Extract appropriate R objects from EML dataTable

[cboettig]

Given the EML file defining a CSV and metadata types, extract the R object information. This should allow the user to reconstruct the following R objects from EML generated by #2

 dat = data.frame(river=c("SAC", "SAC", "AM"), 
                   spp = c("king", "king", "ccho"), 
                   stg = c("smolt", "parr", "smolt"),
                   ct =  c(293L, 410L, 210L))

with the following accompanying metadata:

 col_metadata = c(river = "http://dbpedia.org/ontology/River",
                  spp = "http://dbpedia.org/ontology/Species", 
                  stg = "Life history stage",
                  ct = "count")
 unit_metadata = 
  list(river = c(SAC = "The Sacramento River", AM = "The American River"),
       spp = c(king = "King Salmon", ccho = "Coho Salmon"),
       stg = c(parr = "third life stage", smolt = "fourth life stage"),
       ct = "number")

Ensure that all objects have the correct object type: e.g. (ordered) factors should be (ordered) factors, etc.

[cboettig]

Read should be able to handle local files, not just online files. Likewise an issue for eml_write #2

[cboettig]

Bug in date time parsing:

out <- eml_read("http://harvardforest.fas.harvard.edu/data/eml/hf205.xml")
head(out$dataframe)
out$col_metadata
out$unit_metadata

In other reading checks, note that this EML file also arbitrarily declares that the data has 9999 columns, while we see that it has

dim(out$dataframe)[1]
[1] 279224

Issues and next steps

Of course eml_read is still a work in progress. In particular:

(Also note that eml_read still needs a dateTime parser on the unit_metadata....)

• How do we deal with dateTime when defined across multiple columns?

[cboettig]

• dateTime bug fixed in 8b7ffee by coercing to character. remaining dateTime issues are now in Dealing with dateTimes: when dates are defined over multiple columns #17
• The Harvard Forest hf205.xml example still does some wierd things, e.g. the run id numbers (1-6) are encoded as character strings, where a ordered factor might have been more appropriate. Guess we should just obey the metadata we are given...
• The basic example proposed at the top of this issue does not demonstrate different encodings well, e.g. it uses only a trivial ratio unit (count) and no ordered factors or characters...