2018-02-12-203646.sagews

%r

library("ggplot2")
library("MASS")

if (!file.exists("deaths.rds")) {
  ## from https://github.com/hadley/mexico-mortality/raw/master/deaths/deaths08.csv.bz2
  deaths <- read.csv("deaths08.csv.bz2")
  unlink("deaths08.csv.bz2")
  deaths$hod[deaths$hod == 99] <- NA
  deaths$hod[deaths$hod == 24] <- 0
  deaths$hod[deaths$hod == 0] <- NA
  deaths$hod <- as.integer(deaths$hod)
  deaths <- arrange(deaths, yod, mod, dod, hod, cod)
  deaths <- deaths[c("yod", "mod", "dod", "hod", "cod")]  
  saveRDS(deaths, "deaths.rds")
}

deaths <- readRDS("deaths.rds")

ok <- subset(deaths, yod == 2008 & mod != 0 & dod != 0)
xtable(ok[c(1, 1:14 * 2000), c("yod", "mod", "dod", "hod", "cod")], "raw.tex")

codes <- read.csv("icd-main.csv")
codes$disease <- sapply(codes$disease, function(x) str_c(strwrap(x, width = 30), 
  collapse = "\n"))
names(codes)[1] <- "cod"
codes <- codes[!duplicated(codes$cod), ]

# Display overall hourly deaths
hod_all <- subset(count(deaths, "hod"), !is.na(hod))

Warning message in file(file, "rt"): “cannot open file 'deaths08.csv.bz2': No such file or directory”Error in file(file, "rt"): cannot open the connection Traceback: 1. read.csv("deaths08.csv.bz2") # at line 7 of file <text> 2. read.table(file = file, header = header, sep = sep, quote = quote, . dec = dec, fill = fill, comment.char = comment.char, ...) 3. file(file, "rt")