Created
July 19, 2013 23:55
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> # 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() |
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