Simulate stochastic growth from a sequence of matrices

Created: 2014-07-30 12:39:04      Last updated: 2014-08-14 12:13:05

The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices.

This workflow is based on the popbio package (script: stoch.projection - Simulate stochastic growth from a sequence of matrices, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.3 (Morris and Doak 2002). For more details of the analysis see: Exploring population growth in a variable environment with computer simulations (Morris and Doak 2002, pag: 229-233 and Caswell 2001, Chapter 14).

Outputs:

• Equal selection data • Stochastic projection • Unequal selection data

We use Gentiana pneumonanthe only as example how to run this workflow.

This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.

This workflow was created using and based on Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ==================================================================================

Literature

Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.

Oostermeijer J.G.B., M.L. Brugman; E.R. de Boer; H.C.M. Den Nijs. 1996. Temporal and Spatial Variation in the Demography of Gentiana pneumonanthe, a Rare Perennial Herb. The Journal of Ecology, Vol. 84(2): 153-166.

Morris, W. F., and D. F. Doak. 2002. Quantitative conservation biology: Theory and practice of population viability analysis. Sinauer, Sunderland, Massachusetts, USA. 480 pages

Stubben, C & B. Milligan. 2007. Estimating and Analysing Demographic Models Using the popbio Package in R. Journal of Statistical Software 22 (11): 1-23

Stubben, C., B. Milligan, P. Nantel. 2011. Package ‘popbio’. Construction and analysis of matrix population models. Version 2.3.1.

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