Pack: Matrix Population Models analyses pack

Description:

The Matrix Population Models Workflow provides an environment to perform several analyses on a stage-matrix with no density dependence:

- Eigen analysis; - Age specific survival; - Generation time (T); - Net reproductive rate (Ro); - Transient Dynamics; - Bootstrap of observed census transitions (Confidence intervals of lambda); - Survival curve; - Keyfitz delta; - Cohen's cumulative distance.

This workflow requires an instance of Rserve on localhost

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 uses R packages ‘popbio’ (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011) and 'popdemo' (Stott, Hodgson and Townley 2013).

References:

Caswell, H. 1986. Life cycle models for plants. Lectures on Mathematics in the Life Sciences 18: 171-233.

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

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.

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.

Jongejans E. & H. de Kroon. 2012. Matrix models. Chapter in Encyclopaedia of Theoretical Ecology (eds. Hastings A & Gross L) University of California, p415-423

Mesterton-Gibbons, M. 1993. Why demographic elasticities sum to one: A postscript to de Kroon et al. Ecology 74: 2467-2468.

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.

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

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

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.

Description:

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.

The Matrix Population Models analysis Workflow provides an environment to perform several analyses on a stage-matrix with no density dependence.

Analyses:

• Eigen analysis.

• Age specific survival.

• Generation time (T).

• Net reproductive rate (Ro).

• Transient Dynamics.

• Resample a projection matrix (Confidence intervals of λ).

• Survival curve

• Keyfitz’s Δ

• Cohen’s cumulative distance

Description:

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).

This file allow users to run the workflow Matrix Population Model analysis v10 (http://www.myexperiment.org/workflows/3686.html)

If you use the file please quote as:

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, 84: 153-166.