Create a gist now

Instantly share code, notes, and snippets.

thin.max.R, a function for rarefying point data in any number of dimensions
# Function to rarefy point data in any number of dimensions. The goal here is to
# take a large data set and reduce it in size in such a way as to approximately maximize the
# difference between points. For instance, if you have 2000 points but suspect a lot of
# spatial autocorrelation between them, you can pass in your data frame, the names (or indices)
# of the lat/lon columns, and the number 200, and you get back 200 points from your original data
# set that are chosen to be as different from each other as possible given a randomly chosen
# starting point
# Input is:
# x, a data frame containing the columns to be used to calculate distances along with whatever other data you need
# cols, a vector of column names or indices to use for calculating distances
# npoints, the number of rarefied points to spit out
# e.g., thin.max(, c("latitude", "longitude"), 200)
thin.max <- function(x, cols, npoints){
#Create empty vector for output
inds <- vector(mode="numeric")
#Create distance matrix
this.dist <- as.matrix(dist(x[,cols], upper=TRUE))
#Draw first index at random
inds <- c(inds, as.integer(runif(1, 1, length(this.dist[,1]))))
#Get second index from maximally distant point from first one
#Necessary because apply needs at least two columns or it'll barf
#in the next bit
inds <- c(inds, which.max(this.dist[,inds]))
while(length(inds) < npoints){
#For each point, find its distance to the closest point that's already been selected
min.dists <- apply(this.dist[,inds], 1, min)
#Select the point that is furthest from everything we've already selected
this.ind <- which.max(min.dists)
#Get rid of ties, if they exist
if(length(this.ind) > 1){
print("Breaking tie...")
this.ind <- this.ind[1]
inds <- c(inds, this.ind)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment