search for: xmlroot

R Users: After installing Bioconductor, RSXML and all the relevant Win32 DLLs (libxml2, zlib, iconv), I receive the following error message when using pm.getabst() Error in xmlRoot(absts) : no applicable method for "xmlRoot" I receive this when using the example from help(pm.getabst). Downloading the target XML file, parsing it with xmlTreeParse and applying xmlRoot returns no error. Your thoughts/suggestions are appreciated. Mark Larsen

...<row BRAND="FORD" NUM="1" YEAR="2007" VALUE="17500" /> <row BRAND="GMC" NUM="1" YEAR="2008" VALUE="22000" /> </data> *R Code:* doc< -xmlInternalTreeParse ("Sample2.xml") top <- xmlRoot (doc) xmlName (top) names (top) art <- top [["row"]] art ** *Output:* > art<row BRAND="GMC" NUM="1" YEAR="1999" VALUE="10000"/> * * This is where I am having difficulties. I am unable to "access" additional rows; ( i.e. &...

...I selected GridR package for the distributed programming. *grid.init(service="local",debug=FALSE, localTmpDir="GridRTmp/") grid.apply("x",UCS, wait=TRUE )* UCS is a function. When I execute this statement, I have some errors like : *cannot load local function/variable: xmlRoot extracted from line: : no visible global function definition for 'xmlRoot' cannot load local function/variable: xmlTreeParse extracted from line: : no visible global function definition for 'xmlTreeParse' * In my function I have used the statement: *library("XML")*...

Dear, I want to read XML documents, add child nodes to some elements and store everything back as an XML document. I've tryed the following: doc <- xmlTreeParse("file.xml") QTListNode<-xmlElementsByTagName(xmlRoot(doc)[[1]],"tagname") append.xmlNode(QTListNode[[1]],newXMLNode(name ="Norm", attrs = NULL)) saveXML(doc, file = "out.xml", compression = 0, indent=T) This doesn't seem to work. Can anyone help? Thanks, Steffen

...ue. The RSS feed I would like to use is: > URL <- "http://www.sec.gov/cgi-bin/browse-edgar?action=getcurrent&type=&company=&dateb=&owner=include&start=0&count=40&output=atom" > library(XML) > doc <- xmlTreeParse(URL) > src <- xpathApply(xmlRoot(doc), "//entry") I get an empty list rather than a list of each of the "entry": > src list() attr(,"class") [1] "XMLNodeSet" I'm not sure how to fix this. Any suggestions? Do I need to provide a namespace, or is the RSS malformed? Thanks, James

Dear useRs, I have a simple/RTFM question about XML parsing. Given an XML file, such as (fragment) <A>100</A> <B>23</B> <C>true</C> how do I import it in a data frame or list, so that the values (100, 23, true) can be accessed through the names A, B and C? I installed the XML package and looked over the documentation... however after 20 minutes and a couple of

Is there any function to write a XML structure, after it was read using xmlTreeParse? Ex: library(XML) x <- xmlTreeParse("Irpf2008/aplicacao/dados/12345678901/12345678901.xml") # write it... Alberto Monteiro PS: please, brazilians, don't be offended by my foul language!

...<row BRAND="FORD" NUM="1" YEAR="2007" VALUE="17500" /> <row BRAND="GMC" NUM="1" YEAR="2008" VALUE="22000" /> </data> *R Code:* doc< -xmlInternalTreeParse ("Sample2.xml") top <- xmlRoot (doc) xmlName (top) names (top) art <- top [["row"]] art ** *Output:* > art<row BRAND="GMC" NUM="1" YEAR="1999" VALUE="10000"/> This is where I am having difficulties. I am unable to "access" additional rows; ( i.e. <...

...011-04-05">8.8</v> <v date="2011-04-06">13.5</v> </stationname> </data> I would like to get a table in R like this: stationname date value Aachen 2011-04-01 14.1 Aachen 2011-04-01 17.6 . . . Ahaus 2011-04-06 13.5 I tried to do this: doc = xmlRoot(xmlTreeParse("de.dwd.klis.TADM.xml")) tmp = xmlSApply(doc, function(x) xmlSApply(x, xmlValue)) but the stationname was not parsed because "Aachen" is kind of attribute of stationname. Could anyone give some help? Thanks, kai.

...lesList> </Manifest> I am attempting to use XML package and xpathSApply() to extract, say, the eValue attribute for eName=='0ne' for all <File> nodes that have <FileTypeId>==10. I try the following, amoung several things: doc<-xmlInternalTreeParse(Manifest) Root = xmlRoot(doc) xpathSApply(Root, "//File[FileTypeId=10]/PatientCharacteristics/[@eName='one']", xmlAttrs) and it does not work. Might somebody help me with the syntax here? Thanks a lot!! Aaron [[alternative HTML version deleted]]

...reluctant to paste even a shortened version. The output below shows I can get nodes, but an attempt at value of a single node comes up empty (even though there is data there. One question: Has anybody succeeded parsing Garmin .tcx (xml) files? Thanks! Michael _______________________ >doc2 = xmlRoot(xmlTreeParse("HR.reduced3.tcx",useInternalNodes = TRUE)) >xpathApply(doc2, "//*", xmlName) [[1]] [1] "TrainingCenterDatabase" [[2]] [1] "Activities" [[3]] [1] "Activity" [[4]] [1] "Id" [[5]] [1] "Lap" [[6]] [1] "Tota...

Hello again, Another stumble here that is defeating me. I try: a<-readLines(url("http://feeds.feedburner.com/grokin")) t<-XML::xmlTreeParse(a, ignoreBlanks=TRUE, replaceEntities=FALSE, asText=TRUE) elem<- XML::getNodeSet(XML::xmlRoot(t),"/rss/channel/item")[[1]] And I get: Start tag expected, '<' not found Error: 1: Start tag expected, '<' not found When I modify the second line in "a" to remove the following (just leaving the <rss> tag with its attributes), I do not get the err...

...t;-c('http://www.parl.gc.ca/housechamberbusiness/ChamberSittings.aspx?View=H&Language=E&Mode=1&Parl=41&Ses=1') #Scrape the page with the links doc<-scrape(url=hansard, parse=TRUE, follow=TRUE) #Not sure what exactly this does, but it is necessary doc<-doc[[1]] #Get the xmlRoot directory doc<- xmlRoot(doc) #Get nodes that contain only the links to each day's transcripts links<- getNodeSet(doc, "//a[@class='PublicationCalendarLink']/@href") links<-matrix(links) #Paste those href links to the root URL links<-apply(links, 1, function(x) pa...

...doesn't free up the memory. When I monitor it in windows task manager the memory usage just climbs with each iteration until R crashes. I can replicate the problem with the small example: file.name<-"C:\\MyData.xml.gz" TEMPP<-xmlParse(file.name) xx <- xmlRoot(TEMPP) rm(xx) rm(TEMPP) gc() Even though I remove the root node xx and the document TEMPP, the memory usage remains the same as it was when I first read it in... Any ideas/solutions? I am using a 32bit version of R 2.14.0 on windows XP, and the latest version of XML (3.6.1)...

...some polygons that I would like to extract and use in R. The polygons are nested rather deeply. For example, I found by trial and error that I can extract the coordinates of one of them using functions from the XML package: doc <- xmlInternalTreeParse('doc.kml') docroot <- xmlRoot(doc) pgon <- xmlValue(docroot[[52]][[3]][[7]][[3]][[3]][[1]][[1]]) but this is hardly general! I'm hoping there is some relatively straightforward way to use functions from the XML package to recursively descend the structure and return the text strings representing the polygons in...

...//www.w3.org/2001/XMLSchema.xsd > into genSOAPClientInterface() instead ? Well, it's not possible, at least for me. This is as far as I got, any help appreciated: Thanks in advance, yours, Steffen xsd = XMLSchema:::parseSchemaDoc("http://www.w3.org/2001/XMLSchema.xsd") root = xmlRoot(xsd) types = XMLSchema:::processSchemaTypes(root, root, verbose = TRUE) traceback() > xsd = XMLSchema:::parseSchemaDoc("http://www.w3.org/2001/XMLSchema.xsd") > root = xmlRoot(xsd) > types = XMLSchema:::processSchemaTypes(root, root, verbose = TRUE) processing (sub) schema htt...

...tbios-ssn" method="probed" conf="10"/></port> </ports> <times srtt="647" rttvar="71" to="100000"/> </host>' I want to store this as a list of lists, so I do: mytree<-xmlTreeParse(mydoc) myroot<-xmlRoot(mytree) mylist<-xmlToList(myroot) Now my problem is that when I want to fetch the attributes of the services running of each port, the behavior is not consistent: > mylist[["ports"]][[1]][["service"]]$.attrs["name"] name "msrpc" > mylist[["...

XML is a good tool reading data from web within R. But I wonder how could get the encoding correctly. library(XML) url <- 'http://www.szitic.com/docc/jz-lmzq.html' xml <- htmlTreeParse(url, useInternal=TRUE) q <- "//tbody/tr/td" dat <- unlist(xpathApply(xml, q, xmlValue)) df <- as.data.frame(t(matrix(dat, 4))) dt<-as.character(df[15,1]) The first column of df

...s, including >checking the name of the node to see if you want it >and then storing it somewhere. That's where you'll >need closures (simply viewed the "functions within functions" part) again, >as in my example above. > >But here is a simple example > doc = xmlRoot(xmlTreeParse(URL)) > xmlDOMApply(doc, function(node, ...) > if(xmlName(node) == "PubDate") > print(node) > ) Gorjanc Gregor wrote: > Hello! > > I am trying to get specific fields from an XML document and I am...

...cument and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only node 'pubdate' and its children, but I don't know how to do that unless I try to dig into the structure of the XML file. The problem is that structure can differ and then hardcoded set of list indices i.e. tmp[[i]][[j]]... doesn't help me. I've...