︠dc3651a1-49cf-4b34-ba8e-a549d9194e85︠
%r

library("stringr")
library("reshape2")
library("plyr")
library("ggplot2")
library("MASS")
library("xtable")

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))
qplot(hod, freq, data = hod_all, geom = "line") + scale_y_continuous("Number of deaths", 
  labels = function(x) format(x, big.mark = ",")) + xlab("Hour of day")
︡2128738f-18ba-488f-81d1-e2b3e1b095a2︡{"html":"<table>\n<thead><tr><th></th><th scope=col>yod</th><th scope=col>mod</th><th scope=col>dod</th><th scope=col>hod</th><th scope=col>cod</th></tr></thead>\n<tbody>\n\t<tr><th scope=row>11938</th><td>2008</td><td>1   </td><td> 1  </td><td> 1  </td><td>B20 </td></tr>\n\t<tr><th scope=row>13937</th><td>2008</td><td>1   </td><td> 2  </td><td> 4  </td><td>I67 </td></tr>\n\t<tr><th scope=row>15937</th><td>2008</td><td>1   </td><td> 3  </td><td> 8  </td><td>I50 </td></tr>\n\t<tr><th scope=row>17937</th><td>2008</td><td>1   </td><td> 4  </td><td>12  </td><td>I50 </td></tr>\n\t<tr><th scope=row>19937</th><td>2008</td><td>1   </td><td> 5  </td><td>16  </td><td>K70 </td></tr>\n\t<tr><th scope=row>21937</th><td>2008</td><td>1   </td><td> 6  </td><td>18  </td><td>I21 </td></tr>\n\t<tr><th scope=row>23937</th><td>2008</td><td>1   </td><td> 7  </td><td>20  </td><td>I21 </td></tr>\n\t<tr><th scope=row>25937</th><td>2008</td><td>1   </td><td> 8  </td><td>NA  </td><td>K74 </td></tr>\n\t<tr><th scope=row>27937</th><td>2008</td><td>1   </td><td>10  </td><td> 5  </td><td>K74 </td></tr>\n\t<tr><th scope=row>29937</th><td>2008</td><td>1   </td><td>11  </td><td> 9  </td><td>I21 </td></tr>\n\t<tr><th scope=row>31937</th><td>2008</td><td>1   </td><td>12  </td><td>15  </td><td>I25 </td></tr>\n\t<tr><th scope=row>33937</th><td>2008</td><td>1   </td><td>13  </td><td>20  </td><td>R54 </td></tr>\n\t<tr><th scope=row>35937</th><td>2008</td><td>1   </td><td>15  </td><td> 2  </td><td>I61 </td></tr>\n\t<tr><th scope=row>37937</th><td>2008</td><td>1   </td><td>16  </td><td> 7  </td><td>I21 </td></tr>\n\t<tr><th scope=row>39937</th><td>2008</td><td>1   </td><td>17  </td><td>13  </td><td>I21 </td></tr>\n</tbody>\n</table>\n"}︡{"file":{"filename":"/tmp/tmp3j59pN.png","show":false,"text":null,"uuid":"364756e8-6403-4bca-9bbb-7dc1e1f486ee"},"once":false}︡{"html":"<img src=\"/blobs//tmp/tmp3j59pN.png?uuid=364756e8-6403-4bca-9bbb-7dc1e1f486ee\" smc-image-scaling=\"0.5\" />"}︡{"done":true}︡