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.

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/4349/download?version=1
[ More InfoExpand ]


Information Workflow Components

Information Authors (1)
Information Titles (1)
Information Descriptions (1)
Information Dependencies (0)
Inputs (8)
Processors (14)
Beanshells (1)
Outputs (3)
Datalinks (28)
Coordinations (1)

Information Workflow Type

Taverna 2

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (5)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (13)

Log in to add Tags

Information Shared with Groups (1)

Information Featured In Packs (1)

Log in to add to one of your Packs

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.