scripts/jid.R

In corybrunson/pubmed.network: Network analysis of PubMed data

# Read the file 'J_Entrez' as a data.table

# set working directory
if(file.exists('~/Documents')) {
    setwd('~/Documents/CQM/PubMed')
} else {
    setwd('~/PubMed')
}
# load packages
pkgs <- c('data.table')
for(pkg in pkgs) {
    if(!require(pkg, character.only = TRUE)) {
        install.packages(pkg)
        stopifnot(require(pkg, character.only = TRUE))
    }
}

# Read lines, check that dashes occur at regular intervals
lines <- readLines('data/J_Entrez')
wh <- which(lines == lines[1])
n <- unique(diff(wh))
stopifnot(length(n) == 1)

# Extract header from first "line"
hdr <- gsub('(^[^:]*): .*$', '\\1', lines[2:n])

# Bind remaining "lines"
tab <- t(sapply(wh[-length(wh)], function(i) {
    gsub('^[^:]*: (.*$)', '\\1', lines[i + 1:(n - 1)])
}))

# Coerce to data.table
jids <- as.data.table(tab)
setnames(jids, names(jids), hdr)

# Save as part of the pubmed.network package
save(jids, file = 'pkg/pubmed.network/data/jids.rda')