bcdist {ecodist} | R Documentation |
Returns the Bray-Curtis (also known as Sorenson, 1 - percent similarity) pairwise distances for the objects in the data. It is duplicated by functionality within distance
but remains for backward compatibility and because it is substantially faster.
bcdist(x, rmzero = FALSE)
x |
matrix or data frame with rows as samples and columns as variables (such as species). Distances will be calculated for each pair of rows. |
rmzero |
If rmzero=TRUE, empty rows will be removed from the data before distances are calculated. Otherwise, the distance between two empty rows is assumed to be 0 (the default). |
This function returns a column-order lower-triangular distance matrix. The returned object has an attribute, Size, giving the number of objects, that is, nrow(x). The length of the vector that is returned is nrow(x)*(nrow(x)-1)/2.
Sarah Goslee
data(graze)
system.time(graze.bc <- bcdist(graze[, -c(1:2)]))
# equivalent to but much faster than:
system.time(graze.bc2 <- distance(graze[, -c(1:2)], "bray-curtis"))
all.equal(graze.bc, graze.bc2)