extractJournal.log.R

> # Get data for 2011
> query <- c("cbt" = "'cognitive behavior therapy' OR 'cognitive behavioral therapy' OR 'cognitive therapy' AND 2011[DP]")
> pub.efetch <- searchPubmed(query)
Searching (downloading 1718 articles)
Completed download from PubMed.
> cbt_2011 <- extractJournal()
XML declaration allowed only at the start of the document
StartTag: invalid element name
Error: 1: XML declaration allowed only at the start of the document
2: StartTag: invalid element name
> traceback()
5: stop(e)
4: (function (msg, ...) 
   {
       if (length(grep("\\\n$", msg)) == 0) 
           paste(msg, "\n", sep = "")
       if (immediate) 
           cat(msg)
       if (length(msg) == 0) {
           e = simpleError(paste(1:length(messages), messages, sep = ": ", 
               collapse = ""))
           class(e) = c(class, class(e))
           stop(e)
       }
       messages <<- c(messages, msg)
   })(character(0))
3: .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks), 
       as.logical(replaceEntities), as.logical(asText), as.logical(trim), 
       as.logical(validate), as.logical(getDTD), as.logical(isURL), 
       as.logical(addAttributeNamespaces), as.logical(useInternalNodes), 
       as.logical(isHTML), as.logical(isSchema), as.logical(fullNamespaceInfo), 
       as.character(encoding), as.logical(useDotNames), xinclude, 
       error, addFinalizer, as.integer(options), PACKAGE = "XML")
2: xmlTreeParse(pub.efetch, useInternalNodes = TRUE) at pubmed.R#64
1: extractJournal()