R Dataset / Package HistData / Snow.deaths2
On this Picostat.com statistics page, you will find information about the Snow.deaths2 data set which pertains to John Snow's Map and Data on the 1854 London Cholera Outbreak. The Snow.deaths2 data set is found in the HistData R package. Try to load the Snow.deaths2 data set in R by issuing the following command at the console data("Snow.deaths2"). This may load the data into a variable called Snow.deaths2. If R says the Snow.deaths2 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("Snow.deaths2"). 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 Snow.deaths2 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 Snow.deaths2 R data set. The size of this file is about 12,474 bytes.
John Snow's Map and Data on the 1854 London Cholera Outbreak
The apocryphal story of the significance of Snow's map is that, by closing the Broad Street pump (by removing its handle), Dr. Snow stopped the epidemic, and demonstrated that cholera is a water borne disease. The method of contagion of cholera was not previously understood. Snow's map is the most famous and classical example in the field of medical cartography, even if it didn't happen exactly this way. (the apocryphal part is that the epidemic ended when the pump handle was removed.) At any rate, the map, together with various statistical annotations, is compelling because it points to the Broad Street pump as the source of the outbreak.
data(Snow.deaths) data(Snow.pumps) data(Snow.streets) data(Snow.polygons) data(Snow.dates)
The scale of the source map is approx. 1:2000. The
Of the data in the
One limitation of these data sets is the lack of exact street addresses. Another is the lack of any data that would serve as a population denominator to allow for a comparison of mortality rates in the Broad Street pump area as opposed to others. See Koch (2000), Koch (2004), Koch \& Denike (2009) and Tufte (1999), p. 27-37, for further discussion.
Tobler, W. (1994). Snow's Cholera Map,
The data in these files were first digitized in 1992 by Rusty Dodson of the NCGIA, Santa Barbara, from the map included in the book by John Snow: "Snow on Cholera...", London, Oxford University Press, 1936.
Koch, T. (2000). Cartographies of Disease: Maps, Mapping, and Medicine. ESRI Press. ISBN: 9781589481206.
Koch, T. (2004). The Map as Intent: Variations on the Theme of John Snow Cartographica, 39 (4), 1-14.
Koch, T. and Denike, K. (2009). Crediting his critics' concerns: Remaking John Snow's map of Broad Street cholera, 1854. Social Science \& Medicine 69, 1246-1251.
Snow, J. (1885). On the Mode of Communication of Cholera. London: John Churchill. http://www.ph.ucla.edu/epi/snow/snowbook.html.
Tufte, E. (1997). Visual Explanations. Cheshire, CT: Graphics Press.
data(Snow.deaths) data(Snow.pumps) data(Snow.streets) data(Snow.polygons) data(Snow.deaths)## Plot deaths over time require(lubridate) clr <- ifelse(Snow.dates$date < mdy("09/08/1854"), "red", "darkgreen") plot(deaths ~ date, data=Snow.dates, type="h", lwd=2, col=clr) points(deaths ~ date, data=Snow.dates, cex=0.5, pch=16, col=clr) text( mdy("09/08/1854"), 40, "Pump handle\nremoved Sept. 8", pos=4) ## draw Snow's map and dataSnowMap()# add polygons SnowMap(polygons=TRUE, main="Snow's Cholera Map with Pump Polygons")# zoom in a bit, and show density estimate SnowMap(xlim=c(7.5,16.5), ylim=c(7,16), polygons=TRUE, density=TRUE, main="Snow's Cholera Map, Annotated") ## re-do this the sp way... [thx: Stephane Dray]library(sp)# streets slist <- split(Snow.streets[,c("x","y")],as.factor(Snow.streets[,"street"])) Ll1 <- lapply(slist,Line) Lsl1 <- Lines(Ll1,"Street") Snow.streets.sp <- SpatialLines(list(Lsl1)) plot(Snow.streets.sp, col="gray") title(main="Snow's Cholera Map of London (sp)")# deaths Snow.deaths.sp = SpatialPoints(Snow.deaths[,c("x","y")]) plot(Snow.deaths.sp, add=TRUE, col ='red', pch=15, cex=0.6)# pumps spp <- SpatialPoints(Snow.pumps[,c("x","y")]) Snow.pumps.sp <- SpatialPointsDataFrame(spp,Snow.pumps[,c("x","y")]) plot(Snow.pumps.sp, add=TRUE, col='blue', pch=17, cex=1.5) text(Snow.pumps[,c("x","y")], labels=Snow.pumps$label, pos=1, cex=0.8)
Dataset imported from https://www.r-project.org.
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