ReadPubMed modified function from RefManageR

ReadPubMed.R

ReadPubMed <- function (query, database = "PubMed", ...) 
{
    .params <- list(...)
    bad.ind <- which(!names(.params) %in% c("usehistory", "WebEnv", 
        "query_key", "retstart", "retmax", "field", "datetype", 
        "reldate", "mindate", "maxdate"))
    .parms <- .params
    if (length(bad.ind)) {
        warning("Invalid .params specified and will be ignored")
        .parms <- .parms[-bad.ind]
    }
    base.url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
    stopifnot(!missing(query))
    .parms$term <- query
    .parms$db <- database
    .parms$usehistory = "y"
    results <- try(getForm(base.url, .params = .parms))
    if (inherits(results, "try-error")) 
        return(NA)
    tdoc <- xmlParse(results)
    webenv <- unlist(xpathApply(tdoc, "/eSearchResult/WebEnv", 
        xmlValue))
    query.key <- unlist(xpathApply(tdoc, "/eSearchResult/QueryKey", 
        xmlValue))
    ids <- unlist(xpathApply(tdoc, "/eSearchResult/IdList/Id", 
        xmlValue))
    if (!length(ids)) {
        message("No Results.")
        return()
    }
    res <- GetPubMedByID(id = ids, db = database, WebEnv = webenv, 
        query_key = query.key)
        res$language <- NULL
        #res$language <- paste(res$language, sep=" ")
            #res$language <- gsub(res$language,pattern="c\\(",replacement="")
            #res$language <- gsub(res$language,pattern="\\\"",replacement="")
            #res$language <- gsub(res$language,pattern="\\)",replacement="")
        res$doi <- NULL
        #res$doi <- paste(res$doi, sep="_")
            #res$doi <- gsub(res$doi,pattern="c\\(",replacement="")
            #res$doi <- gsub(res$doi,pattern="\\\"",replacement="")
            #res$doi <- gsub(res$doi,pattern="\\)",replacement="")
    return(res)
}

# message(ReadPubMed function modified successfully)

Differences from the original ReadPubMed function: it removes both "language" and "DOI" fields, to make easier to fit results in a dataframe.