reducedConnMat {ConnMatTools} R Documentation

## Reduced connectivity matrix according to a set of subpopulations

### Description

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`.

### Usage

```reducedConnMat(subpops.lst, conn.mat)
```

### Arguments

 `subpops.lst` A list whose elements are vectors of indices for each subpopulation. If a vector of integers is given, then `subpopsVectorToList` is applied to convert it to a list of subpopulations. `conn.mat` A square connectivity matrix.

### Value

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.

### Author(s)

David M. Kaplan dmkaplan2000@gmail.com

### References

Jacobi, M. N., Andre, C., Doos, K., and Jonsson, P. R. 2012. Identification of subpopulations from connectivity matrices. Ecography, 35: 1004-1016.

See also `qualitySubpops`

### Examples

```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),
"subpopulations."))
pops <- subpopsVectorToList(chile.loco.split\$subpops[,chile.loco.split\$best.splits[]\$index])

reduce.loco <- reducedConnMat(pops,chile.loco)

sr <- selfRecruitment(reduce.loco)
lr <- localRetention(reduce.loco)
rlr <- relativeLocalRetention(reduce.loco)
```

[Package ConnMatTools version 0.3.5 Index]