Mean_matrixstages11 The names of the stages or categories of the input matrix. In the following example, the matrix has 5 stages. The stages of this matrix are called: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D 2014-07-31 14:00:37.437 UTC [S, J, V, G, D] 2014-07-31 13:53:36.576 UTC years11 [1987, 1988, 1989, 1990, 1991, 1992] 2014-07-31 14:01:41.735 UTC Each year represents a matrix and therefore characterizes a period of transition. In this tutorial, we have 6 matrices (see Example Input data) that represent 6 years e.g.: 1987 =data interval between 1987 and 1988 and 1988= data interval between 1988 and 1989 etc. 2014-08-14 13:45:22.856 UTC mean0 the calculated mean matrix from a list of matrices 2014-08-14 14:08:44.342 UTC S J V G D S 0,002459698 0 0 2,227220728 0 J 0,067338404 0,004605797 0 3,194361412 0 V 0,173724733 0,609529672 0,715389978 0,466246955 0,831721022 G 0 0,012105466 0,025024746 0,454641283 0,096747612 D 0 0,011466467 0,032099956 0,0247669 0,071498017 2014-07-31 14:04:05.336 UTC RequestStageMatricesvalues_L1multiple0field0title0forceEqualNumberMatricesPerField0minMatricesPerField0matrices_LL22net.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_file0labels_L1matrix_Rn211net.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.Loop net.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.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList 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.InvokeConvert_LRn2_to_RLn2list_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.Invokemean_calcmatrices1m11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity matrices 1 false m 1 1 false localhost 6311 false false matrices R_EXP m 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 1.0 100 200 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.InvokeYearvalue00net.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.InvokeOutputFundamentalMatrix_3input1output00net.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.InvokeSelect_a_matrixvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select a matrix 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.InvokeminMatricesPerFieldvalue00 Minimum number of matrices per field 2014-08-13 09:39:20.174 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.InvokeRequestStageMatricesvalues_LyearsRequestStageMatricesmultiplemultiplevalueRequestStageMatricesfieldYearvalueRequestStageMatricestitleSelect_a_matrixvalueRequestStageMatricesforceEqualNumberMatricesPerFieldforceEqualNumberMatricesPerFieldvalueRequestStageMatricesminMatricesPerFieldminMatricesPerFieldvalueReadStageMatrixmatrix_fileFlatten_ListoutputlistReadStageMatrixlabels_LstagesFlatten_ListinputlistRequestStageMatricesmatrices_LLConvert_LRn2_to_RLn2list_of_r_expressionsReadStageMatrixmatrix_Rn2mean_calcmatricesConvert_LRn2_to_RLn2r_list_of_expressionsOutputFundamentalMatrix_3inputmean_calcmmeanOutputFundamentalMatrix_3output 9b80b070-a717-4de8-ad28-f6aecba0ed4a 2014-01-22 15:36:19.385 UTC af1ed12c-fb04-490c-9cd8-c9d37050acf3 2014-01-22 15:30:51.591 UTC 57c200ac-9f18-49c8-81e0-73e35275df22 2014-02-04 12:40:15.97 UTC Maria Paula Balcazar-Vargas, Mikolaj Krzyzanowski, Jonathan Giddy, Francisco Quevedo and Gerard Oostermijer . 2014-08-14 14:09:04.23 UTC 0babaaa0-8442-4064-9607-96994e007893 2014-01-30 12:41:59.713 UTC 6f78ab7c-498a-47df-b4d4-734203b129de 2014-01-30 12:44:46.92 UTC a2969a4c-2faf-448c-8de1-d7580e1f4a21 2014-05-21 12:40:51.765 UTC 1dd5ce4f-4c1d-45d8-b4e1-81b41659f19e 2014-01-30 14:22:33.751 UTC 098dbce3-6f92-46cc-a6ff-83502f306561 2014-01-30 14:02:39.207 UTC b925170a-0f46-4fc0-9dfd-b2abd93c28c9 2014-01-30 12:23:36.905 UTC 7a912308-e318-4e70-b4a6-a0f676249f60 2014-08-14 13:45:24.219 UTC df50d7f7-8e37-4649-bbfe-2f179541ea7d 2014-01-30 12:26:33.170 UTC c3ddbb32-e035-4b70-9de5-1430f05039c0 2014-01-30 14:50:17.281 UTC f4b2c9ca-1cc2-4c24-a7fc-084d7d253b31 2014-01-30 12:32:54.963 UTC c54c44a3-8577-4bb0-b667-a2893b179cb8 2014-01-30 14:46:46.164 UTC 18e8a0a7-3e1c-4d14-b0af-1ed6642778c5 2014-05-01 11:02:51.57 UTC c00162c6-aedc-4c4f-aeda-fc39d757e446 2014-07-31 14:04:05.486 UTC 085e1cfd-9e6d-461b-be83-97958fd74c30 2014-01-30 14:06:28.387 UTC 4b09c6e5-5def-4c9a-8a1b-7dbff06e9965 2014-01-30 12:29:36.252 UTC 3660a11a-23e6-4ae8-86c2-45652e978e50 2014-01-22 15:34:57.108 UTC f50211da-b3dc-4499-9694-05f33ab09887 2014-01-22 15:32:42.979 UTC e72bc4ea-d7aa-4b82-86bf-b31c783c8324 2014-01-30 12:19:46.292 UTC 348f209f-f7de-42f1-9a56-9dcb19dc4ec2 2014-01-30 12:52:09.874 UTC 2a5df240-9162-4827-abc7-3a7dfc4352d4 2014-02-04 12:38:51.424 UTC 852d548d-e7d6-4fca-900d-69a0a96d0b9a 2014-08-14 14:09:06.193 UTC 352a165e-e1b7-4081-a39d-098cc18760d1 2014-01-30 12:25:41.905 UTC 59b59c5c-1f95-47d8-89a9-47dc2a92dfa6 2014-01-30 13:06:46.694 UTC 975cd586-3894-44b0-86b3-fbeecd271962 2014-01-30 12:28:04.777 UTC c7fc79f1-1545-48da-a748-a2104f171464 2014-01-30 12:41:13.191 UTC fbc4d358-ab9f-4863-9cbd-25a25434ab39 2014-01-30 12:20:41.104 UTC 6fc10a03-a298-4faf-8841-00e3d4b26dee 2014-01-30 12:43:53.718 UTC 6097442f-eb20-41c9-885a-57944e60c6ec 2014-01-30 14:42:39.118 UTC 7858ebd2-e7ef-4d9f-9399-5238f390a473 2014-01-30 13:52:14.782 UTC e22c8fc0-897d-4851-821a-b52c19f08228 2014-01-30 13:04:03.827 UTC fb493732-b6ed-41a1-bf8d-bb7de95eeb63 2014-01-30 14:41:39.801 UTC 2202d36f-ba99-4c9a-8b5c-6a9c6f90297f 2014-01-30 14:46:01.577 UTC abd83381-19d6-4e3e-92c6-37712176a7f7 2014-01-30 14:43:37.124 UTC c52d1dc4-54e8-4a1c-8f6b-55c448d6f3bd 2014-01-30 14:44:52.348 UTC 4a1a32c9-8ba1-4986-9829-b08bfd97cece 2014-01-22 15:40:58.43 UTC This mean matrix workflow estimates the mean matrix from a list of matrices. This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. This workflow was created using and based on Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ================================================================================== Literature Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts. Oostermeijer J.G.B., M.L. Brugman; E.R. de Boer; H.C.M. Den Nijs. 1996. Temporal and Spatial Variation in the Demography of Gentiana pneumonanthe, a Rare Perennial Herb. The Journal of Ecology, Vol. 84(2): 153-166. Stubben, C & B. Milligan. 2007. Estimating and Analysing Demographic Models Using the popbio Package in R. Journal of Statistical Software 22 (11): 1-23 Stubben, C., B. Milligan, P. Nantel. 2011. Package ‘popbio’. Construction and analysis of matrix population models. Version 2.3.1 2014-07-31 13:51:01.640 UTC e7a10164-5590-46c4-9571-28ea6ec9c107 2014-01-30 15:06:24.96 UTC 79859115-dbbf-4703-bdb3-824678729311 2014-02-19 14:45:20.806 UTC eafd9d19-c984-468f-8c6d-8d3e015e67b4 2014-01-22 15:33:59.286 UTC e70b6d4c-22db-499b-9aec-de5919774765 2014-01-30 14:40:54.996 UTC 4cd83774-63ed-4c4b-a881-33529e3823cd 2014-01-22 14:59:33.446 UTC 2795ee06-1fd8-40ec-bdb6-cc7e4b07b051 2014-02-05 15:42:37.81 UTC 999450f5-0f2c-4340-858c-8833d1d17253 2014-08-14 14:08:45.745 UTC 7b1f06d6-4d8d-49dc-ba61-bd9998b1ad58 2014-08-13 10:37:56.572 UTC Mean matrix 2014-07-31 13:49:59.577 UTC a9cc999a-9d86-4e48-9596-d1b8291102f0 2014-08-04 13:47:20.343 UTC 19920aef-bdc0-4c4c-916a-3ae020cc77f9 2014-01-22 15:37:40.706 UTC 5cad32e9-3dff-4f10-becb-2138b5494d9f 2014-01-30 14:16:24.425 UTC 8346d83d-96d0-4d4d-80f7-9912afacb0a1 2014-01-30 14:49:16.65 UTC 6399b2c3-c7d2-467e-a0fe-36b1b480deff 2014-01-30 12:31:27.856 UTC 314f8085-951d-4f98-a4de-2f31ad1caa47 2014-08-13 10:35:37.795 UTC 217d4dcf-1d99-4b1a-8d24-9c16ae5f6938 2014-01-30 13:26:10.134 UTC f081ac8e-6319-4878-a68c-f0a1b89baece 2014-01-30 12:34:40.860 UTC f9fa6364-e0a6-478f-9f59-f4ce29d28981 2014-07-31 14:01:41.915 UTC 22636a2d-46ec-4711-bad4-06a7edb4d808 2014-07-31 13:51:01.800 UTC ac80823a-6112-469c-9ed6-4f0d797d7765 2014-01-30 12:18:16.259 UTC 785491ad-b0cd-4cc9-949b-d6277ea75927 2014-01-30 12:14:17.602 UTC Convert_Taverna_listlist_of_r_expressions22r_list_of_expressions1FlattenListOfStringsToStringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true concatenated 0 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge UserNameHere 2013-10-14 14:22:51.151 UTC 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.InvokeCombineListOfStringsIntoRListstringlist1output11net.sf.taverna.t2.activitieslocalworker-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true output 1 1 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge UserNameHere 2013-10-14 14:21:14.818 UTC 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.InvokeFlattenListOfStringsToStringstringlistlist_of_r_expressionsCombineListOfStringsIntoRListstringlistFlattenListOfStringsToStringconcatenatedr_list_of_expressionsCombineListOfStringsIntoRListoutput Convert Taverna list of RExpr to R list 2013-09-04 15:13:12.850 UTC Jonathan Giddy 2013-09-04 15:12:34.436 UTC 472c6bef-15bc-4782-ab72-9e041b46e9d0 2013-10-14 14:28:56.870 UTC 1ff54110-840d-474e-95a4-877c8f2c5b5e 2013-09-04 15:26:02.821 UTC 13112099-3efd-42a7-bf18-a93c89de52dd 2013-09-04 15:30:31.850 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. 2013-10-14 14:28:55.280 UTC Workflow188input11output0PrettyPrintRinput1output00net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity input 1 false output 0 0 false localhost 6311 false false input R_EXP output 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.InvokePrettyPrintRinputinputoutputPrettyPrintRoutput deb0863c-b567-4755-af9c-b8b74d5e08e5 2013-06-21 14:31:25.529 UTC 1c210d9a-059f-4c52-8df7-0310db5e211f 2013-06-21 14:30:38.141 UTC 3da1a855-6b93-4760-9496-19703d7ec396 2014-01-22 14:29:59.616 UTC Workflow3values_L11multiple00field00title00minMatricesPerField00forceEqualNumberMatricesPerField00matrices_LL2SelectMatricesInteractionvalues1multiple0field0title0message0forceEqualNumberMatricesPerField0minMatricesPerField0matrices22net.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.interaction.InteractionActivity field 0 text/plain java.lang.String false values 1 text/plain java.lang.String false multiple 0 text/plain java.lang.String false title 0 text/plain java.lang.String false message 0 text/plain java.lang.String false forceEqualNumberMatricesPerField 0 text/plain java.lang.String false minMatricesPerField 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.Invokemessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select a matrix for each year, then click the Confirm button. 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.InvokeSelectMatricesInteractionvaluesvalues_LSelectMatricesInteractionmultiplemultipleSelectMatricesInteractionfieldfieldSelectMatricesInteractiontitletitleSelectMatricesInteractionmessagemessagevalueSelectMatricesInteractionforceEqualNumberMatricesPerFieldforceEqualNumberMatricesPerFieldSelectMatricesInteractionminMatricesPerFieldminMatricesPerFieldmatrices_LLSelectMatricesInteractionmatrices 4dbc4a0b-5962-4f21-96d2-0fb20185b17a 2014-01-16 11:25:38.561 UTC 3682addc-6be9-4f7c-a61c-756ce05a2fdf 2013-11-13 15:33:56.716 UTC 1791ddd6-09f3-4609-83f3-1910f5d7d37f 2014-05-01 11:02:46.628 UTC 5f4b1899-ccf2-474b-b4fb-01a59e02f264 2013-11-13 15:42:43.559 UTC f5456cef-7975-4376-a757-68764ae30f0e 2014-08-13 10:35:34.505 UTC b5e0ea8e-2e1a-409c-aec7-3f4c72ed167a 2013-11-13 15:32:49.843 UTC 9973b049-ee79-4fd7-8a87-8cf191d9509f 2013-10-28 15:04:57.615 UTC 9b37bccc-b963-457b-9efc-66985cb5aba7 2014-05-21 12:39:57.735 UTC 4a0bbebd-3357-48c7-ad1e-b5bcb7b6ec5c 2013-11-13 13:50:35.668 UTC 379602b6-1644-4b9f-a5bb-8161e03da77d 2013-10-28 16:47:25.115 UTC 249fb6a7-886e-4835-8b18-8bc293a6d77e 2013-10-28 16:45:55.371 UTC 47ab6f65-4bec-406a-8560-db17661b13f0 2014-08-13 10:35:20.302 UTC 08912d22-d766-4700-9394-77b1ef8e3a09 2013-10-28 16:49:51.515 UTC e04e4d3f-c7c9-438c-bc0c-c9740084e902 2013-11-13 13:50:47.718 UTC 9b0bff5f-8571-46ca-932e-0804b8324dda 2014-08-13 10:37:16.35 UTC ReadStageMatrixlabels_L11matrix_file00matrix_Rn21Matrix_ReadFromFilematrix_file0labels1read_matrix11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity matrix_file 0 false labels 1 false read_matrix 1 1 false localhost 6311 false false matrix_file TEXT_FILE labels STRING_LIST read_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.InvokeMatrix_ReadFromFilematrix_filematrix_fileMatrix_ReadFromFilelabelslabels_Lmatrix_Rn2Matrix_ReadFromFileread_matrix c8cf946f-3771-4321-870a-26408be164c7 2013-10-14 15:33:20.159 UTC ReadStageMatrix 2013-10-14 14:13:34.18 UTC a6ec62ed-cbc2-4705-812f-9fb8b8010169 2013-10-14 14:12:24.533 UTC 6b5b9009-65c6-45a2-941f-188268b27c59 2013-10-14 14:13:35.986 UTC 19c3521a-2d42-4f77-8dd2-10ab64286ef2 2013-10-15 13:59:10.98 UTC