Stages vectors plots, Survival and Growth rate curves

Created: 2014-07-02 14:58:46 Last updated: 2014-08-29 13:25:45

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The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:

- Survival values calculations per stage per year and its respective plot; - Growth rates (lambda) calculations per year and its respective plot; - Stage Vectors calculations and their respective plots.

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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 the R pack ‘popbio’ (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). References:

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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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (6)

Name	Description
stages	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 as list. 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
surv_graph_title	Is the main title to be display in the Survival Rates Graph. e.g.: Gentiana pneumonanthe survival curves (Gentiana pneumonanthe: species name).
years	Years the data was collected in. The respective years must be filled one by one. First press add value, fill a year and press enter, then press add value and fill once again the next year, repeat the action until you have fill all the years. The years can be display as follow: e.g. 1) 1987 or 2) 1987-1988
growth_graph_title	Is the main title to be display in the Growth rate graph. e.g.: Gentiana pneumonanthe growth rates (Gentiana pneumonanthe: species name).
stage_graph_title	Is the main title to be display in the Stage Vectors Graph. (Note: will appear as Title - Year) The year will automatically be incorporate base on the year of the matix. e.g.: Gentiana pneumonanthe stage vectors - 1987
iterations	This value will be use to plot a output graph that shows a simulation of the number of individuals per stage a few years after the study (e.g. 10). This value represents the years of axis X of the output graph: Stage_Vector_Graph.

Processors (19)

Name	Type	Description
survival_rates	rshell	Script library(popbio) png(survival_curves_plot) par(xpd=T, mar=c(10,5,3,1)) sc <- sapply(matrices, function(x) colSums(splitA(x, r=rows, c=columns)$T)) matplot2(t(sc), legend = FALSE, ylab="Survival", type="b", pch = c(15:18, 20), lcex = .7, col = rainbow(length(matrices)), main=graph_title) legend(0.86, -0.15, colnames(sc), col= rainbow(length(matrices)), pch = c(15:18, 20), cex=0.6, lty=1:length(matrices)) dev.off() R Server localhost:6311
growth_rates	rshell	Script library(popbio) # Plot growth rates png(growth_rates_plot) gr <- sapply(matrices, lambda) plot(gr, type="o", pch=20, axes=FALSE, xlab="years", ylab="Growth rate", col="blue", main=graph_title) axis(1, lab=FALSE) axis(1, at=1:length(years), lab=years) axis(2) box() dev.off() R Server localhost:6311
RequestStageMatrices	workflow
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
ReadStageMatrix	workflow
False	stringconstant	Value false
Convert_LRn2_to_RLn2	workflow
Year	stringconstant	Value Year
AddNames	rshell	Script names(expr) <- labels R Server localhost:6311
Select_matrix_files	stringconstant	Value Select matrix files
stage_vectors	rshell	Script library(popbio) png(growth_rates_plot) projection <- pop.projection(stage_matrix, rep(1,5), iterations) par(xpd=T, mar=c(5,5,4,7)) stage.vector.plot(projection$stage.vectors, ylim=c(0,1), col=rainbow(length(stages)), legend.coords = FALSE, ylab="Proportion in stage clases", xlab="Years", main=paste(graph_title, paste("-", year))) legend((iterations-1)*1.1, 1.04, stages, cex=0.8, lty=1, col=rainbow(length(stages))) dev.off() R Server localhost:6311
CategoriseStages_Interaction	interaction	With this dialogue automatically appears the names of the stages or categories of the census data file. When the dialogue appears, the stages are in disorder, so the user drags and organizes the stages according to the order in the life cycle. Then, the author chooses if the stage belongs to the recruited, reproductive category or it should be excluded. Recruited means that new individuals can be recruited to this (these) stage(s). Reproductive stages are those that reproduce (produce offspring) (in this example the stage G). In the census data file Dt1.txt, x is use to denote when a plant has died in the second year, so the user must selected in the excluded column. Then the user clicks in confirm and you will read stages submitted. In the following example, the life cycle of Gentiana pneumonanthe has 5 stages or categories: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D Interaction Page //biovel.googlecode.com/svn/tags/mpm-20140521/select_fecundity.html
FecundityCols_FromReproductiveStages	rshell	Script indices = match(some_values, all_values) R Server localhost:6311
FecundityRows_FromRecruitedStages	rshell	Script indices = match(some_values, all_values) R Server localhost:6311
OutputFundamentalMatrix	workflow
OutputFundamentalMatrix_2	workflow
OutputFundamentalMatrix_3	workflow
message	stringconstant	Value Select recruited and reproductive stages, then click the Confirm button.
Select_stages	stringconstant	Value Select stages

Beanshells (0)

Outputs (6)

Name	Description
Growth_Rates_Graph	Growth Rates Graph: Plots the population growth rate or lambda values (eigen analyses) of each submitted matrix.
Survival_Rates_Graph	Survival Rates Graph: The graph shows the changes of the survival values per stages across the years.
Stage_Vectors_Graph	Stage Vector Graph: Plots short-term dynamics and convergence to stage distribution. It is a plot that charts the number of individuals per stage vs. years in the short-term (e.g. 5, 10 years).
Population_Projection	Eigen Analysis Calculates the population growth rate and stable stage distribution by repeated projections of the equation n(t+1)=An(t). a) Lambda or dominant eigenvalue: This value describes the population growth rate of a stage matrix. 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). b) The stable stage distribution (w): It is the proportion of the number of individuals per stage. It is given analytically by the right eigenvector (another property of the transition matrix) that corresponds to the dominant eigenvalue c) Stage.vector: A matrix with the number of projected individuals in each stage class. d) Pop.sizes: Total number of projected individuals. e) Pop.changes: Proportional change in population size.
Survival_Rates_Values	Survival Rates Values: It is a table showing the survival rates values per stage per year, these values are plotted in the Survival Rates Graph.
Growth_Rates_Values	Growth Rates Values: It is a table showing the population growth rate or lambda values (eigen analyses) of each submitted matrix.

Datalinks (38)

Source	Sink
AddNames:expr	survival_rates:matrices
surv_graph_title	survival_rates:graph_title
FecundityRows_FromRecruitedStages:indices	survival_rates:rows
FecundityCols_FromReproductiveStages:indices	survival_rates:columns
years	growth_rates:years
AddNames:expr	growth_rates:matrices
growth_graph_title	growth_rates:graph_title
False:value	RequestStageMatrices:multiple
years	RequestStageMatrices:values_L
Year:value	RequestStageMatrices:field
Select_matrix_files:value	RequestStageMatrices:title
RequestStageMatrices:matrices_LL	Flatten_List:inputlist
Flatten_List:outputlist	ReadStageMatrix:matrix_file
stages	ReadStageMatrix:labels_L
ReadStageMatrix:matrix_Rn2	Convert_LRn2_to_RLn2:list_of_r_expressions
Convert_LRn2_to_RLn2:r_list_of_expressions	AddNames:expr
years	AddNames:labels
stages	stage_vectors:stages
stage_graph_title	stage_vectors:graph_title
iterations	stage_vectors:iterations
years	stage_vectors:year
ReadStageMatrix:matrix_Rn2	stage_vectors:stage_matrix
stages	CategoriseStages_Interaction:unsortedStages
message:value	CategoriseStages_Interaction:message
Select_stages:value	CategoriseStages_Interaction:title
CategoriseStages_Interaction:sortedStages	FecundityCols_FromReproductiveStages:all_values
CategoriseStages_Interaction:reproductiveStages	FecundityCols_FromReproductiveStages:some_values
CategoriseStages_Interaction:sortedStages	FecundityRows_FromRecruitedStages:all_values
CategoriseStages_Interaction:recruitedStages	FecundityRows_FromRecruitedStages:some_values
stage_vectors:projection	OutputFundamentalMatrix:input
survival_rates:sc	OutputFundamentalMatrix_2:input
growth_rates:gr	OutputFundamentalMatrix_3:input
growth_rates:growth_rates_plot	Growth_Rates_Graph
survival_rates:survival_curves_plot	Survival_Rates_Graph
stage_vectors:growth_rates_plot	Stage_Vectors_Graph
OutputFundamentalMatrix:output	Population_Projection
OutputFundamentalMatrix_2:output	Survival_Rates_Values
OutputFundamentalMatrix_3:output	Growth_Rates_Values

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Maria Paula Balcazar-Vargas

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Stages vectors plots, Survival and Growth rate curves

Created by Maria Paula Balcazar-Vargas on Wednesday 02 July 2014 14:58:43 (UTC)
Stages vectors plots, Survival and Growth rate curves

Created by Maria Paula Balcazar-Vargas on Friday 25 July 2014 12:37:47 (UTC)

Revision comment:

Changes:
Printing values with 16 digits
Change the default input years and stages
The interactions will be appear always in the same order.