R Dataset / Package HistData / Cholera
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| dataset-66785.csv | 3.48 KB |
| Documentation |
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On this Picostat.com statistics page, you will find information about the Cholera data set which pertains to William Farr's Data on Cholera in London, 1849. The Cholera data set is found in the HistData R package. Try to load the Cholera data set in R by issuing the following command at the console data("Cholera"). This may load the data into a variable called Cholera. If R says the Cholera data set is not found, you can try installing the package by issuing this command install.packages("HistData") and then attempt to reload the data with library("HistData") followed by data("Cholera"). Perhaps strangley, if R gives you no output after entering a command, it means the command succeeded. If it succeeded you can see the data by typing Cholera at the command-line which should display the entire dataset. If you need to download R, you can go to the R project website. You can download a CSV (comma separated values) version of the Cholera R data set. The size of this file is about 3,567 bytes. William Farr's Data on Cholera in London, 1849DescriptionIn 1852, William Farr, published a report of the Registrar-General on mortality due to cholera in England in the years 1848-1849, during which there was a large epidemic throughout the country. Farr initially believed that cholera arose from bad air ("miasma") associated with low elevation above the River Thames. John Snow (1855) later showed that the disease was principally spread by contaminated water. This data set comes from a paper by Brigham et al. (2003) that analyses some tables from Farr's report to examine the prevalence of death from cholera in the districts of London in relation to the available predictors from Farr's table. Usagedata("Cholera")
FormatA data frame with 38 observations on the following 15 variables.
DetailsThe supply of The data frame is sorted by increasing elevation above the high water mark. SourceBingham P., Verlander, N. Q., Cheal M. J. (2004). John Snow, William Farr and the 1849 outbreak of cholera that affected London: a reworking of the data highlights the importance of the water supply. Public Health, 118(6), 387-394, Table 2. (The data was kindly supplied by Neville Verlander, including additional variables not shown in their Table 2.) ReferencesRegistrar-General (1852). Report on the Mortality of Cholera in England 1848-49, W. Clowes and Sons, for Her Majesty's Stationary Office. Written by William Farr. https://ia800309.us.archive.org/22/items/b24751297/b24751297.pdf The relevant tables are at pages clii – clvii. See Also
Examples
data(Cholera)# plot cholera deaths vs. elevation
plot(cholera_drate ~ elevation, data=Cholera,
pch=16, cex.lab=1.2, cex=1.2,
xlab="Elevation above high water mark (ft)",
ylab="Deaths from cholera in 1849 per 10,000")# Farr's mortality ~ 1/ elevation law
elev <- c(0, 10, 30, 50, 70, 90, 100, 350)
mort <- c(174, 99, 53, 34, 27, 22, 20, 6)
lines(mort ~ elev, lwd=2, col="blue")# better plots, using car::scatterplot
library(car)# show separate regression lines for each water supply
scatterplot(cholera_drate ~ elevation | water, data=Cholera,
smooth=FALSE, pch=15:17, lwd=2, id.n=2,
labels=sub(",.*", "", Cholera$district),
col=c("red", "darkgreen", "blue"),
legend.coords="topright", legend.title="Water supply",
xlab="Elevation above high water mark (ft)",
ylab="Deaths from cholera in 1849 per 10,000")scatterplot(cholera_drate ~ poor_rate | water, data=Cholera,
smooth=FALSE, pch=15:17, lwd=2, id.n=2,
labels=sub(",.*", "", Cholera$district),
col=c("red", "darkgreen", "blue"),
legend.coords="topleft", legend.title="Water supply",
xlab="Poor rate per pound of house value",
ylab="Deaths from cholera in 1849 per 10,000")
# fit a logistic regression model a la Bingham etal.
fit <- glm( cbind(cholera_deaths, popn) ~
water + elevation + poor_rate + annual_deaths +
pop_dens + persons_house,
data=Cholera, family=binomial)
summary(fit)# odds ratios
cbind( OR = exp(coef(fit))[-1], exp(confint(fit))[-1,] )if (require(effects)) {
eff <- allEffects(fit)
plot(eff)
}
-- Dataset imported from https://www.r-project.org. |
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