Pack: Matrix Population Model construction and analysis pack

Description:

This is a .txt file of four years demographic data 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 Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysis v19 (http://www.myexperiment.org/workflows/3684.html)

The input data has to have the format of a table containing the demographic data on a series of individuals in two years. Each individual has a table row for each year and is identified by a number (plant column in example). For the year specified in the column 'year', each individual has a certain life stage ('stage'). The stage codes can be chosen by the user, but they have to be specified with a string (limit to characters) . The stages names cannot be longer than 8 characters. For all individuals, the number of offspring is specified in a chosen way (in the example, 'repstr' gives the number of flowers/fruits for each plant. In the example, it can be seen that only generative adults (stage=G) had flowers. Individuals without offspring have to be indicated by filling in '0' in this column, which cannot have empty cells. The column 'recruitment' specifies those individuals that are new in the second year census to the population by means of a code. In the example, 'RS' is a new seedling, and 'RJ' a new juvenile plant. As can be seen in the example, no code is needed in this column for individuals that were already present.

This file allow users to run population modelling workflow.

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.

Description:

This is a .txt file of one year demographic data 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 Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysis v19 (http://www.myexperiment.org/workflows/3684.html)

The input data (a .txt-file) has to have the format of a table containing the demographic data on a series of individuals in two years. Each individual has a table row for each year and is identified by a number (plant column in example). For the year specified in the column 'year', each individual has a certain life stage ('stage'). The stage codes can be chosen by the user, but they have to be specified with a string (limit to characters) . The stages names cannot be longer than 8 characters. For all individuals, the number of offspring is specified in a chosen way (in the example, 'repstr' gives the number of flowers/fruits for each plant. In the example, it can be seen that only generative adults (stage=G) had flowers. Individuals without offspring have to be indicated by filling in '0' in this column, which cannot have empty cells. The column 'recruitment' specifies those individuals that are new in the second year census to the population by means of a code. In the example, 'RS' is a new seedling, and 'RJ' a new juvenile plant. As can be seen in the example, no code is needed in this column for individuals that were already present.

If you use the file please quote as:<o:p></o:p>

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.

Description:

The Matrix Population Models Workflow provides an environment to create stage-matrices with no density dependence and to perform several analyses on them:

- 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.

If multiple year transitions are selected, the results will be ordered by year.

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 construction and analyses 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