# A Brief Introduction to RNeXML

#### Carl Boettiger

#### Scott Chamberlain

#### Rutger Vos

#### Hilmar Lapp

Read in a `nexml` file:

    f <- system.file("examples", "comp_analysis.xml", package="RNeXML")
    nexml <- nexml_read(f)

Pretty-print an overview of the components and metadata that make up the nexml object:

    nexml  # this is the same as show(nexml)

    ## A nexml object representing:
    ##       1 phylogenetic tree block(s), where:
    ##     block 1 contains 1 phylogenetic tree(s)
    ##       2 character block(s), where:
    ##     block 1 defines 1 continuous character(s)
    ##     matrix 1 has 10 row(s)
    ##     block 2 defines 1 standard/discrete character(s), with 2 states each
    ##      and  0 polymorphic or uncertain state(s) defined
    ##     matrix 2 has 10 row(s)
    ##       10 taxonomic units in 1 block(s)
    ##   Taxa:   taxon_1, taxon_2, taxon_3, taxon_4, taxon_5, taxon_6 ...
    ##   Metadata annotations:
    ##  2 at top level
    ##  0 in block 1 at otu level
    ##  0 in block 1 at char level
    ##  0 in block 2 at char level
    ##  0 in block 1 at state level
    ##  0 in block 2 at state level
    ##
    ## Author(s): rvosa
    ##
    ## NeXML generated by Bio::Phylo::Project v.0.56 using schema version: 0.9
    ## Size: 289.3 Kb

Create a summary object of various component and metadata counts (the `show()` method uses this):

    summary(nexml)

    ## $nblocks
    ##      trees       otus characters
    ##          1          1          2
    ##
    ## $ncharacters
    ## block.1 block.2
    ##       1       1
    ##
    ## $nstates
    ##         block.1 block.2
    ## Min.         NA       2
    ## 1st Qu.      NA       2
    ## Median       NA       2
    ## Mean         NA       2
    ## 3rd Qu.      NA       2
    ## Max.         NA       2
    ##
    ## $nnonstdstatedefs
    ##         polymorphic uncertain
    ## block.1          NA        NA
    ## block.2           0         0
    ##
    ## $nmatrixrows
    ## block.1 block.2
    ##      10      10
    ##
    ## $ntrees
    ## block.1
    ##       1
    ##
    ## $notus
    ## block.1
    ##      10
    ##
    ## $nmeta
    ## $nmeta$nexml
    ## [1] 2
    ##
    ## $nmeta$otu
    ## block.1
    ##       0
    ##
    ## $nmeta$char
    ## block.1 block.2
    ##       0       0
    ##
    ## $nmeta$state
    ## block.1 block.2
    ##       0       0

Extract trees from nexml into the `ape::phylo` format:

    tr <- get_trees(nexml) # or: as(nexml, "phylo")
    plot(tr)

plot of chunk unnamed-chunk-5

Write an `ape::phylo` tree into the `nexml` format:

    data(bird.orders)
    nexml_write(bird.orders, "test.xml", creator = "Carl Boettiger")

    ## [1] "test.xml"

A key feature of NeXML is the ability to formally validate the construction of the data file against the standard (the lack of such a feature in nexus files had lead to inconsistencies across different software platforms, and some files that cannot be read at all). While it is difficult to make an invalid NeXML file from `RNeXML`, it never hurts to validate just to be sure:

    nexml_validate("test.xml")

    ## [1] TRUE

Extract metadata from the NeXML file:

    birds <- nexml_read("test.xml")
    get_taxa(birds)

    ##     otu            label xsi.type otus
    ## 1  ou37 Struthioniformes       NA  os3
    ## 2  ou38     Tinamiformes       NA  os3
    ## 3  ou39      Craciformes       NA  os3
    ## 4  ou40      Galliformes       NA  os3
    ## 5  ou41     Anseriformes       NA  os3
    ## 6  ou42    Turniciformes       NA  os3
    ## 7  ou43       Piciformes       NA  os3
    ## 8  ou44    Galbuliformes       NA  os3
    ## 9  ou45   Bucerotiformes       NA  os3
    ## 10 ou46      Upupiformes       NA  os3
    ## 11 ou47    Trogoniformes       NA  os3
    ## 12 ou48    Coraciiformes       NA  os3
    ## 13 ou49      Coliiformes       NA  os3
    ## 14 ou50     Cuculiformes       NA  os3
    ## 15 ou51   Psittaciformes       NA  os3
    ## 16 ou52      Apodiformes       NA  os3
    ## 17 ou53   Trochiliformes       NA  os3
    ## 18 ou54  Musophagiformes       NA  os3
    ## 19 ou55     Strigiformes       NA  os3
    ## 20 ou56    Columbiformes       NA  os3
    ## 21 ou57       Gruiformes       NA  os3
    ## 22 ou58    Ciconiiformes       NA  os3
    ## 23 ou59    Passeriformes       NA  os3

    get_metadata(birds)

    ##           property   datatype                 content     xsi.type                                              href Meta
    ## 1       dc:creator xsd:string          Carl Boettiger  LiteralMeta                                              <NA> m278
    ## 2 dcterms:modified xsd:string 2020-01-28 23:24:19 GMT  LiteralMeta                                              <NA> m279
    ## 3       cc:license       <NA>                    <NA> ResourceMeta http://creativecommons.org/publicdomain/zero/1.0/ m280

Add basic additional metadata:

      nexml_write(bird.orders, file="meta_example.xml",
                  title = "My test title",
                  description = "A description of my test",
                  creator = "Carl Boettiger <cboettig@gmail.com>",
                  publisher = "unpublished data",
                  pubdate = "2012-04-01")

    ## [1] "meta_example.xml"

By default, `RNeXML` adds certain metadata, including the NCBI taxon id numbers for all named taxa. This acts a check on the spelling and definitions of the taxa as well as providing a link to additional metadata about each taxonomic unit described in the dataset.

### Advanced annotation

We can also add arbitrary metadata to a NeXML tree by define `meta` objects:

    modified <- meta(property = "prism:modificationDate",
                     content = "2013-10-04")

Advanced use requires specifying the namespace used. Metadata follows the RDFa conventions. Here we indicate the modification date using the prism vocabulary. This namespace is included by default, as it is used for some of the basic metadata shown in the previous example. We can see from this list:

    RNeXML:::nexml_namespaces

    ##                                              nex                                              xsi
    ##                      "http://www.nexml.org/2009"      "http://www.w3.org/2001/XMLSchema-instance"
    ##                                              xml                                             cdao
    ##           "http://www.w3.org/XML/1998/namespace"                "http://purl.obolibrary.org/obo/"
    ##                                              xsd                                               dc
    ##              "http://www.w3.org/2001/XMLSchema#"               "http://purl.org/dc/elements/1.1/"
    ##                                          dcterms                                            prism
    ##                      "http://purl.org/dc/terms/" "http://prismstandard.org/namespaces/1.2/basic/"
    ##                                               cc                                             ncbi
    ##                 "http://creativecommons.org/ns#"          "http://www.ncbi.nlm.nih.gov/taxonomy#"
    ##                                               tc
    ##  "http://rs.tdwg.org/ontology/voc/TaxonConcept#"

This next block defines a resource (link), described by the `rel` attribute as a homepage, a term in the `foaf` vocabulary. Because `foaf` is not a default namespace, we will have to provide its URL in the full definition below.

    website <- meta(href = "http://carlboettiger.info",
                    rel = "foaf:homepage")

Here we create a history node using the `skos` namespace. We can also add id values to any metadata element to make the element easier to reference externally:

      history <- meta(property = "skos:historyNote",
                      content = "Mapped from the bird.orders data in the ape package using RNeXML",
                      id = "meta123")

For this kind of richer annotation, it is best to build up our NeXML object sequentially. First we will add `bird.orders` phylogeny to a new phylogenetic object, and then we will add the metadata elements created above to this object. Finally, we will write the object out as an XML file:

      birds <- add_trees(bird.orders)
      birds <- add_meta(meta = list(history, modified, website),
                        namespaces = c(skos = "http://www.w3.org/2004/02/skos/core#",
                                       foaf = "http://xmlns.com/foaf/0.1/"),
                        nexml=birds)
      nexml_write(birds,
                  file = "example.xml")

    ## [1] "example.xml"

### Taxonomic identifiers

Add taxonomic identifier metadata to the OTU elements:

    nex <- add_trees(bird.orders)
    nex <- taxize_nexml(nex)

## Working with character data

NeXML also provides a standard exchange format for handling character data. The R platform is particularly popular in the context of phylogenetic comparative methods, which consider both a given phylogeny and a set of traits. NeXML provides an ideal tool for handling this metadata.

### Extracting character data

We can load the library, parse the NeXML file and extract both the characters and the phylogeny.

    library(RNeXML)
    nexml <- read.nexml(system.file("examples", "comp_analysis.xml", package="RNeXML"))
    traits <- get_characters(nexml)
    tree <- get_trees(nexml)

(Note that `get_characters` would return both discrete and continuous characters together in the same data.frame, but we use `get_characters_list` to get separate data.frames for the continuous `characters` block and the discrete `characters` block).

We can then fire up `geiger` and fit, say, a Brownian motion model the continuous data and a Markov transition matrix to the discrete states:

    library(geiger)
    fitContinuous(tree, traits[1], ncores=1)
    fitDiscrete(tree, traits[2], ncores=1)