EML

Note: EML is work in progress. Please see the Issues tracker in this repository for details about current issues and development milestonds.

Installation

EML has not yet been released. Please install from GitHub after installing the devtools package (from CRAN):

devtools::install_github("cboettig/EML")

Quickstart

Load the package and read in an EML file:

library("EML")
f <- system.file("xsd/test/eml.xml", package = "EML")
eml <- read_eml(f)

This creates a native R object called eml. Although this is an "S4 object" type, it uses a "show" method which displays in an XML-like layout for convenience:

eml
#> <eml packageId="eml.1.1" system="knb" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.1 eml.xsd">
#>   <dataset>
#>     <title>Sample dataset Description</title>
#>     <creator id="23445" scope="document">
#>       <individualName>
#>         <surName>Smith</surName>
#>       </individualName>
#>     </creator>
#>     <creator id="23446" scope="document">
#>       <individualName>
#>         <surName>Smith</surName>
#>       </individualName>
#>     </creator>
#>     <additionalInfo>
#>       <para>My comments go here.</para>
#>     </additionalInfo>
#>     <intellectualRights>
#>       <section>
#>         <para>Anyone can use it.</para>
#>       </section>
#>     </intellectualRights>
#>     <distribution>
#>       <online>
#>         <connectionDefinition scope="document">
#>           <schemeName system="CAP">sde</schemeName>
#>           <description>
#>             <para>The SDE scheme used at CAP LTER</para>
#>           </description>
#>           <parameterDefinition>
#>             <name>hostname</name>
#>             <definition>The host</definition>
#>             <defaultValue>mohave.asu.edu</defaultValue>
#>           </parameterDefinition>
#>           <parameterDefinition>
#>             <name>databaseName</name>
#>             <definition>The name of the database or catalog</definition>
#>           </parameterDefinition>
#>           <parameterDefinition>
#>             <name>owner</name>
#>             <definition>The owner catalog</definition>
#>             <defaultValue>dbo</defaultValue>
#>           </parameterDefinition>
#>         </connectionDefinition>
#>       </online>
#>     </distribution>
#>     <purpose>
#>       <para>Provide data to the whole world.</para>
#>     </purpose>
#>     <contact>
#>       <individualName>
#>         <surName>Johnson</surName>
#>       </individualName>
#>     </contact>
#>     <contact>
#>       <references>23445</references>
#>     </contact>
#>   </dataset>
#> </eml>

Validate EML against the official schema

eml_validate(eml)
#> $status
#> [1] 0
#> 
#> $errors
#> list()
#> attr(,"class")
#> [1] "XMLStructuredErrorList"
#> 
#> attr(,"class")
#> [1] "XMLSchemaValidationResults"

Write out as EML:

write_eml(eml, "example.xml")
#> [1] "example.xml"

Manipulating EML objects

Eventually EML will provide constructor and extract methods to create and extract common metadata sections from convenient R stuctures (e.g. data.frames with unit metadata, common R classes like Person, bibtype). For now, the only method to access and modify EML is to use the standard S4 subsetting and constructor methods.

Our current example does not have a publication date. Let's add one:

eml@dataset@ResourceGroup@pubDate <- new("pubDate", "2016")

Note that we use the constructor method new() to create an object.

Working with repeating elements

Developer notes

Creating EML class definitions

Class definitions (classes.R) and methods (methods.R) are created programmatically. From the root of the package, run: source("inst/create-package/create_package.R").