R Dataset / Package HistData / Snow.deaths2

On this R-data 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. You can load the Snow.deaths2 data set in R by issuing the following command at the console data("Snow.deaths2"). This will 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 the library() command. 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

Description

The Snow data consists of the relevant 1854 London streets, the location of 578 deaths from cholera, and the position of 13 water pumps (wells) that can be used to re-create John Snow's map showing deaths from cholera in the area surrounding Broad Street, London in the 1854 outbreak. Another data frame provides boundaries of a tesselation of the map into Thiessen (Voronoi) regions which include all cholera deaths nearer to a given pump than to any other.

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.

Usage

data(Snow.deaths)
data(Snow.pumps)
data(Snow.streets)
data(Snow.polygons)
data(Snow.dates)

Format

Snow.deaths: A data frame with 578 observations on the following 3 variables, giving the address of a person who died from cholera. When many points are associated with a single street address, they are "stacked" in a line away from the street so that they are more easily visualized. This is how they are displayed on John Snow's original map. The dates of the deaths are not individually recorded in this data set.

case: Sequential case number, in some arbitrary, randomized order
x: x coordinate
y: y coordinate

Snow.pumps: A data frame with 13 observations on the following 4 variables, giving the locations of water pumps within the boundaries of the map.

pump: pump number
label: pump label: Briddle St Broad St ... Warwick
x: x coordinate
y: y coordinate

Snow.streets: A data frame with 1241 observations on the following 4 variables, giving coordinates used to draw the 528 street segment lines within the boundaries of the map. The map is created by drawing lines connecting the n points in each street segment.

street: street segment number: 1:528
n: number of points in this street line segment
x: x coordinate
y: y coordinate

Snow.polygons: A list of 13 data frames, giving the vertices of Thiessen (Voronoi) polygons containing each pump. Their boundaries define the area that is closest to each pump relative to all other pumps. They are mathematically defined by the perpendicular bisectors of the lines between all pumps. Each data frame contains:

x: x coordinate
y: y coordinate

Snow.deaths2: An alternative version of Snow.deaths correcting some possible duplicate and missing cases, as described in vignette("Snow_deaths-duplicates").

Snow.dates: A data frame of 44 observations and 3 variables from Table 1 of Snow (1855), giving the number of fatal attacks and number of deaths by date from Aug. 19 – Sept. 30, 1854. There are a total of 616 deaths represented in both columns attacks and deaths; of these, the date of the attack is unknown for 45 cases.

Details

The scale of the source map is approx. 1:2000. The (x, y) coordinate units are 100 meters, with an arbitrary origin.

Of the data in the Snow.dates table, Snow says, “The deaths in the above table are compiled from the sources mentioned above in describing the map; but some deaths which were omitted from the map on account of the number of the house not being known, are included in the table.”

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.

Source

Tobler, W. (1994). Snow's Cholera Map, http://www.ncgia.ucsb.edu/pubs/snow/snow.html; data files were obtained from http://ncgia.ucsb.edu/Publications/Software/cholera/, but these sites seem to be down.

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.

References

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.

Examples

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.

Attachments: csv, json

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