Dear all, I would like to obtain a data.frame with some data selected from pubmed information. For example, I would like to do an specific search and obtain a data.frame with the title of each article and the publication type.
Example of syntax: > library(reutils) > library(XML) > > pmid <- esearch('"Epidemiology" [Journal]', "pubmed", mindate="2013/01/01", > maxdate=paste("2013/12/31", sep=""), retmax="10000000") Mensajes de aviso perdidos NCBI requests that you provide an email address with each query to their API. Set the global option 'reutils.email' to your address to make this message go away. > > articles <- efetch(pmid, db="pubmed", retmax="10000000") Mensajes de aviso perdidos NCBI requests that you provide an email address with each query to their API. Set the global option 'reutils.email' to your address to make this message go away. > > journal <- articles$xmlValue("//Title") > BUT HERE I HAVE THE PROBLEM Each article (PMID) can have more than one type of publication. > ptype <- articles$xmlValue("//PublicationType") With this syntax I can select the first type of publication > ptype1 <- articles$xmlValue("//PublicationTypeList//PublicationType[1]") > length(ptype1) [1] 181 > With this syntax I can select the second type of publication. > ptype2 <- articles$xmlValue("//PublicationTypeList//PublicationType[2]") > length(ptype2) [1] 152 > But I would like to obtain a vector of length 181 (as ptype1) with NA's when there is no information of publication list Therefore I cannot obtain a data.frame because I don't obtain a NA when there is no data in ptype2 > df1 <- data.frame(journal=journal, ptype1=ptype1, ptype2=ptype2 ) Error en data.frame(journal = journal, ptype1 = ptype1, ptype2 = ptype2) : arguments imply differing number of rows: 181, 152 How can I do this data.frame??? Best Regards, Marc ______________________________________________ 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.