Reduces a connectivity matrix based on a set of subpopulations. If there are
N subpopulations, then the reduced matrix will have dimensions NxN. The
reduced matrix will be ordered according to the order of subpopulations in
subpops.lst
.
1  reducedConnMat(subpops.lst, conn.mat)

subpops.lst 
A list whose elements are vectors of indices for each
subpopulation. If a vector of integers is given, then

conn.mat 
A square connectivity matrix. 
A reduced connectivity matrix. The sum of all elements of this reduced connectivity matrix will be equal to the sum of all elements of the original connectivity matrix.
David M. Kaplan dmkaplan2000@gmail.com
Jacobi, M. N., Andre, C., Doos, K., and Jonsson, P. R. 2012. Identification of subpopulations from connectivity matrices. Ecography, 35: 10041016.
See also qualitySubpops
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  library(ConnMatTools)
data(chile.loco)
num < prod(dim(chile.loco)) / sum(chile.loco)
betas < betasVectorDefault(n=num,steps=4)
chile.loco.split < optimalSplitConnMat(chile.loco,normalize.cols=FALSE,
betas=betas)
# Extra 3rd division
print(paste("Examining split with",names(chile.loco.split$best.splits)[1],
"subpopulations."))
pops < subpopsVectorToList(chile.loco.split$subpops[,chile.loco.split$best.splits[[1]]$index])
reduce.loco < reducedConnMat(pops,chile.loco)
sr < selfRecruitment(reduce.loco)
lr < localRetention(reduce.loco)
rlr < relativeLocalRetention(reduce.loco)

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