Description Usage Arguments Value Author(s) References See Also Examples
View source: R/jacobi_etal_2012.R
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 [email protected]
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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