  5.926926
52   ou75           Callithrix_jacchus  5.673323
53   ou76            Callithrix_kuhlii  5.926926
54   ou77       Callithrix_penicillata  5.828946
55   ou78           Callithrix_pygmaea  4.828314
56   ou79              Cebus_albifrons  7.832014
57   ou80                 Cebus_apella  7.922986
58   ou81              Cebus_capucinus  8.009695
59   ou82              Cebus_olivaceus  7.937375
60   ou83            Cercocebus_agilis  8.870663
61   ou84         Cercocebus_galeritus  8.865029
62   ou85         Cercocebus_torquatus  8.894259
63   ou86       Cercopithecus_ascanius  8.171882
64   ou87      Cercopithecus_campbelli  8.199739
65   ou88         Cercopithecus_cephus  8.143227
66   ou89          Cercopithecus_diana  8.382518
67   ou90          Cercopithecus_dryas  7.930206
68   ou91  Cercopithecus_erythrogaster  8.143227
69   ou92     Cercopithecus_erythrotis  8.086410
70   ou93        Cercopithecus_hamlyni  8.438150
71   ou94        Cercopithecus_lhoesti  8.579229
72   ou95          Cercopithecus_mitis  8.525161
73   ou96           Cercopithecus_mona  8.289037
74   ou97      Cercopithecus_neglectus  8.579229
75   ou98      Cercopithecus_nictitans  8.567886
76   ou99     Cercopithecus_petaurista  8.083329
77  ou100       Cercopithecus_pogonias  8.183118
78  ou101        Cercopithecus_preussi  8.544808
79  ou102       Cercopithecus_sclateri  8.029433
80  ou103        Cercopithecus_solatus  8.567886
81  ou104          Cercopithecus_wolfi  8.089482
82  ou105           Cheirogaleus_major  6.104793
83  ou106          Cheirogaleus_medius  5.283204
84  ou107         Chiropotes_albinasus  7.937375
85  ou108           Chiropotes_satanas  7.996317
86  ou109         Chlorocebus_aethiops  8.301522
87  ou110           Colobus_angolensis  9.103868
88  ou111              Colobus_guereza  9.210340
89  ou112            Colobus_polykomos  9.060680
90  ou113              Colobus_satanas  9.121509
91  ou114 Daubentonia_madagascariensis  7.919356
92  ou115           Erythrocebus_patas  8.988446
93  ou116            Eulemur_coronatus  7.438384
94  ou117               Eulemur_fulvus  7.779049
95  ou118               Eulemur_macaco  7.816014
96  ou119               Eulemur_mongoz  7.478735
97  ou120          Eulemur_rubriventer  7.620705
98  ou121         Euoticus_elegantulus  5.690359
99  ou122            Euoticus_pallidus  5.627621
100 ou123                Galago_alleni  5.521461
101 ou124              Galago_gallarum  5.365976
102 ou125             Galago_matschiei  5.267858
103 ou126                Galago_moholi  5.375278
104 ou127          Galago_senegalensis  5.594711
105 ou128          Galagoides_demidoff  4.206184
106 ou129      Galagoides_zanzibaricus  4.997212
107 ou130              Gorilla_gorilla 11.643954
108 ou131             Hapalemur_aureus  7.358831
109 ou132            Hapalemur_griseus  6.862758
110 ou133              Hapalemur_simus  7.620705
111 ou134                 Homo_sapiens 10.980195
112 ou135             Hylobates_agilis  8.675905
113 ou136           Hylobates_concolor  8.768730
114 ou137         Hylobates_gabriellae  9.047821
115 ou138            Hylobates_hoolock  8.809863
116 ou139            Hylobates_klossii  8.674197
117 ou140                Hylobates_lar  8.635865
118 ou141         Hylobates_leucogenys  8.898366
119 ou142             Hylobates_moloch  8.677610
120 ou143           Hylobates_muelleri  8.687779
121 ou144           Hylobates_pileatus  8.630522
122 ou145        Hylobates_syndactylus  9.296518
123 ou146                  Indri_indri  9.065315
124 ou147         Lagothrix_flavicauda  9.020390
125 ou148         Lagothrix_lagotricha  8.743532
126 ou149                  Lemur_catta  7.878534
127 ou150      Leontopithecus_caissara  6.405228
128 ou151    Leontopithecus_chrysomela  6.352629
129 ou152   Leontopithecus_chrysopygus  6.486161
130 ou153       Leontopithecus_rosalia  6.385194
131 ou154           Lepilemur_dorsalis  6.232448
132 ou155           Lepilemur_edwardsi  6.711740
133 ou156           Lepilemur_leucopus  6.396930
134 ou157           Lepilemur_microdon  6.863803
135 ou158         Lepilemur_mustelinus  6.508769
136 ou159       Lepilemur_ruficaudatus  6.637258
137 ou160    Lepilemur_septentrionalis  6.638568
138 ou161          Lophocebus_albigena  8.903815
139 ou162            Loris_tardigradus  5.517453
140 ou163             Macaca_arctoides  9.148465
141 ou164            Macaca_assamensis  9.054855
142 ou165              Macaca_cyclopis  8.658693
143 ou166          Macaca_fascicularis  8.431635
144 ou167               Macaca_fuscata  9.220291
145 ou168                 Macaca_maura  8.894259
146 ou169               Macaca_mulatta  8.771835
147 ou170            Macaca_nemestrina  8.970813
148 ou171                 Macaca_nigra  8.906529
149 ou172              Macaca_ochreata  7.919356
150 ou173               Macaca_radiata  8.517193
151 ou174               Macaca_silenus  8.699515
152 ou175                Macaca_sinica  8.446771
153 ou176              Macaca_sylvanus  9.350102
154 ou177             Macaca_thibetana  9.268609
155 ou178              Macaca_tonkeana  9.220291
156 ou179       Mandrillus_leucophaeus  9.560997
157 ou180            Mandrillus_sphinx  9.729134
158 ou181         Microcebus_coquereli  5.793014
159 ou182           Microcebus_murinus  4.198705
160 ou183             Microcebus_rufus  3.881564
161 ou184         Miopithecus_talapoin  7.130899
162 ou185             Nasalis_concolor  8.979354
163 ou186             Nasalis_larvatus  9.417355
164 ou187           Nycticebus_coucang  6.878326
165 ou188          Nycticebus_pygmaeus  5.840642
166 ou189      Otolemur_crassicaudatus  7.130899
167 ou190           Otolemur_garnettii  6.701960
168 ou191                 Pan_paniscus 10.468801
169 ou192              Pan_troglodytes 10.716638
170 ou193              Papio_hamadryas  9.735069
171 ou194           Perodicticus_potto  6.984716
172 ou195              Phaner_furcifer  6.016157
173 ou196       Pithecia_aequatorialis  7.774856
174 ou197            Pithecia_albicans  7.937375
175 ou198            Pithecia_irrorata  7.749322
176 ou199            Pithecia_monachus  7.654443
177 ou200            Pithecia_pithecia  7.420579
178 ou201               Pongo_pygmaeus 10.860920
179 ou202             Presbytis_comata  9.039552
180 ou203          Presbytis_femoralis  8.797851
181 ou204           Presbytis_frontata  8.853665
182 ou205              Presbytis_hosei  8.725832
183 ou206         Presbytis_melalophos  8.748305
184 ou207         Presbytis_potenziani  8.774931
185 ou208          Presbytis_rubicunda  8.773385
186 ou209            Presbytis_thomasi  8.765615
187 ou210            Procolobus_badius  8.808369
188 ou211         Procolobus_pennantii  9.122601
189 ou212           Procolobus_preussi  9.094930
190 ou213      Procolobus_rufomitratus  8.995909
191 ou214             Procolobus_verus  8.289037
192 ou215          Propithecus_diadema  8.794825
193 ou216      Propithecus_tattersalli  8.171882
194 ou217        Propithecus_verreauxi  8.202482
195 ou218          Pygathrix_avunculus  9.164296
196 ou219              Pygathrix_bieti  9.118225
197 ou220           Pygathrix_brelichi  9.305651
198 ou221            Pygathrix_nemaeus  9.417355
199 ou222          Pygathrix_roxellana  9.510445
200 ou223             Saguinus_bicolor  6.142037
201 ou224         Saguinus_fuscicollis  5.976351
202 ou225           Saguinus_geoffroyi  6.200509
203 ou226           Saguinus_imperator  6.016157
204 ou227             Saguinus_inustus  6.688355
205 ou228            Saguinus_labiatus  6.234411
206 ou229            Saguinus_leucopus  6.124683
207 ou230               Saguinus_midas  6.293419
208 ou231              Saguinus_mystax  6.326149
209 ou232         Saguinus_nigricollis  6.109248
210 ou233             Saguinus_oedipus  6.139885
211 ou234         Saguinus_tripartitus  5.953243
212 ou235          Saimiri_boliviensis  6.690842
213 ou236            Saimiri_oerstedii  6.570883
214 ou237             Saimiri_sciureus  6.620073
215 ou238                Saimiri_ustus  6.791221
216 ou239           Saimiri_vanzolinii  6.664409
217 ou240       Semnopithecus_entellus  9.441452
218 ou241             Tarsius_bancanus  4.736198
219 ou242               Tarsius_dianae  4.709530
220 ou243              Tarsius_pumilus  4.808111
221 ou244             Tarsius_spectrum  5.111988
222 ou245             Tarsius_syrichta  4.753590
223 ou246         Theropithecus_gelada  9.680344
224 ou247       Trachypithecus_auratus  9.181941
225 ou248     Trachypithecus_cristatus  8.872067
226 ou249     Trachypithecus_francoisi  9.008224
227 ou250          Trachypithecus_geei  9.031214
228 ou251        Trachypithecus_johnii  9.268609
229 ou252      Trachypithecus_obscurus  8.870663
230 ou253       Trachypithecus_phayrei  8.948976
231 ou254      Trachypithecus_pileatus  9.323669
232 ou255       Trachypithecus_vetulus  8.969542
233 ou256            Varecia_variegata  8.261010
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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.