Life_Table_Response_years11 Years: All years which start a period of transition. This should indicate two consecutive study periods. In the following example, we have six years (e.g.: 1988 =data interval between 1988 and 1989 and 1989= data interval between 1989 and 1990). 2014-04-17 09:47:02.55 UTC [1987, 1988, 1989, 1990, 1991, 1992] 2014-04-02 11:50:44.473 UTC stages11 [S, J, V, G, D] 2014-04-02 11:50:23.417 UTC 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, enter a stage name (not longer than 8 characters) and press Enter; then click Add Value and enter the next stage name, repeat the action until you have entered all the stage 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 09:46:02.872 UTC Pooled_matrix_file00 Pooled_matrix_file: Weighted main Matrix in a .txt file format 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. MT_pooled data.txt) and then clicks the Open button. Then the link to the file will appear on the Taverna window. 2014-04-17 09:45:33.331 UTC 0.0074 0 0 6.0510 0 0.1953 0.0092 0 5.9154 0 0.3167 0.6710 0.6999 0.4621 0.7636 0 0.0258 0.0663 0.4818 0.1287 0 0.0214 0.0473 0.0561 0.1077 2014-03-28 13:35:49.687 UTC plot_title00 Plot_Title: Descriptive main title for labelling generated outputs (graphs). Click Add Value, enter a title and press Enter. 2014-04-17 09:45:05.223 UTC LTRE, Gentiana pneumonanthe 2014-03-28 13:45:47.950 UTC LTRE_Analysis0 $`1987` S J V G D S -0,000427437 0 0 0,017977128 0 J -0,018948429 0,000125413 0 0,063000672 0 V 0,02217648 0,027240295 0,08050301 -0,005123488 0,001407312 G 0 0,02999793 -0,28293633 0,04915813 -0,002225181 D 0 0,002716886 -0,02162583 -0,003004855 -0,002262304 $`1988` S J V G D S -6,95E-05 0 0 -0,015389513 0 J 4,96E-03 -0,000558645 0 0,01926612 0 V -7,30E-03 0,020735759 0,04387892 -0,019217928 -0,001781114 G 0,00E+00 -0,017338168 0,09869957 0,16998346 0,011994002 D 0,00E+00 -0,006333278 -0,01669189 -0,004617703 0,000357214 $`1989` S J V G D S 4,81E-05 0,00E+00 0 -0,079033122 0 J -1,37E-02 -1,11E-03 0 -0,137816922 0 V -1,63E-02 -2,39E-02 -0,004376839 0,002379802 -0,001615473 G 0,00E+00 -1,11E-02 -0,190435466 -0,039096363 0,003208923 D 0,00E+00 -6,95E-05 0,004850583 0,000120345 0,002089625 $`1990` S J V G D S -0,000269809 0 0 -0,063011581 0 J -0,013011246 0,000303558 0 -0,160845614 0 V -0,046430953 -0,046785723 -0,006004358 0,008516046 0,002694165 G 0 -0,024276849 -0,169262225 -0,054201685 -0,020216428 D 0 -0,002132282 -0,020610214 -0,003466185 0,001150681 $`1991` S J V G D S -0,000324936 0 0 -0,082567502 0 J -0,019091282 -0,001030737 0 -0,168009967 0 V -0,030504132 -0,052268343 -0,07184465 0,007067617 0,003212066 G 0 -0,028415235 -0,16602744 -0,05199214 -0,007222026 D 0 -0,006109288 -0,03369773 -0,004342381 -0,003520319 $`1992` S J V G D S -0,000189651 0 0 -0,051219954 0 J -0,017605964 -0,001154529 0 -0,119286554 0 V -0,033613991 0,019059924 -0,03514813 0,006108974 0,008998567 G 0 -0,028684697 -0,2645677 -0,055151583 -0,03686409 D 0 -0,004550707 0,01982567 0,001756256 -0,005900316 2014-03-28 13:55:01.421 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. 2014-04-02 11:30:16.422 UTC LTRE_Results0 LTRE_ Results: The results of the LTRE per year. These are the generated values of the plotted LTRE graph. 2014-04-02 11:30:36.167 UTC 1987 1988 1989 1990 1991 1992 -0.0422506 0.2805752 -0.5058927 -0.6178607 -0.7166884 -0.5981885 2014-03-28 13:59:24.93 UTC LTRE_Graph0 LTRE_Graph: Creates a histogram to display the LTRE_Results. The year effect is shown in the Figure. In this example: The year 1988 had the largest positive effect on lambda, and the other years had a negative effect. 2014-04-02 11:30:23.231 UTC ReadStageMatrixmatrix_file0xlabels1ylabels1matrix11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeReadPooledMatrixmatrix_file0xlabels1ylabels1matrix11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAddNameslabels1expr1expr11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculateYearEffectmatrices1pooled_matrix1xlabel0xticks1ylabel0plot_colour0plot_title0LTRE_Analysis11LTRE_Results_RLn11graph00net.sf.taverna.t2.activitiesdataflow-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeListRtoRListlist_of_r_expressions2r_list_of_expressions11net.sf.taverna.t2.activitiesdataflow-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokexlabelvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Years net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeylabelvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Year Effect net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeplot_colourvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity lightblue net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrintAnalysisrexpr1text00net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrintResultsrexpr1text00net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricesvalues1matrices11 Request the user the introduction of stage matrices 2014-08-13 09:40:21.490 UTC net.sf.taverna.t2.activitiesdataflow-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeReadStageMatrixmatrix_fileRequestStageMatricesmatricesReadStageMatrixxlabelsstagesReadStageMatrixylabelsstagesReadPooledMatrixmatrix_filePooled_matrix_fileReadPooledMatrixxlabelsstagesReadPooledMatrixylabelsstagesAddNameslabelsyearsAddNamesexprListRtoRListr_list_of_expressionsCalculateYearEffectmatricesAddNamesexprCalculateYearEffectpooled_matrixReadPooledMatrixmatrixCalculateYearEffectxlabelxlabelvalueCalculateYearEffectxticksyearsCalculateYearEffectylabelylabelvalueCalculateYearEffectplot_colourplot_colourvalueCalculateYearEffectplot_titleplot_titleListRtoRListlist_of_r_expressionsReadStageMatrixmatrixPrintAnalysisrexprCalculateYearEffectLTRE_AnalysisPrintResultsrexprCalculateYearEffectLTRE_Results_RLnRequestStageMatricesvaluesyearsLTRE_AnalysisPrintAnalysistextLTRE_ResultsPrintResultstextLTRE_GraphCalculateYearEffectgraph 95c803bc-8325-408a-bd8c-10d5f6ada6a2 2014-04-02 11:50:44.640 UTC 18c4eeb8-867b-4c95-88ea-e05b8595cc00 2014-01-09 10:38:48.222 UTC The Life Table Response Experiments Effect of Years in One Place workflow provides an environment to analyse two or more matrices from different years in one location. The objective of this workflow is to determine the effects of the research years (2 or more) in one place 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 in one location) (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 in one location or place 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 2014-04-17 09:44:37.246 UTC Maria Paula Balcázar-Vargas, Jonathan Giddy, Francisco Quevedo and Gerard Oostermeijer 2014-08-13 15:06:53.953 UTC cf5d4da2-05ba-4d0a-9be6-6394a5b3479f 2014-03-28 14:59:48.772 UTC 912c941a-280a-462e-b2d7-5d677e5470ea 2014-03-28 13:24:34.661 UTC 42b0b3cc-f24a-45f0-9c70-7ee6b642c6db 2014-03-28 13:48:51.759 UTC bb2abaa0-6770-4154-8fe7-f73253f9cf49 2014-04-17 09:47:04.603 UTC 0f74d343-dea2-4b8e-ba47-78035b22525d 2014-08-13 15:06:55.504 UTC 37d391e2-3f0f-4582-8865-3e60c8539c1c 2014-01-09 10:37:15.381 UTC 95a33542-c8d6-498d-b246-8e85697055e1 2014-08-13 10:30:26.487 UTC 19d711bf-10e6-4cc3-aff6-949fe866e46e 2014-04-02 11:30:37.237 UTC 2de008d8-f612-4e55-9aae-bcbe99767a58 2014-08-11 10:55:37.675 UTC ea1a70de-8996-4713-99ba-222ae76a32f8 2014-01-09 10:34:46.590 UTC e5145e38-9a49-42ed-a93d-4059e934f210 2014-01-09 10:38:14.641 UTC 04551d66-4d11-4071-8f90-3dc44ff4c27c 2014-01-09 10:39:28.414 UTC f6f707d4-2315-4b39-84c8-8e06eb732009 2014-08-13 09:46:47.128 UTC Life Table Response Experiment Year Effect in One Location or Place 2014-04-02 11:23:31.382 UTC a185a5b8-f620-4553-8da5-79c80b888aa9 2014-04-17 09:44:39.189 UTC d6c4e74a-c2b5-4328-b178-669b1508bbef 2014-03-28 13:59:24.276 UTC 3b27b1f8-f1d7-47be-94d4-d0646e9d24e9 2014-03-28 14:55:32.14 UTC 4c2bae6b-69c6-4e9f-9f8e-431051560b0f 2014-03-28 13:45:45.608 UTC 66c08fd8-d1cf-4b84-8a1c-c2b99d8f3b38 2014-04-17 09:44:06.366 UTC 69113e1e-6ee6-45eb-94cf-f44aec06abef 2014-03-28 13:46:49.704 UTC ea8ef35f-341c-4bd7-858d-594854efdb06 2014-03-28 13:35:49.846 UTC 3c786ca1-5d23-4907-9a83-43c9622ba306 2014-08-13 10:06:24.805 UTC 89b9d79d-225c-4e44-b652-ce0efedf0aa0 2014-04-02 11:30:35.317 UTC 067e249a-3afe-4cb1-8787-1b5d5d440ecc 2014-04-17 09:45:59.652 UTC 63c96824-2e52-4c18-8e7e-55edcaa26b47 2014-08-11 10:51:13.778 UTC e4d115e7-82d2-42db-b46f-c8b38e989e7f 2014-03-28 13:55:16.499 UTC d88716c4-8891-4e0a-964e-d43a400be9fc 2014-03-28 13:50:11.912 UTC fb0ff3e3-4525-4bcf-9a5a-ce62c620f911 2014-03-28 13:57:13.223 UTC Life_Table_Response_matrices11pooled_matrix11xticks11xlabel00plot_colour00plot_title00ylabel00LTRE_Analysis1graph0LTRE_Results1LTRE_Results_RLn1LTREmatrices1pooled_matrix1LTRE_Analysis11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePlotLTRELTRE_Analysis1xticks1xlabel0plot_colour0plot_title0ylabel0graph00LTRE_Results11LTRE_Results_RLn11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeLTREmatricesmatricesLTREpooled_matrixpooled_matrixPlotLTRELTRE_AnalysisLTRELTRE_AnalysisPlotLTRExticksxticksPlotLTRExlabelxlabelPlotLTREplot_colourplot_colourPlotLTREplot_titleplot_titlePlotLTREylabelylabelLTRE_AnalysisLTRELTRE_AnalysisgraphPlotLTREgraphLTRE_ResultsPlotLTRELTRE_ResultsLTRE_Results_RLnPlotLTRELTRE_Results_RLn 627ddba7-2980-423b-b333-6988e033c310 2014-01-09 10:34:46.784 UTC Life Table Response Experiment 2013-11-27 14:27:50.10 UTC RequestStageMatricesvalues11matrices1RequestStageMatricestitle0field0values1message0minMatricesPerField0multiple0forceEqualNumberMatricesPerField0matrices22net.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.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 matrices 2 2 http://biovel.googlecode.com/svn/tags/mpm-20140811/select_matrices.html LocallyPresentedHtml false net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefieldvalue00 Name of the field to introduce the stage matrices 2014-08-13 09:46:27.925 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Year net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.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 anot 2014-08-13 09:40:42.463 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity false net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemessagevalue00 Message to show to the user the action s/he needs to perform in the interaction page 2014-08-13 09:40:51.74 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select matrix files, then click Confirm net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeminMatricesPerFieldvalue00 Minimum number of matrices per field 2014-08-13 09:41:01.365 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemultiplevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity false net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketitlevalue00 Title to be shown in the interaction page 2014-08-13 09:41:34.771 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select a stage matrix for each year net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlattenListinputlist2outputlist11net.sf.taverna.t2.activitiesbeanshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity inputlist 2 text/plain java.lang.String true outputlist 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricestitletitlevalueRequestStageMatricesfieldfieldvalueRequestStageMatricesvaluesvaluesRequestStageMatricesmessagemessagevalueRequestStageMatricesminMatricesPerFieldminMatricesPerFieldvalueRequestStageMatricesmultiplemultiplevalueRequestStageMatricesforceEqualNumberMatricesPerFieldforceEqualNumberMatricesPerFieldvalueFlattenListinputlistRequestStageMatricesmatricesmatricesFlattenListoutputlist 1629a676-0820-432d-a5e0-c2b63dfe216a 2014-08-11 10:37:09.774 UTC eb7ff995-6def-43c9-9248-422a828fb6d2 2014-08-11 10:48:09.842 UTC 53df2b6d-fc40-46f1-9ccc-f72c7011dd57 2014-08-13 10:30:16.788 UTC RequestStageMatrices 2014-08-11 10:35:59.628 UTC b5df8a82-43c1-4126-afda-73a7a47ee637 2014-08-11 10:55:22.947 UTC 2b747eb4-5df4-455e-b118-82b57c02d194 2014-08-13 09:46:46.757 UTC Convert_Taverna_listlist_of_r_expressions22r_list_of_expressions1RExpressionToStringstringlist1concatenated00net.sf.taverna.t2.activitiesbeanshell-activity1.5-SNAPSHOTnet.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-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJoinListOfStringsIntoRListstringlist1output11net.sf.taverna.t2.activitiesbeanshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity stringlist 1 text/plain java.lang.String true output 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRExpressionToStringstringlistlist_of_r_expressionsJoinListOfStringsIntoRListstringlistRExpressionToStringconcatenatedr_list_of_expressionsJoinListOfStringsIntoRListoutput e138fe4e-acf6-4e88-a83f-f7dd8b7d4511 2014-01-09 10:34:46.821 UTC Convert Taverna list of RExpr to R list 2013-11-27 14:27:50.10 UTC Jonathan Giddy 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