Transient Dynamics.

Created: 2012-11-02 14:54:47 Last updated: 2014-07-31 10:17:38

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This workflow produces plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.

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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 based on Package ‘popbio’ in R.

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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For further details see:

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

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

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (6)

Name	Description
stage_matrix_file	Here comes the stage matrix without the stage names (as you see in the example). It should be provied as a txt-file. Example from: J. Gerard B. Oostermeijer; 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.
stages	Stage input port: Here come the names of the stages or categories of the input matrix. It is very important that the stages names are not longer than 8 characters. The name of the stages must be added one by one. The respective name stages must be filled one by one. First press add value, fill a stage name (not longer than 8 characters) and press enter, then press add value and fill once again the next stage name, repeat the action until you have fill all the stages names. In the following example, the matrix has 5 stages or categories: S J V G D S 0.0000 0.0000 0.0000 7.6660 0.0000 J 0.0579 0.0100 0.0000 8.5238 0.0000 V 0.4637 0.8300 0.9009 0.2857 0.8604 G 0.0000 0.0400 0.0090 0.6190 0.1162 D 0.0000 0.0300 0.0180 0.0000 0.0232 The stages of this matrix are called: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D
short_term_years	This value will be use to plot a graph that shows a simulation of the number of individuals per stage a few years after the study. This value represents the years of axis X of the output graph: Stage_Vector_Plot_Short_Term.
abundances	The initial abundance on the field or the observed structure per stage. Gentiana pneumonanthe stage matrix has 5 stages with its respective abundance: stage abundance 1 S (seedlings) 69 2 J (Juveniles) 100 3 V (vegetative) 111 4 G (reproductive individuals) 21 5 D (dormant plants) 43 The respective abundance numbers must be filled one by one. Fill a number and then press enter, then press add value and fill again the next number, repeat the action until you have fill all the abundance values.
long_term_years	This value contains the maximum number of iterations in the transient dynamic analysis, and hence the total number of years for the long term graphs. The number of years will be used in two output graphs: 1) StageVectorPlotLongTermProportional: the proportion of individuals per stage in the long term. 2) StageVectorPlotLongTermLogarithmic: the number of individuals per stage in the long term.
plot_title	Here come the title of the plots. It can be the name of the species or the name of the place where the research has been conducted.

Processors (2)

Name	Type	Description
StageMatrix_ReadFromFile	rshell	Script stageData <- read.table(stageMatrixFile) stageMatrix <- as.matrix(stageData) dimnames(stageMatrix) <- list(stages,stages) R Server localhost:6311
TransientDynamics	workflow

Beanshells (0)

Outputs (5)

Name	Description
damping_ratio	The ratio between the dominant eigenvalue and the second highest eigenvalue of a transition matrix is called the damping ratio, and it 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 damping ratio, the quicker the population converges) (Caswell 2001, p. 95). High damping ratios tell you that the dominant stable stage distribution is reached fairly soon.
pop_projection	Population projection: Lambda or dominant eigenvalue: The population will be stable, grow or decrease at a rate given by lambda: e.g.: λ = 1 (population is stable), λ > 1 (population is growing) and finally λ < 1 (population is decreasing). e.g. The projected population growth rate (λ) is 1.237, meaning that the population is projected to increase with 23% per year if these model parameters remain unchanged. The stable stage distribution (stable.stage): It is the proportion of the number of individuals per stage and it is given by (w). Stage vector (stage.vectors): it is the projection of the number of individuals per category per year in the long term, the long term was stipulated in the input port (long term years) (e.g. 50 years). Population sizes (pop.sizes): it is the total population size per year in the long-term (e.g. 50 years). Population change (pop.changes): are the lambda values per year in the long-term (e.g. 50 years).
stage_vector_plot_short_term	It is a plot that charts the number of individuals per stage vs years in the short-term (e.g. 5, 10 years). This value (5 or 10 years) is related to the short-term years input value.
stage_vector_plot_long_term_proportional	It is a plot which shows the stable stage distribution (w) of the analyzed matrix or in other words It plots the proportion of individuals per stage in the population.
stage_vector_plot_long_term_logarithmic	It is a plot that charts the number of individuals in a logarithmic scale per stage vs years in the long-term (e.g. 50 years). This value (50 years) is related to the long_term_years input value.

Datalinks (12)

Source	Sink
stages	StageMatrix_ReadFromFile:stages
stage_matrix_file	StageMatrix_ReadFromFile:stageMatrixFile
StageMatrix_ReadFromFile:stageMatrix	TransientDynamics:stage_matrix
short_term_years	TransientDynamics:short_term_years
abundances	TransientDynamics:abundances
long_term_years	TransientDynamics:long_term_years
plot_title	TransientDynamics:plot_title
TransientDynamics:damping_ratio	damping_ratio
TransientDynamics:pop_projection	pop_projection
TransientDynamics:stage_vector_plot_short_term	stage_vector_plot_short_term
TransientDynamics:stage_vector_plot_long_term_proportional	stage_vector_plot_long_term_proportional
TransientDynamics:stage_vector_plot_long_term_logarithmic	stage_vector_plot_long_term_logarithmic

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Taverna 2

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Maria Paula Balcazar-Vargas

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Version History

In chronological order:

Transient Dynamics.

Created by Maria Paula Balcazar-Vargas on Friday 02 November 2012 14:54:46 (UTC)
Transient Dynamics.

Created by Maria Paula Balcazar-Vargas on Friday 25 July 2014 12:19:03 (UTC)

Revision comment:

Changes:
Print values with 16 digits
Liberate sink memory
Change default inputs Stages [S,J,V,GD] and Abundances [69,100,111,21,43]
Change springer version for localhost
Transient Dynamics.

Created by Maria Paula Balcazar-Vargas on Thursday 31 July 2014 10:17:38 (UTC)

Revision comment:

In this version, an error with the Rscript to print the graphic is corrected.