Snapshot of the Pack: Matrix Population Model construction and analysis pack

Description

This pack contains a workflow, a file and documentation (tutorial to run the workflow).

The Matrix Population Models Workflow provides an environment for create a stage-matrix with no density dependence and perform several analyses on it.

Analyses:

• Eigen analysis.
• Age specific survival.
• Generation time (T).
• Net reproductive rate (Ro).
• Transient Dynamics.
• Bootstrap of observed census transitions (Confidence intervals of λ).
• Survival curve
• Keyfitz’s Δ
• Cohen’s cumulative distance

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) and popdemo (Stott, Hodgson and Townley, 2013)

References
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1. Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.
2. Cohen, J.E. 1979. The cumulative distance from an observed to a stable age structure. SIAM Journal on Applied Mathematics, 36:169–175.
3. de Kroon, H. J., A. Plaiser, J. van Groenendael, and H. Caswell. 1986. Elasticity: The relative contribution of demographic parameters to population growth rate. Ecology 67: 1427-1431.
4. Horvitz, C., D.W. Schemske, and Hal Caswell. 1997. The relative "importance" of life-history stages to population growth: Prospective and retrospective analyses. In S. Tuljapurkar and H. Caswell. Structured population models in terrestrial and freshwater systems. Chapman and Hall, New York.
5. Jongejans E. & H. de Kroon. 2012. Matrix models. Chapter in Encyclopaedia of Theoretical Ecology (eds. Hastings A & Gross L) University of California, p415-423
6. Keyfitz, N. 1968. Introduction to the Mathematics of Populations. Addison-Wesley, Reading, MA, USA.
7. Mesterton-Gibbons, M. 1993. Why demographic elasticities sum to one: A postscript to de Kroon et al. Ecology 74: 2467-2468.
8. 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.
9. Stott, I., S. Townley and D.J. Hodgson 2011. A framework for studying transient dynamics of population projection matrix models. Ecology Letters 14: 959–970
10. Stott, I., D.J. Hodgson and S. Townley. 2013. popdemo: Provides Tools For Demographic Modelling Using Projection Matrices. Version 0.1-3.
11. Stubben, C & B. Milligan. 2007. Estimating and Analysing Demographic Models Using the popbio Package in R. Journal of Statistical Software 22 (11): 1-23
12. Stubben, C., B. Milligan, P. Nantel. 2011. Package ‘popbio’. Construction and analysis of matrix population models. Version 2.3.1
13. van Groenendael, J., H. de Kroon, S. Kalisz, and S. Tuljapurkar. 1994. Loop analysis: Evaluating life history pathways in population projection matrices. Ecology 75: 2410-2415.
14. Williams, J.L., M.M. Ellis, M.C. Bricker, J.F. Brodie and E.W. Parsons. 2011. Distance to stable stage distribution in plant populations and implications for near-term population projections. Journal of Ecology, 99, 1171–1178.