[R-sig-eco] subsetting lower triangle distance matrix based on variable in another object

[Jari Oksanen]

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: "<r-sig-ecology at r-project.org>" <r-sig-ecology at r-project.org>
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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