R/readabsnew.R

In pubmed.mineR: Text Mining of PubMed Abstracts

readabsnew = function (x) 
{
    xa <- readLines(con = x, warn=FALSE)
    xa <- c("PMID: MOCK", "", xa)
    xb <- regexpr("PMID", xa)
    xc = unlist(lapply(1:length(xb), function(x) {
        if (xb[x] == 1) 
            return(x)
    }))
    jn <- NULL
    abs <- NULL
    pmid <- NULL
    xd = lapply(1:length(xc), function(x) {
        k = x + 1
        if (k <= length(xc)) {
            tempjn <- xc[x] + 3
            jn = xa[tempjn]
            tempabs1 <- tempjn + 1
            tempabs2 <- xc[k] - 1
            abs = paste(xa[tempabs1:tempabs2], collapse = " ")
            temppmid <- xc[k]
            temppmid2 <- unlist(strsplit(xa[temppmid], " ", fixed = TRUE))
            pmid = temppmid2[2]
            return(c(jn, abs, pmid))
        }
    })
    jn = unlist(lapply(xd, function(x) {
        return(x[1])
    }))
    abs = unlist(lapply(xd, function(x) {
        return(x[2])
    }))
    pmid = unlist(lapply(xd, function(x) {
        return(x[3])
    }))
    abs = unlist(lapply(abs,function(x){space_quasher(x)}))
    write.table(cbind(jn, abs, pmid), file = "newabs.txt", quote = FALSE, 
        sep = "\t", row.names = FALSE)
    resultabs <- new("Abstracts", Journal = jn, Abstract = abs, 
        PMID = as.numeric(pmid))
    return(resultabs)
}