ConnMatTools - Tools for working with connectivity matrices
Collects several different methods for analyzing and working with connectivity matrices in R. Though primarily oriented towards marine larval dispersal, many of the methods are general and useful for terrestrial systems as well.
Installation of latest version via github
Once this is done, one can install the development version with:
Replace "master" with another branch, tag or commit to obtain a different version of the package.
Methods from the following publications are implemented in the package:
Jacobi, M. N., and Jonsson, P. R. 2011. Optimal networks of nature reserves can be found through eigenvalue perturbation theory of the connectivity matrix. Ecological Applications, 21: 1861–1870.
Jacobi, M. N., André, C., Döös, K., and Jonsson, P. R. 2012. Identification of subpopulations from connectivity matrices. Ecography, 35: 1004-1016.
Grüss, A., Kaplan, D. M., and Lett, C. 2012. Estimating local settler-recruit relationship parameters for complex spatially explicit models. Fisheries Research, 127-128: 34-39.
Kaplan, D. M., Botsford, L. W., and Jorgensen, S. 2006. Dispersal per recruit: An efficient method for assessing sustainability in marine reserve networks. Ecological Applications, 16: 2248-2263.
Kaplan DM, Cuif M, Fauvelot C, Vigliola L, Nguyen-Huu T, Tiavouane J and Lett C (in press) Uncertainty in empirical estimates of marine larval connectivity. ICES Journal of Marine Science. doi:10.1093/icesjms/fsw182.
White, J. W. 2010. Adapting the steepness parameter from stock-recruit curves for use in spatially explicit models. Fisheries Research, 102: 330-334.
Grüss A, Kaplan DM, Hart DR (2011) Relative Impacts of Adult Movement, Larval Dispersal and Harvester Movement on the Effectiveness of Reserve Networks. PLoS ONE 6:e19960
Beverton RJH, Holt SJ (1957) On the dynamics of exploited fish populations. H.M.S.O., London. 533 pp.