Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements

None

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);

Name	Description
stages	The names of the stages or categories of the input matrix. In the following example, the matrix has 5 stages. The stages of this matrix are called: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D
years	Each year represents a matrix and therefore characterizes a period of transition. In this tutorial, we have 6 matrices (see Input data) that represent 6 years e.g.: 1987 =data interval between 1987 - 1988 and 1988= data interval between 1988 - 1989 etc.

Name	Type	Description
RequestStageMatrices	workflow
ReadStageMatrix	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);
Convert_LRn2_to_RLn2	workflow
graph20b	rshell	Script library(popbio) png(pfister_plot2) vr1<-pfister.plot(matrices) temp <- c() for (rn in rownames(vr1)) { rc = substring(rn, 2, 3) i1 = strtoi(substring(rc, 1, 1)) i2 = strtoi(substring(rc, 2, 2)) if (rc %in% fec_xy) { x = 'F' } else if (i1 < i2) { x = 'R' } else if (i1 == i2) { x = 'S' } else { x = 'G' } temp = c(temp, paste0(x, '[', i1, '.', i2, ']')) } plot(vr1$cv, vr1$elas, xlab="CV", ylab="Elasticity", log="xy", type='n') y2<-parse(text=temp) text(vr1$cv, vr1$elas, y2) abline(lm(log10(vr1$elas)~log10(vr1$cv)), col="red") spr<-cor.test(vr1$cv, vr1$elas, method="spearman") minCV= min(vr1$cv) minElat= min(vr1$elas) text(minCV+5, minElat, substitute(rho == x, list(x=round(spr$estimate,3))), col="blue") dev.off() R Server localhost:6311
multiple	stringconstant	Value false
Year	stringconstant	Value Year
OutputFundamentalMatrix_3	workflow
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-20140626/select_fecundity_matrix.html
graph20a	rshell	Script library(popbio) png(pfister_plot) tab<-pfister.plot(matrices) dev.off() R Server localhost:6311
OutputFundamentalMatrix_3_2	workflow
message	stringconstant	Value Select fecundity stage transitions, then click the Confirm button.
Select_stages	stringconstant	Value Select fecundity transitions
Select_a_matrix	stringconstant	Value Select a matrix

Name	Description
pfister_graph	Graph plotting CV vs. Elasticity in matrix elements, showing the regression line (red line) and the Spearman correlation value (ρ) between these two values.
spearman_rank	Spearman correlation results of the CV vs. Elasticity in matrix elements
pfister_plot	Graphs of the calculated values of Sensitivity vs. Variance and CV vs. Elasticity in matrix elements.
pfister_plot_table	A table of calculated values of mean, variance, CV, sensitivity and elasticity of the matrix elements.

Source	Sink
years	RequestStageMatrices:values_L
multiple:value	RequestStageMatrices:multiple
Year:value	RequestStageMatrices:field
Select_a_matrix:value	RequestStageMatrices:title
Flatten_List:outputlist	ReadStageMatrix:matrix_file
stages	ReadStageMatrix:labels_L
RequestStageMatrices:matrices_LL	Flatten_List:inputlist
ReadStageMatrix:matrix_Rn2	Convert_LRn2_to_RLn2:list_of_r_expressions
Convert_LRn2_to_RLn2:r_list_of_expressions	graph20b:matrices
CategoriseStages_Interaction:fecundityIndices	graph20b:fec_xy
graph20b:spr	OutputFundamentalMatrix_3:input
message:value	CategoriseStages_Interaction:message
Select_stages:value	CategoriseStages_Interaction:title
stages	CategoriseStages_Interaction:stages
Convert_LRn2_to_RLn2:r_list_of_expressions	graph20a:matrices
graph20a:tab	OutputFundamentalMatrix_3_2:input
graph20b:pfister_plot2	pfister_graph
OutputFundamentalMatrix_3:output	spearman_rank
graph20a:pfister_plot	pfister_plot
OutputFundamentalMatrix_3_2:output	pfister_plot_table

Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Script

Script

R Server

Value

Value

Interaction Page

Script

R Server

Value

Value

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (0)