The_Life_Table_Respoplaces11[Dwingeloo 1, Dwingeloo 2, Dwingeloo 3, Lochem, Terschelling]2013-11-27 14:27:50.10 UTCPlaces: The list of places (two or more) where the research has being carried out. The respective name places must be filled one by one. First, click Add Value, fill a place name (not longer than 12 characters) and press Enter; then click Add Value and fill once again the next place name, repeat the action until you have filled all the place names.2014-04-17 09:05:31.511 UTCyears11[1988, 1989]2013-11-27 14:27:50.10 UTCYears: All years which start a period of transition. This should indicate two consecutive study periods. In the following example, we have two years (1988 =data interval between 1988 and 1989 and 1989= data interval between 1989 and 1990).2014-04-17 09:08:41.749 UTCstages11Stages: the names of the stages or categories of the input matrix. In the following example, the matrix has 5 stages or categories. The respective name stages must be filled one by one. First click Add Value, fill a stage name (not longer than 8 characters) and press Enter; then click 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:
The stages of this matrix are called:
1) Seedlings S
2) Juveniles J
3) Vegetative V
4) Reproductive individuals G
5) Dormant plants D2014-04-17 09:08:00.942 UTC[S, J, V, G, D]2013-11-27 14:27:50.10 UTCpooled_matrix_file000.0074 0 0 7.9915 0
0.1981 0.0056 0 4.4289 0
0.2467 0.7087 0.7015 0.4220 0.3380
0.0369 0.0508 0.1609 0.4973 0.1939
0 0.0388 0.0848 0.0808 0.46812013-11-27 14:27:50.10 UTCPooled_matrix_file: Weighted main Matrix in a .txt file format or what popbio (R package) calls pooled matrix (to see more details: Horvitz, Schemske and Caswell 1997; Horvitz, and Schemske 1995). Click in Set file location, a window dialog appears and the user selects the file (e.g. Pooled_matrix_Gentiana.txt) and then clicks the Open button. Then the link to the file will appear on the Taverna window. 2014-04-17 09:06:43.790 UTCplot_title00LTRE, Gentiana pneumonanthe2013-11-27 14:27:50.10 UTCPlot_Title: Descriptive main title for labelling generated outputs (graphs). Click Add Value, fill a title and press Enter.2014-04-17 09:05:55.128 UTCLTRE_Analysis$`1988`
S J V G D
S -0,00052453 0 0 -0,103043507 0
J -0,03495754 -0,000665156 0 -0,152312111 0
V -0,03814084 -0,00607003 -0,04351741 -0,023654522 -0,003417825
G -0,058844293 0,002606578 0,037617619 0,129540602 -0,00450503
D 0 -0,00236353 -0,008211038 -0,008574729 0,005021163
$`1989`
S J V G D
S -0,000495382 0 0 -0,112706023 0
J -0,02925375 -0,000790648 0 -0,111478812 0
V -0,019606058 0,036731763 -0,025998876 0,009560876 0,005126723
G -0,027846831 -0,033431783 -0,10417847 -0,066688407 -0,014491732
D 0 -0,008364033 0,001389627 0,000672706 -0,002462745
2013-11-27 14:27:50.10 UTCLTRE_Analysis: Intermediary results showing the matrices calculated on the LTRE analysis per year. After this step the workflow sums up all the values per matrix giving us the final result: LTRE_ Results. 2014-04-17 09:09:18.906 UTCLTRE_Results1988 1989
-0.3140161 -0.50431192013-11-27 14:27:50.10 UTCLTRE_ Results: The results of the LTRE per year. These are the generated values of the plotted LTRE graph. 2014-04-17 09:10:45.371 UTCLTRE_GraphLTRE_Graph: Creates a histogram to display the LTRE_Results. The year effect is shown in the Figure. In the Tutorial: The year 1989 had the largest negative effect on λ, and no year had a positive effect.2014-04-17 09:10:25.585 UTCReadStageMatrixmatrix_file0xlabels1ylabels1matrix11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityxlabels1falseylabels1falsematrix_file0falsematrix11falselocalhost6311falsefalsexlabelsSTRING_LISTylabelsSTRING_LISTmatrix_fileTEXT_FILEmatrixR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeReadPooledMatrixmatrix_file0xlabels1ylabels1matrix11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityxlabels1falseylabels1falsematrix_file0falsematrix11falselocalhost6311falsefalsexlabelsSTRING_LISTylabelsSTRING_LISTmatrix_fileTEXT_FILEmatrixR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTransposelistDepth33transposed33net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitylistDepth33text/plainjava.lang.Stringtruetransposed33workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMeanMatrixmatrices1mean_matrix11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivitymatrices1falsemean_matrix11falselocalhost6311falsefalsematricesR_EXPmean_matrixR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeListRtoRListlist_of_r_expressions2r_list_of_expressions11net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAddNameslabels1expr1expr11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityexpr1falselabels1falseexpr11falselocalhost6311falsefalseexprR_EXPlabelsSTRING_LISTexprR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculatePlaceEffectmatrices1pooled_matrix1xlabel0xticks1ylabel0plot_colour0plot_title0LTRE_Analysis11LTRE_Results_RLn11graph00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeListRtoRList_2list_of_r_expressions2r_list_of_expressions11net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexlabelvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivityYearnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeylabelvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivityYear Effectnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeplot_colourvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitylightbluenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrintAnalysisrexpr1text00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityrexpr1falsetext00falselocalhost6311falsefalserexprR_EXPtextTEXT_FILEnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrintResultsrexpr1text00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityrexpr1falsetext00falselocalhost6311falsefalserexprR_EXPtextTEXT_FILEnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricesvalues1matrices22Request the user the introduction of stage matrices 2014-08-13 09:37:19.218 UTCnet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeReadStageMatrixmatrix_fileReadStageMatrixxlabelsReadStageMatrixylabelsReadPooledMatrixmatrix_fileReadPooledMatrixxlabelsReadPooledMatrixylabelsTransposelistDepth3MeanMatrixmatricesListRtoRListlist_of_r_expressionsAddNameslabelsAddNamesexprCalculatePlaceEffectmatricesCalculatePlaceEffectpooled_matrixCalculatePlaceEffectxlabelCalculatePlaceEffectxticksCalculatePlaceEffectylabelCalculatePlaceEffectplot_colourCalculatePlaceEffectplot_titleListRtoRList_2list_of_r_expressionsPrintAnalysisrexprPrintResultsrexprRequestStageMatricesvaluesLTRE_AnalysisLTRE_ResultsLTRE_GraphMaria Paula Balcázar-Vargas, Jonathan Giddy, Francisco Quevedo and Gerard Oostermeijer2014-08-13 14:27:14.774 UTCe3dfdddf-fb55-41b3-a662-d7405aaa20852014-08-11 10:43:07.46 UTC0a8050aa-38bd-49ff-9c94-777b0a3aba202014-08-13 10:30:27.477 UTCLife Table Response Experiment year effect for multiple places2014-04-17 09:18:33.879 UTCf8ad1325-17c7-4d90-93bb-d34012d4178a2014-04-17 09:04:32.294 UTCeed98302-824a-4eeb-bddb-129910c423e92014-08-13 10:06:25.846 UTCbd00c099-bc21-46cf-8f14-454bc324b2c32014-04-17 09:18:35.458 UTCcf501376-a801-44de-8710-04808df615372014-04-17 09:09:58.547 UTCThe Life Table Response Experiments Year Effect for Multiple Places workflow provides an environment to analyse two or more matrices (e.g., two or more matrices of different years from one place) at two or more different locations. The objective of this workflow is to determine the effects of the research years (2 or more) on λ. This workflow performs a fixed LTRE, one way design (Caswell 2001).
LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on λ under two or more sets of environmental conditions (in this case 2 or more years from different places) (Horvitz, Schemske and Caswell 1997). The goal of the analysis is to quantify the contribution of each of the vital rates to the variability in λ. (Caswell 1989, 1996, 2001 in Horvitz, Schemske and Caswell 1997).
Fixed Treatments: Decomposing Years Treatment Effects for multiple places
A fixed-effect analysis treats the matrices as representative of particular conditions, either experimental or natural (high vs. low nutrients in a one-way model, for example, or year and spatial location in a two-way model). The goal is to determine how much a treatment level (in this case year) on λ is contributed by each of the vital rates. The analysis uses a linear approximation in which the sensitivities appear as slopes. The effect of a treatment on λ depends on its effect on each matrix entry and on the sensitivity of λ to that entry. (Horvitz, Schemske and Caswell 1997).
For more details of the analysis see: Retrospective Analyses: Fixed Treatments (page 262 in Horvitz, Schemske and Caswell 1997) and Chapter 10 Life Table Response Experiments (page 258 in Caswell 2001).
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. 1989. The analysis of life table response experiments. I. Decomposition of treatment effects on population growth rate. Ecological Modelling 46: 221-237.
Caswell, H. 1996. Demography meets ecotoxicology: Untangling the population level effects of toxic substances. Pp. 255-292 in M. C. Newman and C. H. Jagoe, eds., Ecotoxicology: A Hierarchical Treatment. Lewis, Boca Raton, Fla.
Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.
Horvitz, C.C. and D.W. Schemske. 1995. Spatiotemporal Variation in Demographic Transitions of a Tropical Understory Herb: Projection Matrix Analysis. Ecological Monographs, 65:155-192
Horvitz, C., D.W. Schemske, and Hal Caswell. 1997. The relative "importance" of life-history stages to population growth: Prospective and retrospective analyses. In S. Tuljapurkar and H. Caswell. Structured population models in terrestrial and freshwater systems. Chapman and Hall, New York.
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
ion 2.3.12014-04-17 09:37:55.580 UTC7af908a6-1d7e-4554-b87a-24af600ec3412014-08-18 11:20:37.124 UTC6ac7dbb2-eb4e-42c1-ace8-257ed0992cf12014-08-13 09:39:49.859 UTCc63e4ff2-db75-4e9a-9481-4a647b8a1b5f2014-08-13 14:27:16.185 UTCffc835d9-1b75-4585-88a9-60eb05d447712014-08-18 11:23:00.639 UTC53726ae2-444b-4467-86f1-127489aa1b502014-08-14 10:22:56.636 UTC6e4b5de5-26b7-4e4a-9ef7-09776e9b97f62014-04-17 09:32:27.906 UTC12936c59-cc33-4399-8bd4-adbe8c442c562014-04-17 09:37:52.308 UTC6d82302e-25ff-48ad-a41d-b73926e85a972014-08-18 11:04:20.909 UTC870bb249-90b7-4fa0-9c8b-028c41473a5f2014-08-14 09:41:46.934 UTCa8319edd-d5a4-4059-9595-312f0c21914f2014-04-17 09:05:22.398 UTCafa45cce-ad01-4e88-b849-6f378fe0f0422014-04-17 09:10:47.377 UTC19997faf-c3bd-414a-b22e-f44d13117d4f2014-04-17 09:38:00.146 UTC213baa8c-e424-482a-b6f1-c48bef85c13c2014-08-13 09:46:47.968 UTCdcda0930-e759-4ec5-9afc-309ca08ee4202014-08-14 09:21:49.776 UTCConvert_Taverna_listlist_of_r_expressions22r_list_of_expressionsRExpressionToStringstringlist1concatenated00net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityseperator0text/plainjava.lang.Stringtruestringlist1text/plainjava.lang.Stringtrueconcatenated00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJoinListOfStringsIntoRListstringlist1output11net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitystringlist1text/plainjava.lang.Stringtrueoutput11workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRExpressionToStringstringlistJoinListOfStringsIntoRListstringlistr_list_of_expressionsConvert Taverna list of RExpr to R list2013-11-27 14:27:50.10 UTCThis workflow accepts a Taverna list of arbitrary R expressions and returns a single R expression representing an R list containing the original expressions.
This workflow relies on the current Taverna behaviour of an R expression being represented by a list of strings containing the deparsed expression. If this changes, this workflow will likely break.
The first BeanShell converts each R expression (actually a list of strings) to a single string. This uses implicit iteration to do this for each R expression, so input port depth is 2 but the BeanShell input depth is 1.
The second Beanshell creates a comma-separated list of the deparsed R expressions and wraps the string with the R list() function. So now we have a single string s that can be turned into an R list using eval(parse(text=s)).
But RShell already does that parsing for us, so we just need to ensure the string looks like an R expression by turning it into a list of strings. So we actually output a 1-element list containing the string.
Version 1: initial implementation
Version 2: reduce number of BeanShells
2013-11-27 14:27:50.10 UTC35194dda-0e05-4a31-ac5b-84cd050ef7322014-04-17 09:04:32.563 UTCJonathan Giddy2013-11-27 14:27:50.10 UTCLife_Table_Response_matrices11pooled_matrix11xticks11xlabel00plot_colour00plot_title00ylabel00LTRE_AnalysisgraphLTRE_ResultsLTRE_Results_RLnLTREmatrices1pooled_matrix1LTRE_Analysis11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivitymatrices1falsepooled_matrix1falseLTRE_Analysis11falselocalhost6311falsefalsematricesR_EXPpooled_matrixR_EXPLTRE_AnalysisR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePlotLTRELTRE_Analysis1xticks1xlabel0plot_colour0plot_title0ylabel0graph00LTRE_Results11LTRE_Results_RLn11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityplot_colour0falseLTRE_Analysis1falsexticks1falsexlabel0falseylabel0falseplot_title0falseLTRE_Results11LTRE_Results_RLn11graph00falselocalhost6311falsefalseplot_colourSTRINGLTRE_AnalysisR_EXPxticksSTRING_LISTxlabelSTRINGylabelSTRINGplot_titleSTRINGLTRE_ResultsDOUBLE_LISTLTRE_Results_RLnR_EXPgraphPNG_FILEnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeLTREmatricesLTREpooled_matrixPlotLTRELTRE_AnalysisPlotLTRExticksPlotLTRExlabelPlotLTREplot_colourPlotLTREplot_titlePlotLTREylabelLTRE_AnalysisgraphLTRE_ResultsLTRE_Results_RLnLife Table Response Experiment2013-11-27 14:27:50.10 UTC08e4641c-aa76-4499-ac7a-4f2643f770f72014-04-17 09:04:32.600 UTCRequestStageMatricesvalues11matricesRequestStageMatricestitle0field0values1message0minMatricesPerField0multiple0forceEqualNumberMatricesPerField0matrices22net.sf.taverna.t2.activitiesinteraction-activity1.0.4net.sf.taverna.t2.activities.interaction.InteractionActivityfield0text/plainjava.lang.Stringfalsetitle0text/plainjava.lang.Stringfalsevalues1text/plainjava.lang.Stringfalsemultiple0text/plainjava.lang.Stringfalsemessage0text/plainjava.lang.StringfalseminMatricesPerField0text/plainjava.lang.StringfalseforceEqualNumberMatricesPerField0text/plainjava.lang.StringfalseextraValidationMessage0text/plainjava.lang.Stringfalsematrices22http://biovel.googlecode.com/svn/tags/mpm-20140811/select_matrices.htmlLocallyPresentedHtmlfalsenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefieldvalue00Name of the field to introduce the stage matrices2014-08-13 09:46:01.240 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivityLocationnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeforceEqualNumberMatricesPerFieldvalue00Boolean 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 another
2014-08-13 09:38:04.761 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitytruenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeactionMessagevalue00Message to show to the user the action s/he needs to perform in the interaction page2014-08-13 09:38:28.954 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect matrix files, then click Confirmnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeminMatricesPerFieldvalue00Minimum number of matrices per field2014-08-13 09:39:10.12 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity2net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemultiplevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitytruenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketitlevalue00Title to be shown in the interaction page2014-08-13 09:41:40.682 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect multiple stage matrices from different years for each locationnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricestitleRequestStageMatricesfieldRequestStageMatricesvaluesRequestStageMatricesmessageRequestStageMatricesminMatricesPerFieldRequestStageMatricesmultipleRequestStageMatricesforceEqualNumberMatricesPerFieldmatricesf908ef4d-6e39-4607-8cc3-30644f3ee39f2014-08-14 09:41:36.822 UTCae40df9f-64b8-478c-aa80-c934651002e32014-08-18 11:22:56.929 UTC1629a676-0820-432d-a5e0-c2b63dfe216a2014-08-11 10:37:09.774 UTCc9f0c332-fede-422b-a1d2-20a1f14c8d552014-08-13 09:46:47.638 UTCRequestStageMatrices2014-08-11 10:35:59.628 UTCe0da9a8e-c59e-473b-ac64-0c353ef27bf82014-08-14 10:22:49.940 UTC90b4b6b2-1f85-426d-8d35-225d1d251a602014-08-14 09:21:44.869 UTC2ca1f58f-8e3f-44c0-b6a2-b91016a4e60f2014-08-13 09:39:49.489 UTC37811903-e1ae-4e34-87b5-78a09b0154302014-08-18 11:04:13.359 UTCd24a591d-1a5d-4225-b15a-4b6929decd862014-08-11 10:43:02.482 UTC12f411ec-70cd-4759-9b2f-e169c1f1d7532014-08-14 10:05:41.627 UTCd8c492fe-c128-4014-8db8-59376764d9bd2014-08-18 11:20:15.185 UTC3fab5cb5-6a01-4972-b11f-565da26a87932014-08-13 10:30:27.87 UTC