Mean matrix

Created: 2014-08-14 14:11:04

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This mean matrix workflow estimates the mean matrix from a list of matrices.

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 using and based on Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ==================================================================================

Literature

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

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 (2)

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 Example Input data) that represent 6 years e.g.: 1987 =data interval between 1987 and 1988 and 1988= data interval between 1988 and 1989 etc.

Processors (11)

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
mean_calc	rshell	Script library(popbio) m<-mean(matrices) R Server localhost:6311
multiple	stringconstant	Value false
Year	stringconstant	Value Year
OutputFundamentalMatrix_3	workflow
Select_a_matrix	stringconstant	Value Select a matrix
forceEqualNumberMatricesPerField	stringconstant	Boolean to force or not that the user introduces the same number of matrices in each field. Possible values: true => all elements should have the same number of matrices false => the elements can have different number of matrices from one to anot Value false
minMatricesPerField	stringconstant	Minimum number of matrices per field Value 1

Beanshells (0)

Outputs (1)

Name	Description
mean	the calculated mean matrix from a list of matrices

Datalinks (13)

Source	Sink
years	RequestStageMatrices:values_L
multiple:value	RequestStageMatrices:multiple
Year:value	RequestStageMatrices:field
Select_a_matrix:value	RequestStageMatrices:title
forceEqualNumberMatricesPerField:value	RequestStageMatrices:forceEqualNumberMatricesPerField
minMatricesPerField:value	RequestStageMatrices:minMatricesPerField
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	mean_calc:matrices
mean_calc:m	OutputFundamentalMatrix_3:input
OutputFundamentalMatrix_3:output	mean