Tools for hotspot mapping in R
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README.md

Hotspot Mapping in R

Simple hotspot mapping. Currently based on the distance-based-mapping algorithm of Jeffery et al. This package is functional but under active development.

Requires ggplot2.

To install, make sure you have the devtools package installed and loaded and run:

require(devtools)
install_github("jzelner/hotspotr")

Demo

The following is a quick demo showing how a simple hotspot map can be generated from a set a dataset consisting of a set of (x,y) points and a vector of case/control designations labeled z.

Import hotspotr:

require(hotspotr)

Generate a set of (x,y) points in the unit square:

x <- runif(1000)
y <- runif(1000)

plot of chunk unnamed-chunk-4

Using the random_hotspot function in hotspotr, place an area of increased risk in the center of the square. In this case, we'll select an area covering the middle 30% of the unit square where 80% of individuals within this are are cases and only 20% outside of it are cases, for a relative risk of 4:

hs <- random_hotspot(x, y, 0.3, 0.8, 0.2)

Create a new data frame with case points labeled as z = 1 and controls as z = 0:

hs <- data.frame(x = x, y = y, z = as.factor(hs[["z"]]))

We can plot this and see anecdotally that there is a greater density of cases (represented by triangles) in the center:

plot of chunk unnamed-chunk-7

We can verify whether this area of increased density is statistically significant using the hotspot_map function in hotspotr.

The first argument to hotspot_map is the data frame with columns x, y, and z with x and y coordinates and case/control designations, respectively. The second argument is the density estimation method to use (currently only the distance-based-mapping method of Jeffery et al. is supported (as the function dbm_score_rr).

User-defined density functions can easily be written. All that is required is a function of the form fn(hs) that returns a density measure at each (x,y) point in the hs dataframe. p specifies the width of the smoothing window, and color_samples specifies the number of random permutations of case/control designations to use when generating the color scale for the map:

hm <- hotspot_map(hs, dbm_score_rr, p = 0.03, color_samples = 100, pbar = FALSE)

We can then plot the resulting map and see that in fact the area at the center of the map represents a likely hotspot:

plot(hm)

plot of chunk unnamed-chunk-9