Log_log_plots_of_varstages11 [S, J, V, G, D] 2014-08-13 10:58:38.493 UTC 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 2014-08-13 11:00:43.617 UTC years11 [1987, 1988, 1989, 1990, 1991, 1992] 2014-08-13 10:59:02.855 UTC Each year represents a matrix and therefore characterizes a period of transition. In this tutorial, we have 6 matrices (see Input data) that represent 6 years e.g.: 1987 =data interval between 1987 - 1988 and 1988= data interval between 1988 - 1989 etc. 2014-08-14 12:58:31.269 UTC pfister_graph0 Graph plotting CV vs. Elasticity in matrix elements, showing the regression line (red line) and the Spearman correlation value (ρ) between these two values. 2014-08-14 12:58:38.518 UTC spearman_rank0 Spearman correlation results of the CV vs. Elasticity in matrix elements 2014-08-13 12:59:24.274 UTC "Spearman's rank correlation rho" data: vr1$cv and vr1$elas S = 1488, p-value = 0.02377 alternative hypothesis: true rho is not equal to 0 sample estimates: rho -0.5356037 2014-08-13 12:36:53.4 UTC pfister_plot0 Graphs of the calculated values of Sensitivity vs. Variance and CV vs. Elasticity in matrix elements. 2014-08-13 12:37:16.812 UTC pfister_plot_table0 A table of calculated values of mean, variance, CV, sensitivity and elasticity of the matrix elements. 2014-08-13 12:37:34.494 UTC mean var cv sens elas a11 0,002459698 1,26E-05 144,05386 0,021023792 5,47E-05 a21 0,067350239 6,32E-03 118,07172 0,066912895 4,77E-03 a31 0,173736086 2,66E-02 93,93399 0,088205265 1,62E-02 a22 0,004605797 2,48E-05 108,22858 0,099776711 4,86E-04 a32 0,609529672 3,73E-02 31,68504 0,131526685 8,48E-02 a42 0,012105466 2,09E-04 119,40443 0,919475709 1,18E-02 a52 0,011466467 1,23E-04 96,55131 0,226904442 2,75E-03 a33 0,715390128 1,28E-02 15,84439 0,576723463 4,36E-01 a43 0,025026248 1,17E-03 136,89433 4,031753836 1,07E-01 a53 0,032102959 5,30E-04 71,69679 0,994939665 3,38E-02 a14 2,227331845 9,11E+00 135,51451 0,008903495 2,10E-02 a24 3,154680462 9,60E+00 98,19777 0,028337352 9,45E-02 a34 0,466249338 4,43E-02 45,12835 0,037354589 1,84E-02 a44 0,454649217 5,63E-02 52,20394 0,261138165 1,26E-01 a54 0,0247669 1,32E-03 146,62524 0,064442605 1,69E-03 a35 0,831731875 1,60E-02 15,20576 0,023961774 2,11E-02 a45 0,09676079 7,56E-03 89,85414 0,167511778 1,71E-02 a55 0,071507318 4,15E-03 90,12403 0,041337869 3,13E-03 2014-08-13 12:37:51.667 UTC RequestStageMatricesvalues_L1multiple0field0title0matrices_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.Invokegraph20bmatrices1fec_xy1pfister_plot200spr11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity matrices 1 false fec_xy 1 false pfister_plot2 0 0 spr 1 1 false localhost 6311 false false matrices R_EXP fec_xy STRING_LIST pfister_plot2 PNG_FILE spr 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.InvokeCategoriseStages_Interactionmessage0title0stages1fecundityIndices11 With this dialogue automatically appears the names of the stages or categories of the census data file. When the dialogue appears, the stages are in disorder, so the user drags and organizes the stages according to the order in the life cycle. Then, the author chooses if the stage belongs to the recruited, reproductive category or it should be excluded. Recruited means that new individuals can be recruited to this (these) stage(s). Reproductive stages are those that reproduce (produce offspring) (in this example the stage G). In the census data file Dt1.txt, x is use to denote when a plant has died in the second year, so the user must selected in the excluded column. Then the user clicks in confirm and you will read stages submitted. In the following example, the life cycle of Gentiana pneumonanthe has 5 stages or categories: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D 2012-11-01 14:53:35.21 UTC net.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.interaction.InteractionActivity stages 1 text/plain java.lang.String false message 0 text/plain java.lang.String false title 0 text/plain java.lang.String false fecundityIndices 1 1 //biovel.googlecode.com/svn/tags/mpm-20140626/select_fecundity_matrix.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.Invokegraph20amatrices1pfister_plot00tab11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity matrices 1 false pfister_plot 0 0 tab 1 1 false localhost 6311 false false matrices R_EXP pfister_plot PNG_FILE tab 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.InvokeOutputFundamentalMatrix_3_2input1output00net.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.Invokemessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select fecundity stage transitions, 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.InvokeSelect_stagesvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select fecundity transitions 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.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.InvokeRequestStageMatricesvalues_LyearsRequestStageMatricesmultiplemultiplevalueRequestStageMatricesfieldYearvalueRequestStageMatricestitleSelect_a_matrixvalueReadStageMatrixmatrix_fileFlatten_ListoutputlistReadStageMatrixlabels_LstagesFlatten_ListinputlistRequestStageMatricesmatrices_LLConvert_LRn2_to_RLn2list_of_r_expressionsReadStageMatrixmatrix_Rn2graph20bmatricesConvert_LRn2_to_RLn2r_list_of_expressionsgraph20bfec_xyCategoriseStages_InteractionfecundityIndicesOutputFundamentalMatrix_3inputgraph20bsprCategoriseStages_InteractionmessagemessagevalueCategoriseStages_InteractiontitleSelect_stagesvalueCategoriseStages_Interactionstagesstagesgraph20amatricesConvert_LRn2_to_RLn2r_list_of_expressionsOutputFundamentalMatrix_3_2inputgraph20atabpfister_graphgraph20bpfister_plot2spearman_rankOutputFundamentalMatrix_3outputpfister_plotgraph20apfister_plotpfister_plot_tableOutputFundamentalMatrix_3_2output 23ac88cc-a1ca-4307-b37e-81bb4ffb977a 2014-08-13 12:35:25.67 UTC 2bfb4912-f75b-409a-b8f0-e401d1aa288e 2014-06-09 11:30:39.493 UTC 026c2803-8198-4b45-ac58-286c58bb73d1 2014-01-30 15:06:30.379 UTC d9df7dc7-ff05-420d-8552-9d8d93c10785 2014-01-30 15:15:14.703 UTC 6399b2c3-c7d2-467e-a0fe-36b1b480deff 2014-01-30 12:31:27.856 UTC 6f78ab7c-498a-47df-b4d4-734203b129de 2014-01-30 12:44:46.92 UTC 217d4dcf-1d99-4b1a-8d24-9c16ae5f6938 2014-01-30 13:26:10.134 UTC 287c70cb-a73c-4762-a645-2f03bba95387 2014-08-19 08:50:16.336 UTC 7a79e657-35a3-42d8-979d-4878384fd112 2014-05-01 11:10:26.483 UTC c968ca36-13de-4606-8bcf-455186a2ed62 2014-01-30 15:16:28.95 UTC 67369ce6-3783-41ed-9d1a-09edd0615d98 2014-03-12 13:56:21.508 UTC 514ceb09-013e-444d-8f7a-5e50e7608e43 2014-06-09 10:48:28.347 UTC 0babaaa0-8442-4064-9607-96994e007893 2014-01-30 12:41:59.713 UTC aa94cc1e-117a-48f8-a3ee-9c4b3fa8615d 2014-03-12 14:24:14.586 UTC fbc4d358-ab9f-4863-9cbd-25a25434ab39 2014-01-30 12:20:41.104 UTC ba7b6ae2-1a23-4049-8ae7-031ea06668b9 2014-06-09 12:29:07.138 UTC 616b6248-a39e-4724-a0d5-186d0e084012 2014-08-13 12:36:53.134 UTC 156c2607-3107-4265-b7a3-c9bff4be75b5 2014-06-09 12:15:46.613 UTC 498d9ea4-ddd2-4036-845e-d9da698cffd2 2014-02-19 13:28:23.718 UTC 0f434d33-5836-4460-9074-9f0e808f5164 2014-06-09 12:23:40.12 UTC e0b5af5a-ec95-4cd9-8ed5-fc666c425fc6 2014-06-09 12:30:55.275 UTC 098dbce3-6f92-46cc-a6ff-83502f306561 2014-01-30 14:02:39.207 UTC 1dd5ce4f-4c1d-45d8-b4e1-81b41659f19e 2014-01-30 14:22:33.751 UTC e22c8fc0-897d-4851-821a-b52c19f08228 2014-01-30 13:04:03.827 UTC e72bc4ea-d7aa-4b82-86bf-b31c783c8324 2014-01-30 12:19:46.292 UTC 37a3d6c0-367e-4df6-bba4-1cfe17034daa 2014-07-02 12:33:19.933 UTC 9b80b070-a717-4de8-ad28-f6aecba0ed4a 2014-01-22 15:36:19.385 UTC 785491ad-b0cd-4cc9-949b-d6277ea75927 2014-01-30 12:14:17.602 UTC 480620c4-5a62-4d77-b32e-523bbea340b5 2014-05-30 08:32:01.943 UTC 44642922-7ed1-45e5-9bf4-6d0b087d4ad1 2014-03-12 14:26:47.907 UTC 0ffe2b8c-307c-4604-924a-d9a6d23aba7c 2014-03-12 14:09:41.930 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 19920aef-bdc0-4c4c-916a-3ae020cc77f9 2014-01-22 15:37:40.706 UTC 02f9be04-9ad9-4f7c-a42e-35ee0bc50aff 2014-05-21 12:46:15.738 UTC e167e277-3b91-4339-a2a6-66e65a7b385a 2014-08-19 08:49:36.438 UTC 3660a11a-23e6-4ae8-86c2-45652e978e50 2014-01-22 15:34:57.108 UTC aa234bcf-72bf-4e4d-a2d1-f3f434e161a1 2014-08-21 08:52:40.347 UTC 5cad32e9-3dff-4f10-becb-2138b5494d9f 2014-01-30 14:16:24.425 UTC c5a0629e-47de-4574-84b8-15d21f43edc0 2014-02-04 11:18:29.32 UTC bcaaa4a0-0663-4d39-b61b-2bae44ce940a 2014-02-19 13:32:24.458 UTC c3b208b7-bef2-4582-a3a1-82174e4ba8fb 2014-06-09 12:24:22.521 UTC bba5fbd2-997b-4b0d-b8d4-12c530301ff6 2014-06-09 11:19:11.929 UTC 6fc10a03-a298-4faf-8841-00e3d4b26dee 2014-01-30 12:43:53.718 UTC 1f6d5764-6e50-4994-a068-350a28bfdc32 2014-08-13 12:37:51.797 UTC This workflow creates log-log plots of both variance vs. sensitivity and CV vs. elasticity in matrix elements. Plots are based on Figure 2 in Pfister (1998). This workflow calculates as well the summary mean, variance, CV, sensitivities and elasticities of each matrix element of the submitted matrices. Please if you want to know more about this analyses please refer to: Pfister, C.A. 1998. Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications. Proc. Natl. Acad. Sci. USA, 95: 213–218. 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. Pfister, C.A. 1998. Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications. Proc. Natl. Acad. Sci. USA, 95: 213–218. 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 2014-08-13 12:03:08.509 UTC eafd9d19-c984-468f-8c6d-8d3e015e67b4 2014-01-22 15:33:59.286 UTC 84fd477e-e0b4-4238-9485-4edf3b0ccf44 2014-03-12 14:08:28.629 UTC 4cd83774-63ed-4c4b-a881-33529e3823cd 2014-01-22 14:59:33.446 UTC 7858ebd2-e7ef-4d9f-9399-5238f390a473 2014-01-30 13:52:14.782 UTC f50211da-b3dc-4499-9694-05f33ab09887 2014-01-22 15:32:42.979 UTC 348f209f-f7de-42f1-9a56-9dcb19dc4ec2 2014-01-30 12:52:09.874 UTC df50d7f7-8e37-4649-bbfe-2f179541ea7d 2014-01-30 12:26:33.170 UTC 54cd8e08-0449-43ed-9709-ca7479210f7d 2014-03-12 14:31:47.816 UTC ac80823a-6112-469c-9ed6-4f0d797d7765 2014-01-30 12:18:16.259 UTC 2656c68b-ca75-4dda-af1d-c58f9fb2934a 2014-03-12 14:13:44.667 UTC 36b91a6c-30fc-41de-8e7a-0dbdbca60eb5 2014-01-30 14:32:56.847 UTC 7afc63c9-2618-432c-821f-6165b08bf54d 2014-08-13 10:59:16.736 UTC b96375e3-a69f-4d54-bce3-99260f0a6f8b 2014-06-09 12:19:38.858 UTC c7fc79f1-1545-48da-a748-a2104f171464 2014-01-30 12:41:13.191 UTC 22821b95-408a-4c8a-afd2-b950caa590d0 2014-08-13 11:01:02.499 UTC 266a7a30-65df-41d5-bb63-f9c83ca3bdec 2014-08-13 12:59:26.166 UTC c22c065d-0fdb-4329-a297-aa5d3aad73a0 2014-03-12 13:59:55.640 UTC 997f319b-0449-4dc5-8ad4-739e4b940860 2014-08-13 12:03:09.579 UTC 352a165e-e1b7-4081-a39d-098cc18760d1 2014-01-30 12:25:41.905 UTC 23155441-913d-432b-bd4f-3460251e149b 2014-05-30 07:37:53.918 UTC af1ed12c-fb04-490c-9cd8-c9d37050acf3 2014-01-22 15:30:51.591 UTC 950f497c-df88-4dbc-871a-ea89d2170d26 2014-07-02 12:34:44.876 UTC 9e35a27b-f46e-4803-b2fa-76fef46873c3 2014-03-12 14:01:23.66 UTC 1377d9cd-8d15-4573-8b15-e08609260016 2014-06-26 11:24:23.283 UTC 8c8b409b-60c3-4536-8ffc-51b97c8ea2e7 2014-03-12 14:19:45.770 UTC 01690407-98aa-493f-95fe-6d147522daa0 2014-08-13 11:00:28.334 UTC 085e1cfd-9e6d-461b-be83-97958fd74c30 2014-01-30 14:06:28.387 UTC 21c3d918-a29b-4200-b602-e88cad1206e8 2014-03-12 13:58:05.817 UTC e2de2fe5-ff6b-4623-927f-f68ceab4a922 2014-06-09 11:17:02.530 UTC 5e567feb-8018-4c7f-a287-59a8ef7279e8 2014-02-19 13:30:59.164 UTC f376f4a9-7892-4d4f-aa0a-175a8248065c 2014-01-30 14:35:00.282 UTC 09652be8-35a0-4006-aba5-6a75aa3c9695 2014-03-12 14:23:20.728 UTC f081ac8e-6319-4878-a68c-f0a1b89baece 2014-01-30 12:34:40.860 UTC a5f0cc4d-5b1a-4470-b61e-28c82afff02c 2014-08-14 12:58:48.623 UTC 68d0c67a-d7b9-4f0d-a801-64d4de50d088 2014-05-01 11:12:06.251 UTC 4f245bd7-2aca-4366-bb00-623e680aafe4 2014-03-12 14:18:28.428 UTC 4a1a32c9-8ba1-4986-9829-b08bfd97cece 2014-01-22 15:40:58.43 UTC 2268c4fd-52e1-48e5-8d2f-8e578f90319a 2014-06-09 12:17:48.467 UTC Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements 2014-08-13 10:59:42.703 UTC 633c0842-97be-43cc-b8a2-faf8b211991d 2014-01-30 14:37:41.374 UTC be591851-207d-4dd1-9fae-ac07c1d8eb76 2014-02-19 13:30:22.407 UTC Maria Paula Balcazar-Vargas, Mikolaj Krzyzanowski, Jonathan Giddy, Francisco Quevedo and Gerard Oostermijer . 2014-08-21 08:52:38.897 UTC 0abc668e-9c29-4464-8677-26793e4e8bb0 2014-03-12 14:33:38.456 UTC 4b09c6e5-5def-4c9a-8a1b-7dbff06e9965 2014-01-30 12:29:36.252 UTC f4b2c9ca-1cc2-4c24-a7fc-084d7d253b31 2014-01-30 12:32:54.963 UTC b925170a-0f46-4fc0-9dfd-b2abd93c28c9 2014-01-30 12:23:36.905 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 ReadStageMatrix 2013-10-14 14:13:34.18 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 c8cf946f-3771-4321-870a-26408be164c7 2013-10-14 15:33:20.159 UTC a6ec62ed-cbc2-4705-812f-9fb8b8010169 2013-10-14 14:12:24.533 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 3da1a855-6b93-4760-9496-19703d7ec396 2014-01-22 14:29:59.616 UTC 1c210d9a-059f-4c52-8df7-0310db5e211f 2013-06-21 14:30:38.141 UTC deb0863c-b567-4755-af9c-b8b74d5e08e5 2013-06-21 14:31:25.529 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 Jonathan Giddy 2013-09-04 15:12:34.436 UTC Convert Taverna list of RExpr to R list 2013-09-04 15:13:12.850 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 1ff54110-840d-474e-95a4-877c8f2c5b5e 2013-09-04 15:26:02.821 UTC 472c6bef-15bc-4782-ab72-9e041b46e9d0 2013-10-14 14:28:56.870 UTC Workflow3values_L11multiple00field00title00matrices_LL2SelectMatricesInteractionvalues1multiple0field0title0message0matrices22net.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 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, the 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_LSelectMatricesInteractionmultiplemultipleSelectMatricesInteractionfieldfieldSelectMatricesInteractiontitletitleSelectMatricesInteractionmessagemessagevaluematrices_LLSelectMatricesInteractionmatrices 249fb6a7-886e-4835-8b18-8bc293a6d77e 2013-10-28 16:45:55.371 UTC 3682addc-6be9-4f7c-a61c-756ce05a2fdf 2013-11-13 15:33:56.716 UTC 379602b6-1644-4b9f-a5bb-8161e03da77d 2013-10-28 16:47:25.115 UTC aa1bce37-9305-46fe-94ce-54147fc9dbbc 2014-05-01 11:11:23.650 UTC 9973b049-ee79-4fd7-8a87-8cf191d9509f 2013-10-28 15:04:57.615 UTC 4a0bbebd-3357-48c7-ad1e-b5bcb7b6ec5c 2013-11-13 13:50:35.668 UTC e1d2b65a-5760-4545-ab45-093ff6af8b53 2014-08-19 08:49:23.864 UTC e04e4d3f-c7c9-438c-bc0c-c9740084e902 2013-11-13 13:50:47.718 UTC 6a5b3b94-e9e7-4a3c-adfe-827a28db11fc 2014-05-21 12:45:46.881 UTC 5f4b1899-ccf2-474b-b4fb-01a59e02f264 2013-11-13 15:42:43.559 UTC 3eb71377-6971-4010-ae33-7f620c9efbcc 2014-05-01 11:11:59.305 UTC 08912d22-d766-4700-9394-77b1ef8e3a09 2013-10-28 16:49:51.515 UTC 4dbc4a0b-5962-4f21-96d2-0fb20185b17a 2014-01-16 11:25:38.561 UTC b5e0ea8e-2e1a-409c-aec7-3f4c72ed167a 2013-11-13 15:32:49.843 UTC