search for: useinternalnod

Hi, Why is the following retuning a nodset of length 0: > library(XML) > test <- xmlTreeParse( > "http://www.unimod.org/xml/unimod_tables.xml",useInternalNodes=TRUE) > getNodeSet(test,"//modifications_row") Thanks for any hint. Joh

...know that the html code is malformed, but for my purposes i can ignore that output. Is there a way to achieve this? ### Example: library(RCurl); library(XML) doc <- getURL('http://www.google.co.uk/search?q=%22R%20Project %22&as_qdr=d1&num=100') html.tree <- htmlTreeParse(doc, useInternalNodes = TRUE) ### Output - this is what i would like to suppress Tag nobr invalid htmlParseEntityRef: expecting ';' htmlParseEntityRef: expecting ';' ### etc. I attempted to use try(expr, silent=TRUE) but that didn't work for me: > try(htmlTreeParse(doc, useInternalNodes = TRU...

I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse("

...ry large, I mean going up to 5-10Gb, although I am using a 'small' 40M file to test my code.) My first attempt at parsing the 40M file, using the XML package, took more than 2200 seconds and left me quite disappointed. I managed to cut that down to around 40 seconds by: -using the 'useInternalNodes' option of the XML package when parsing the xml tree; -vectorizing the parsing (i.e., replacing loops like "for(node in group.of.nodes) {...}" by "sapply(group.of.node, function(node){...}") I gained another 5 seconds by making small changes to the functions used (like...

...encoding right in htmlTreeParse command. See below > library(RCurl) > library(XML) > > site <- getURL("http://www.aarresaari.net/jobboard/jobs.html") > txt <- readLines(tc <- textConnection(site)); close(tc) > txt <- htmlTreeParse(txt, error=function(...){}, useInternalNodes = TRUE) > > g <- xpathSApply(txt, "//p", function(x) xmlValue(x)) > head(grep(" ", g, value=T)) [1] "????PART-TIME EXPORT SALES ASSOCIATES (ALSO SUMMER WORK) ? Valuatum Oy ??Helsinki ??Ilmoitus lis??tty: 31.12.2009. Viimeinen hakup??iv??: 28.02.2010" [2]...

...gt; The following code shows that i cannot extract the Value of "Länge" correctly. Any help is very welcom. ---------------------------------------- Code Start ------------ > fname1 <- "test1.xml" > fname2 <- "test2.xml" > doc <- xmlTreeParse(fname1,useInternalNodes=T) > show(doc) <?xml version="1.0" encoding="ISO-8859-1"?> <Daten> <ITEM> <Messdaten> <MESSUNG> <BEZEICHNUNG>Länge</BEZEICHNUNG> </MESSUNG> </Messdaten> </ITEM> </Daten> > x...

...teniendo en cuenta que puede que haya semanas que no haya puntuado (en el ejemplo, la segunda semana). De momento lo estoy obteniendo de la siguiente forma: url_jugador<-"http://localhost:8080/jugadores/Luis" txt_jugador <- getURL(url_jugador) doc<-htmlTreeParse(txt_jugador, useInternalNodes = TRUE) puntos_nodo<- xpathApply(doc, "//table[@class='points']/tr") puntos_nodo [[1]] <tr> <td class="semana">1</td> <td class="neg"/> <td> <div class="bar">6</div> </td> </tr>...

...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] "TotalTimeSeconds" > xpathApply(doc2, "//Total...

...objects in each iteraction. As in the following example (which doesn't work quite well) my_list<-c("A","B","C","D","E","F") for(i in c(1:length(my_list))){ url<- "http://finance.yahoo.com" doc = htmlTreeParse(url, useInternalNodes = T) tab_nodes = xpathApply(doc, "//table[@cellpadding = '3']") *my_list[i]*=lapply(tab_nodes, readHTMLTable) #problem is in this line names(*my_list[i]*)=c("Ins","outs") } The problem is that in iteraction #1, I need the info to be stored at an...

...Ocular. I am using the following code: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300", sep="") docId <- xmlTreeParse(getURL(paste(url, search, sep="")), useInternalNodes=TRUE) I want to get the reply where BOTH the terms exist in abstract. But it is not doing that now. Any idea? Thanks john [[alternative HTML version deleted]]

...search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax=100&usehistory=y", sep="") docId <- xmlTreeParse(getURL(paste(url, search, sep="")), useInternalNodes=TRUE) I want to fetch abstracts containing queryTerm1 AND queryTerm2 Or queryTerm3 OR queryTerm4. The code runs without error, but from the result I find that conjunction and disjunction is not working. Can anyone suggest a correct syntax for doing AND and OR pubmed query? Thanks John [[alte...

Hi All: I would like to extract the provider name, address, and phone number from multiple webpages like this: http://oasasapps.oasas.state.ny.us/portal/pls/portal/oasasrep.providersearch.take_to_rpt?P1=3489&P2=11490 Based on searching R-help archives, it seems like the XML package might have something useful for this task. I can load the XML package and supply the url as an argument to

...The "nodes" object is either the argument nor generated in the function. How can R find the "nodes" object? What am I missing here? Thanks Zheng Jk parseXmlEntryNodeSet <- function(psimi25file, psimi25source, verbose=TRUE) { psimi25Doc <- xmlTreeParse(psimi25file, useInternalNodes = TRUE) psimi25NS <- getDefaultNamespace(psimi25Doc) namespaces <- c(ns = psimi25NS) entry <- getNodeSet(psimi25Doc, "/ns:entrySet/ns:entry", namespaces) if(verbose) statusDisplay(paste(length(entry),"Entries found\n",sep=" ")) entryCount &l...

...in htmlParse code:     ans <- .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") By the way, readHTMLTable(htmlParse(url)) works fine on other pages, so the problem is some...

Hi All, First method:- >library(XML) >theurl <- "http://home.sina.com" >download.file(theurl, "tmp.html") >txt <- readLines("tmp.html") >txt <- htmlTreeParse(txt, error=function(...){}, useInternalNodes = TRUE) >g <- xpathSApply(txt, "//p", function(x) xmlValue(x)) >head(grep(" ", g, value=T)) [1] " | | ENGLISH" " " [3] " ()" " " [5] " "...

...ddress" hm <- function(x) { url.zill <-paste("http://www.zillow.com/webservice/GetDeepSearchResults.htm?zws-id=X1-ZWz1bup03e49vv_5kvb6&address=",x, sep="") ############## problem line is next ################################# zdoc <-xmlTreeParse(url.zill, useInternalNode=TRUE, isURL=TRUE) ############# problem line above ################################## f$zpid <- sapply(getNodeSet(zdoc, "//result/zpid"), xmlValue) f$zest.low <-sapply(getNodeSet(zdoc, "//valuationRange/low"), xmlValue) f$zest <- sapply(getNodeSet(zdoc, "...

Dear all, for my diploma thesis I have to import huge XML-Files into R for statistical processing - huge means a size about 33 MB. I'm using the XML-Package version 1.9 As far as reading the complete file into R via xmlTreeParse doesn't work or is too slow, I'm trying to use xmlEventParse but I got completely stuck. I have many different type of nodes + <configuration>

...atements are wrong or getNodeSet needs something else to get to information contained in a bubble on a webpage. Any suggestions or ideas would be GREATLY appreciated. library(XML) url <- "http://www.zillow.com/homes/511 W Lafayette St, Norristown, PA_rb" doc <- htmlTreeParse(url, useInternalNode=TRUE, isURL=TRUE) f1 <- getNodeSet(doc, "//a[contains(@href,'homedetails')]") f2 <- getNodeSet(doc, "//span[contains(@class,'price')]") f3 <- getNodeSet(doc, "//LIST[@Beds]") f4 <- getNodeSet(doc, "//LIST[@Baths]") f5 <- getNod...

...as que no haya puntuado (en el ejemplo, la segunda semana). De >> momento lo estoy obteniendo de la siguiente forma: >> >> url_jugador<-"http://localhost:8080/jugadores/Luis" >> txt_jugador <- getURL(url_jugador) >> doc<-htmlTreeParse(txt_jugador, useInternalNodes = TRUE) >> puntos_nodo<- xpathApply(doc, "//table[@class='points']/tr") >> puntos_nodo >> [[1]] >> <tr> >> <td class="semana">1</td> >> <td class="neg"/> >> <td> >> &...

...#39; Traceback: 1: .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), FALSE, as.logical(isSchema), as.logical(fullNamespaceInfo), as.character(encoding), as.logical(useDotNames), xinclude, error, addFinalizer, PACKAGE = "XML") 2: xmlTreeParse(fileName) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R witho...