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Description

The Damping ratio Workflow provides an environment to calculate the damping ratio of several matrices and plot them.

The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the population converges (Caswell 2001).

A detailed description of resampling methods to estimate confidence intervals for demographic estimates is described Caswell (2001, Chapter 12)

 

Biovel Portal Tutorial

To run this workflow in the Biovel Portal please refer to Tutorial Manual 

 

General

Name of the workflow and its myExperiment identifier

Name: Damping ratio Workflow

The workflow pack can be downloaded from myExperiment pack 632or only the workflow: myExperiment workflow 4317

Date, version and licensing

Last updated: 25th July 2014
Version: 2
Licensing: CC-BY-SA

How to cite this workflow

To report work that has made use of this workflow, please add the following credit acknowledgement to your research publication:

The input data and results reported in this publication (tutorial) come from data (Dr. Gerard Oostermeijer unpublished results and publication: Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 1996.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.) using BioVeL workflows and services (www.biovel.eu). Damping ratio workflow was run on <date of the workflow run>. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.

 

Scientific specifications

Keywords

Matrix Population Models, stage matrix, damping ratio, demography.

Scientific workflow description

The Damping ratio Workflow provides an environment to calculate the damping ratio of several matrices and plot them. The workflow accepts input data in a .txt format. The output is provided as a set of R results and a graphic plot. 

 

Technical specifications

The Workflow requires a Taverna Engine. The simplest way to install a Taverna Engine is to install Taverna Workbench. The workflow also requires an Rserve installation with popbio package installed. It is possible to setup the workflow to use a remote Rserve. However, instructions for installing a local Rserve are provided below.

Dependencies

Install R software in your computer. See: http://www.r-project.org/

  • Start R, and install package Rserve:
    • install.packages(“Rserve”)
  • Install package popbio
    • install.packages(“popbio”)
  • Local R Server: (Rserve) running at port 6311. See https://wiki.biovel.eu/x/3ICD for additional information.

How it works

First, open R, once R is opened, type library(Rserve) and press enter; then type Rserve() and press enter again. You will see then something similar to the following message:


After this operation you can open Taverna and run the workflow.

 

Bibliography

This workflow was created using and based on Packages ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011) and popdemo (Stott, Hodgson and Townley, 2013)

  • Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.
  • Jongejans E. & H. de Kroon. 2012. Matrix models. Chapter in Encyclopaedia of Theoretical Ecology (eds. Hastings A & Gross L) University of California, p415-423
  • 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.
  • 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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