The_Life_Table_Respoplaces11 [Dwingeloo 1, Dwingeloo 2, Dwingeloo 3, Lochem, Terschelling] 2013-11-27 14:27:50.10 UTC Places: 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 UTC years11 [1988, 1989] 2013-11-27 14:27:50.10 UTC Years: 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 UTC stages11 Stages: 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 D 2014-04-17 09:08:00.942 UTC [S, J, V, G, D] 2013-11-27 14:27:50.10 UTC pooled_matrix_file00 0.0074 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 0.4681 2013-11-27 14:27:50.10 UTC Pooled_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 UTC plot_title00 LTRE, Gentiana pneumonanthe 2013-11-27 14:27:50.10 UTC Plot_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 UTC LTRE_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 UTC LTRE_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 UTC LTRE_Results 1988 1989 -0.3140161 -0.5043119 2013-11-27 14:27:50.10 UTC LTRE_ 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 UTC LTRE_Graph LTRE_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 UTC ReadStageMatrixmatrix_file0xlabels1ylabels1matrix11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity xlabels 1 false ylabels 1 false matrix_file 0 false matrix 1 1 false localhost 6311 false false xlabels STRING_LIST ylabels STRING_LIST matrix_file TEXT_FILE matrix R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.RshellActivity xlabels 1 false ylabels 1 false matrix_file 0 false matrix 1 1 false localhost 6311 false false xlabels STRING_LIST ylabels STRING_LIST matrix_file TEXT_FILE matrix R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity listDepth3 3 text/plain java.lang.String true transposed 3 3 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.RshellActivity matrices 1 false mean_matrix 1 1 false localhost 6311 false false matrices R_EXP mean_matrix R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.RshellActivity expr 1 false labels 1 false expr 1 1 false localhost 6311 false false expr R_EXP labels STRING_LIST expr R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity Year net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 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net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity lightblue net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.RshellActivity rexpr 1 false text 0 0 false localhost 6311 false false rexpr R_EXP text TEXT_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 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net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricesvalues1matrices22 Request the user the introduction of stage matrices 2014-08-13 09:37:19.218 UTC net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeReadStageMatrixmatrix_fileRequestStageMatricesmatricesReadStageMatrixxlabelsstagesReadStageMatrixylabelsstagesReadPooledMatrixmatrix_filepooled_matrix_fileReadPooledMatrixxlabelsstagesReadPooledMatrixylabelsstagesTransposelistDepth3ReadStageMatrixmatrixMeanMatrixmatricesListRtoRListr_list_of_expressionsListRtoRListlist_of_r_expressionsTransposetransposedAddNameslabelsyearsAddNamesexprListRtoRList_2r_list_of_expressionsCalculatePlaceEffectmatricesAddNamesexprCalculatePlaceEffectpooled_matrixReadPooledMatrixmatrixCalculatePlaceEffectxlabelxlabelvalueCalculatePlaceEffectxticksyearsCalculatePlaceEffectylabelylabelvalueCalculatePlaceEffectplot_colourplot_colourvalueCalculatePlaceEffectplot_titleplot_titleListRtoRList_2list_of_r_expressionsMeanMatrixmean_matrixPrintAnalysisrexprCalculatePlaceEffectLTRE_AnalysisPrintResultsrexprCalculatePlaceEffectLTRE_Results_RLnRequestStageMatricesvaluesplacesLTRE_AnalysisPrintAnalysistextLTRE_ResultsPrintResultstextLTRE_GraphCalculatePlaceEffectgraph Maria Paula Balcázar-Vargas, Jonathan Giddy, Francisco Quevedo and Gerard Oostermeijer 2014-08-13 14:27:14.774 UTC e3dfdddf-fb55-41b3-a662-d7405aaa2085 2014-08-11 10:43:07.46 UTC 0a8050aa-38bd-49ff-9c94-777b0a3aba20 2014-08-13 10:30:27.477 UTC Life Table Response Experiment year effect for multiple places 2014-04-17 09:18:33.879 UTC f8ad1325-17c7-4d90-93bb-d34012d4178a 2014-04-17 09:04:32.294 UTC eed98302-824a-4eeb-bddb-129910c423e9 2014-08-13 10:06:25.846 UTC bd00c099-bc21-46cf-8f14-454bc324b2c3 2014-04-17 09:18:35.458 UTC cf501376-a801-44de-8710-04808df61537 2014-04-17 09:09:58.547 UTC The 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 2.3.1 2014-04-17 09:37:55.580 UTC 7af908a6-1d7e-4554-b87a-24af600ec341 2014-08-18 11:20:37.124 UTC 6ac7dbb2-eb4e-42c1-ace8-257ed0992cf1 2014-08-13 09:39:49.859 UTC c63e4ff2-db75-4e9a-9481-4a647b8a1b5f 2014-08-13 14:27:16.185 UTC ffc835d9-1b75-4585-88a9-60eb05d44771 2014-08-18 11:23:00.639 UTC 53726ae2-444b-4467-86f1-127489aa1b50 2014-08-14 10:22:56.636 UTC 6e4b5de5-26b7-4e4a-9ef7-09776e9b97f6 2014-04-17 09:32:27.906 UTC 12936c59-cc33-4399-8bd4-adbe8c442c56 2014-04-17 09:37:52.308 UTC 6d82302e-25ff-48ad-a41d-b73926e85a97 2014-08-18 11:04:20.909 UTC 870bb249-90b7-4fa0-9c8b-028c41473a5f 2014-08-14 09:41:46.934 UTC a8319edd-d5a4-4059-9595-312f0c21914f 2014-04-17 09:05:22.398 UTC afa45cce-ad01-4e88-b849-6f378fe0f042 2014-04-17 09:10:47.377 UTC 19997faf-c3bd-414a-b22e-f44d13117d4f 2014-04-17 09:38:00.146 UTC 213baa8c-e424-482a-b6f1-c48bef85c13c 2014-08-13 09:46:47.968 UTC dcda0930-e759-4ec5-9afc-309ca08ee420 2014-08-14 09:21:49.776 UTC Convert_Taverna_listlist_of_r_expressions22r_list_of_expressionsRExpressionToStringstringlist1concatenated00net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity seperator 0 text/plain java.lang.String true stringlist 1 text/plain java.lang.String true concatenated 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity stringlist 1 text/plain java.lang.String true output 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRExpressionToStringstringlistlist_of_r_expressionsJoinListOfStringsIntoRListstringlistRExpressionToStringconcatenatedr_list_of_expressionsJoinListOfStringsIntoRListoutput Convert Taverna list of RExpr to R list 2013-11-27 14:27:50.10 UTC This 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 UTC 35194dda-0e05-4a31-ac5b-84cd050ef732 2014-04-17 09:04:32.563 UTC Jonathan Giddy 2013-11-27 14:27:50.10 UTC Life_Table_Response_matrices11pooled_matrix11xticks11xlabel00plot_colour00plot_title00ylabel00LTRE_AnalysisgraphLTRE_ResultsLTRE_Results_RLnLTREmatrices1pooled_matrix1LTRE_Analysis11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity matrices 1 false pooled_matrix 1 false LTRE_Analysis 1 1 false localhost 6311 false false matrices R_EXP pooled_matrix R_EXP LTRE_Analysis R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.RshellActivity plot_colour 0 false LTRE_Analysis 1 false xticks 1 false xlabel 0 false ylabel 0 false plot_title 0 false LTRE_Results 1 1 LTRE_Results_RLn 1 1 graph 0 0 false localhost 6311 false false plot_colour STRING LTRE_Analysis R_EXP xticks STRING_LIST xlabel STRING ylabel STRING plot_title STRING LTRE_Results DOUBLE_LIST LTRE_Results_RLn R_EXP graph PNG_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeLTREmatricesmatricesLTREpooled_matrixpooled_matrixPlotLTRELTRE_AnalysisLTRELTRE_AnalysisPlotLTRExticksxticksPlotLTRExlabelxlabelPlotLTREplot_colourplot_colourPlotLTREplot_titleplot_titlePlotLTREylabelylabelLTRE_AnalysisLTRELTRE_AnalysisgraphPlotLTREgraphLTRE_ResultsPlotLTRELTRE_ResultsLTRE_Results_RLnPlotLTRELTRE_Results_RLn Life Table Response Experiment 2013-11-27 14:27:50.10 UTC 08e4641c-aa76-4499-ac7a-4f2643f770f7 2014-04-17 09:04:32.600 UTC RequestStageMatricesvalues11matricesRequestStageMatricestitle0field0values1message0minMatricesPerField0multiple0forceEqualNumberMatricesPerField0matrices22net.sf.taverna.t2.activitiesinteraction-activity1.0.4net.sf.taverna.t2.activities.interaction.InteractionActivity field 0 text/plain java.lang.String false title 0 text/plain java.lang.String false values 1 text/plain java.lang.String false multiple 0 text/plain java.lang.String false message 0 text/plain java.lang.String false minMatricesPerField 0 text/plain java.lang.String false forceEqualNumberMatricesPerField 0 text/plain java.lang.String false extraValidationMessage 0 text/plain java.lang.String false matrices 2 2 http://biovel.googlecode.com/svn/tags/mpm-20140811/select_matrices.html LocallyPresentedHtml false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefieldvalue00 Name of the field to introduce the stage matrices 2014-08-13 09:46:01.240 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Location net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeforceEqualNumberMatricesPerFieldvalue00 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 another 2014-08-13 09:38:04.761 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity true net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeactionMessagevalue00 Message to show to the user the action s/he needs to perform in the interaction page 2014-08-13 09:38:28.954 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select matrix files, then click Confirm net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeminMatricesPerFieldvalue00 Minimum number of matrices per field 2014-08-13 09:39:10.12 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 2 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity true net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketitlevalue00 Title to be shown in the interaction page 2014-08-13 09:41:40.682 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select multiple stage matrices from different years for each location net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricestitletitlevalueRequestStageMatricesfieldfieldvalueRequestStageMatricesvaluesvaluesRequestStageMatricesmessageactionMessagevalueRequestStageMatricesminMatricesPerFieldminMatricesPerFieldvalueRequestStageMatricesmultiplemultiplevalueRequestStageMatricesforceEqualNumberMatricesPerFieldforceEqualNumberMatricesPerFieldvaluematricesRequestStageMatricesmatrices f908ef4d-6e39-4607-8cc3-30644f3ee39f 2014-08-14 09:41:36.822 UTC ae40df9f-64b8-478c-aa80-c934651002e3 2014-08-18 11:22:56.929 UTC 1629a676-0820-432d-a5e0-c2b63dfe216a 2014-08-11 10:37:09.774 UTC c9f0c332-fede-422b-a1d2-20a1f14c8d55 2014-08-13 09:46:47.638 UTC RequestStageMatrices 2014-08-11 10:35:59.628 UTC e0da9a8e-c59e-473b-ac64-0c353ef27bf8 2014-08-14 10:22:49.940 UTC 90b4b6b2-1f85-426d-8d35-225d1d251a60 2014-08-14 09:21:44.869 UTC 2ca1f58f-8e3f-44c0-b6a2-b91016a4e60f 2014-08-13 09:39:49.489 UTC 37811903-e1ae-4e34-87b5-78a09b015430 2014-08-18 11:04:13.359 UTC d24a591d-1a5d-4225-b15a-4b6929decd86 2014-08-11 10:43:02.482 UTC 12f411ec-70cd-4759-9b2f-e169c1f1d753 2014-08-14 10:05:41.627 UTC d8c492fe-c128-4014-8db8-59376764d9bd 2014-08-18 11:20:15.185 UTC 3fab5cb5-6a01-4972-b11f-565da26a8793 2014-08-13 10:30:27.87 UTC