analysis/word_clouds.R

In sbfnk/flusurvey: Packages for analysing flusurvey data

library(RColorBrewer)
library(data.table)
library(wordcloud)
library(plotrix)

dt <- readRDS("flusurvey_201213.rds")

## lwords =
##   c("Fever", "Watery eyes", "Runny nose", "Sneezing", "Sore throat", "Cough",
##   "Coloured sputum", "Headache", "Muscle pain", "Chest pain", "Feeling tired",
##   "Loss of appetite", "Nausea", "Vomiting", "Diarrhoea", "Other", "Chills",
##   "Shortness of breath", "Stomach ache")

lwords =
    c("Fever", "Chills", "Runny nose", "Sneezing", "Sore throat", "Cough",
      "Shortness of Breath", "Headache", "Joint pain", "Chest pain",
      "Feeling tired", "Loss of appetite", "Phlegm", "Watery eyes", "Nausea",
      "Vomiting", "Diarrhoea", "Stomach ache")

#df <- read.csv('ill.csv', header=T, sep=',')
## df$date <- as.Date(df$date, "%Y/%m/%d")
df <- dt[, c(1,2,166:183), with = F]
for (symptom in names(df)[3:21]) {
    df[,eval(symptom) := as.numeric(get(symptom) == "t"), with = F]
}

m <- data.matrix(df)
m_fever <- data.matrix(subset(df, fever==1))

counts <- rep(0, 18)
counts_fever <- rep(0, 17)

for (i in 1:18) {
  counts[i] <- sum(m[,i+2])
}

for (i in 1:17) {
  counts_fever[i] <- sum(m_fever[,i+3])
}

colpal <- colorRampPalette(c("blue", "red"))

pdf('word_cloud.pdf')
wordcloud(lwords,counts_fever, rot.per=.35, random.order = F, col = colpal(17))
## plot(x, y, type = "n", axes = FALSE)
## tagcloudspiral(lwords, counts_fever, col = rev(brewer.pal(9, "PuBu"))[1:5], maxcex=5)
dev.off()

png('word_cloud.png')
wordcloud(lwords,counts_fever, rot.per=.35, random.order = F, col = colpal(17))
## plot(x, y, type = "n", axes = FALSE)
## tagcloudspiral(lwords, counts_fever, col = rev(brewer.pal(9, "PuBu"))[1:5], maxcex=5)
dev.off()

pdf('word_cloud_all.pdf')
wordcloud(lwords,counts, rot.per=.35, random.order = F, col = colpal(18))
## plot(x, y, type = "n", axes = FALSE)
## tagcloudspiral(lwords, counts, col = rev(brewer.pal(9, "PuBu"))[1:5], maxcex=5)
dev.off()

png('word_cloud_all.png')
wordcloud(lwords,counts, rot.per=.35, random.order = F, col = colpal(18))
## plot(x, y, type = "n", axes = FALSE)
## tagcloudspiral(lwords, counts, col = rev(brewer.pal(9, "PuBu"))[1:5], maxcex=5)
dev.off()

## slices <- 5

## df_sorted$date_cut <- cut(df_sorted$date, slices)
## m_counts <- matrix(0,ncol=length(lwords),nrow=slices)
## m_counts_fever<- matrix(0,ncol=length(lwords),nrow=slices)

## for (i in 1:slices) {
##   for (j in 1:length(lwords)) {
##     m_counts[i,j] <- sum(subset(df_sorted, date_cut==levels(df_sorted$date_cut)[i])[,j+2])
##     m_counts_fever[i,j] <- sum(subset(df_sorted,
##                                       date_cut==levels(df_sorted$date_cut)[i] &
##                                       Fever == 1)[,j+2])
##   }
## }

## for (i in 1:slices) {
##   pdf(paste("word_cloud_all_", i, ".pdf", sep=""))
##   plot(x, y, type = "n", axes = FALSE)
##   tagcloudspiral(lwords, m_counts[i,], col = rev(brewer.pal(9, "PuBu"))[1:5],
##                  maxcex=max(m_counts[i,])/max(m_counts)*5)
##   dev.off()
##   png(paste("word_cloud_all_", i, ".png", sep=""))
##   plot(x, y, type = "n", axes = FALSE)
##   tagcloudspiral(lwords, m_counts[i,], col = rev(brewer.pal(9, "PuBu"))[1:5],
##                  maxcex=max(m_counts[i,])/max(m_counts)*5)
##   dev.off()
##   pdf(paste("word_cloud_", i, ".pdf", sep=""))
##   plot(x, y, type = "n", axes = FALSE)
##   tagcloudspiral(lwords, m_counts_fever[i,], col = rev(brewer.pal(9, "PuBu"))[1:5],
##                  maxcex=max(m_counts_fever[i,])/max(m_counts_fever)*5)
##   dev.off()
##   png(paste("word_cloud_", i, ".png", sep=""))
##   plot(x, y, type = "n", axes = FALSE)
##   tagcloudspiral(lwords, m_counts_fever[i,], col = rev(brewer.pal(9, "PuBu"))[1:5],
##                  maxcex=max(m_counts_fever[i,])/max(m_counts_fever)*5)
##   dev.off()
## }