R: John Snow's map and data on the 1854 London Cholera outbreak

Snow	R Documentation

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 apochrophal 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. 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)

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 recorded.

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 data frame with 54 observations on the following 3 variables, giving 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. The outlines of these polygons can be drawn by connecting all points sequentially starting at each value of start==0. Here, each line segment consists of two sequential points.

start: line start indicator. The value start==0 indicates the start of a new line, including all following points having start==1
x: x coordinate
y: y coordinate

Details

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

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. A third is the lack of dates of death that could allow analysis of the time course of the outbreak. 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/

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.

Tufte, E. (1997). Visual Explanations. Cheshire, CT: Graphics Press.

Examples

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

## draw a rough approximation to Snow's map and data

# define some funtions to make the pieces re-usable
Sdeaths <- function(col="red", pch=15, cex=0.6) {
		# make sure that the plot limits include all the other stuff
   plot(Snow.deaths[,c("x","y")], col=col, pch=pch, cex=cex, 
   	xlab="", ylab="", xlim=c(3,20), ylim=c(3,20),
   	main="Snow's Cholera Map of London")
	}
# function to plot and label the pump locations
Spumps <- function(col="blue", pch=17, cex=1.5)  {
   points(Snow.pumps[,c("x","y")], col=col, pch=pch, cex=cex)
   text(Snow.pumps[,c("x","y")], labels=Snow.pumps$label, pos=1, cex=0.8)
}

# function to draw the streets 
Sstreets <- function(col="gray") {
	slist <- split(Snow.streets[,c("x","y")],as.factor(Snow.streets[,"street"]))
	invisible(lapply(slist, lines, col=col))
}

# draw a scale showing distance in meters in upper left
mapscale <- function(xs=3.5, ys=19.7) {
   scale <- matrix(c(0,0, 4,0, NA, NA), nrow=3, ncol=2, byrow=TRUE)
   colnames(scale)<- c("x","y")
	# tick marks
   scale <- rbind(scale, expand.grid(y=c(-.1, .1, NA), x=0:4)[,2:1])
   lines(xs+scale[,1], ys+scale[,2])
	# value and axis labels
   stext <- matrix(c(0,0, 2,0, 4,0, 4, 0.1), nrow=4, ncol=2, byrow=TRUE)
   text(xs+stext[,1], ys+stext[,2], labels=c("0", "2", "4", "100 m."), pos=c(1,1,1,4), cex=0.8)
}

# draw the map with the pieces
Sdeaths()
Spumps()
Sstreets()
mapscale()


# draw the Thiessen polygon boundaries
starts <- which(Snow.polygons$start==0)
for(i in 1:length(starts)) {
	this <- starts[i]:(starts[i]+1)
	lines(Snow.polygons[this,2:3], col="blue", lwd=2, lty=2)
	}


## overlay bivariate kernel density contours of deaths
Sdeaths()
Spumps()
Sstreets()
mapscale()
require(KernSmooth)
kde2d <- bkde2D(Snow.deaths[,2:3], bandwidth=c(0.5,0.5))
contour(x=kde2d$x1, y=kde2d$x2,z=kde2d$fhat, add=TRUE)

## 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)