I am trying to generate what I can best describe as a pairwise distance matrix from a data frame containing the distance between two neighboring points. These are not Euclidean distances, they are essentially the distance between points on a shoreline, so the distance is not a straight line. I was able to generate a distance matrix in the package riverdist using geospatial data, but that only did the complete distance between the two points, I am now trying to do a subset of this distance between the points.
I have been looking for a way to do this for a little while and keep coming up empty handed. Any help would be much appreciated.
Here is an exampe:
I have this data:
mat <- matrix(
c(
3, #distance between 1 and 2
10, #distance between 2 and 3
7, #distance between 3 and 4
9 #distance between 4 and 5
),
nrow=4, ncol=1, dimnames = list(c("site1","site2","site3","site4"),c("dist")))
> mat
dist
site1 3
site2 10
site3 7
site4 9
And I would like to produce the following 'distance' matrix:
site1 site2 site3 site4 site5
site1 0
site2 3 0
site3 13 10 0
site4 20 17 7 0
site5 29 26 16 9 0
The original data might be better organized as follows for this task:
SiteA SiteB Dist
1 site1 site2 3
2 site2 site3 10
3 site3 site4 7
4 site4 site5 9
Any advice out there?
This is a cumulative distance, so take a cumulative sum and then do the distance calculation:
mat <- c(3,10,7,9)
dist(cumsum(c(0,mat)))
# 1 2 3 4
#2 3
#3 13 10
#4 20 17 7
#5 29 26 16 9