#!/usr/bin/Rscript
library(RISmed)
library(mineR)
# Get abstracts of data
# Store the input string for reuse
search_topic <- "anaphylaxis genetics"
search_query <- EUtilsSummary(search_topic, mindate=2014, maxdate=2015)
pull <- EUtilsGet(search_query)
data <- data.frame('Abstracts' = AbstractText(pull))
# Get rid of first entry for some reason, seems to always be blank
data[,1] <- as.character(data[,1])
data <- data[-1,]
search_topic <- "immunology genetics"
search_query <- EUtilsSummary(search_topic, # Find all articles matching the string
mindate=2014, # From 2014
maxdate=2015, # to 2015
retmax = 1000) # This is the default but explicit
pull_control <- EUtilsGet(search_query)
control <- data.frame('Abstracts' = AbstractText(pull_control))
# Get rid of first entry for some reason, seems to always be blank
control[,1] <- as.character(control[,1])
control <- control[-1,]
### Load in the preconstructed TDM
data(package = "mineR", "TDM.go.df")
TDM.go.df <- TDM.go.df[, !duplicated(colnames(TDM.go.df))]
lims <- c(1,2,2,3,4,5,6,7,7,8,10)
results <- list()
for(i in 1:length(data)){
if(!data[i] == ""){
results[[i]] <- mineR(doc = data[i],
terms = terms,
lims = lims,
syn = F,
object = T,
log = "/dev/null",
reader = "local",
output = "/dev/null",
term_tdm = TDM.go.df)
}
}
results <- do.call("rbind", results)
#### ------ CONTROLS ------- ###
control_results <- list()
for(i in 1:length(control)){
if(!control[i] == ""){
control_results[[i]] <- mineR(doc = control[i],
terms = terms,
lims = lims,
syn = F,
object = T,
log = "/dev/null",
reader = "local",
output = "/dev/null",
term_tdm = TDM.go.df)
}
}
control_results <- do.call("rbind", control_results)
save(results, file = "~/repos/mineR/data/results.Rda")
save(control_results, file = "~/repos/mineR/data/control_results.Rda")
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