Kendra,
Subset a matrix an convert to dist. You must subset both rows and columns in
the same way, and therefore you must use subsetting index instead of a subset()
function. Let k be a vector that is TRUE for selected items;
as.dist(yoursymmetricmatrix[k, k]) is what you are looking for.
Cheers, Jari Oksanen
alkuperäinen viesti
Lähettäjä: Mitchell, Kendra
Lähetetty: 31.07.2013, 02:38
Vastaanottaja: ""
Aihe: [R-sig-eco] subsetting lower triangle distance matrix based on variable
in another object
I have a number of dissimilarity matrices built in another program that I'd
like to subset then run NMS.
#read in distance matrix
b_bc03 <-data.matrix(read.table("bac_final.an.thetayc.0.03.lt.ave.dist",
row.names=1, header=T, fill=TRUE)) # creates a 736x736 double matrix
#read in environmental variables
bac_env<-read.csv("bac_samples.csv", row.names=1, header=T) # 736 obs. of 6
variables
#The only way that I've figured out how to subset a lt matrix is to convert to
dist object first
bc_dist<-as.dist(b_bc03) # dist[27048]
tx_dist<-subset(bc_dist, bac_env$zone=="TX") # numeric[54316]
Here is where it falls apart, the subset doesn't keep the labels, just the
values so I can't convert it back to a distance matrix. I've looked through
ecodist but can't find anyway in that package to select only certain samples.
Help please?
thanks
Kendra
--
Kendra Maas Mitchell, Ph.D.
Post Doctoral Research Fellow
University of British Columbia
604-822-5646
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