On Dec 15, 2007 6:31 PM, David Winsemius <[EMAIL PROTECTED]> wrote: > > pm.srch<- function (){ > srch.stem > <-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=" > query <-as.character(scan(file="",what="character")) > doc <-xmlTreeParse(paste(srch.stem,query,sep=""),isURL = TRUE, > useInternalNodes = TRUE) > sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue) > } > > pm.srch() > 1: "laryngeal neoplasms[mh]" > 2: > Read 1 item > //Id > [1,] "18042931" > [2,] "18038886" > [3,] "17978930" > [4,] "17974987" > [5,] "17972507" > [6,] "17970149" > [7,] "17967299" > [8,] "17962724" > [9,] "17954109" > [10,] "17942038" > [11,] "17940076" > [12,] "17848290" > [13,] "17848288" > [14,] "17848287" > [15,] "17848278" > [16,] "17938330" > [17,] "17938329" > [18,] "17918311" > [19,] "17910347" > [20,] "17908862" > >
I tried the above function with simple search terms and it worked fine for me (also more output thanks to Martin's post) but when I use search terms attributed to certain fields, i.e. with [au] or [ta], I get the following error message: > pm.srch() 1: "laryngeal neoplasms[mh]" 2: Read 1 item Fehler in .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks), : error in creating parser for http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=laryngeal neoplasms[mh] I/O warning : failed to load external entity "http%3A//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi%3Fdb=pubmed&term=laryngeal%20neoplasms%5Bmh%5D" > What's wrong? Thanks for any help -- Armin Goralczyk, M.D. -- Universitätsmedizin Göttingen Abteilung Allgemein- und Viszeralchirurgie Rudolf-Koch-Str. 40 39099 Göttingen -- Dept. of General Surgery University of Göttingen Göttingen, Germany -- http://www.chirurgie-goettingen.de ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.