Simulate_stochastic_stages11 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 press add value (see arrow in Fig), fill a stage name (not longer than 8 characters) and press enter; then press add value and fill once again the next stage name, repeat the action until you have fill all the stages names. In the following example, the matrix has 5 stages or categories: The stages of this matrix are called: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D 2014-07-11 13:17:44.858 UTC [S, J, V, G, D] 2014-05-21 14:40:23.268 UTC graph_title00 Projection of stochastic growth for Gentiana using equal and unequal probabilities 2014-05-21 14:40:55.852 UTC Is the main title to be display in the stochastic projection graph. Click in add value and then write the text in the right space. Please do not use a title longer than the suggest it. 2014-07-11 13:12:42.334 UTC intervals00 This value is the number of time steps or projection intervals to predict future population size or in other words the time to predict future population size. Click in add value and write the number in the right space. 2014-07-11 13:13:29.437 UTC 25 2014-05-21 14:41:02.962 UTC iterations00 1000 2014-07-11 13:21:02.274 UTC It is the number of iterations or the number of realizations of population growth to simulate. Click in add value and write the number in the right space. 2014-07-11 13:14:18.297 UTC probabilities11 [0.1, 0.1, 0.1, 0.1, 0.2, 0.4] 2014-07-25 13:55:13.956 UTC It is a vector of probability weights used by sample for selecting the projection matrices. In the following example, we use 6 matrices of 6 consecutive years, so if the user selects probabilities weights, the user must fill in 6 probabilities in total that sum up 1. No probability weights: If the user wants to use no probability weights, this is established by: First, click in add value, then in the left window a List is added with a "Some input data goes here" element in the right window. Delete that text. After, deletion the "List" have no elements. When running the workflow, Rshell script will assign NULL to the input. (this is when you are running the wf in Taverna workbench) Probability weights: The respective probabilities must be filled one by one, they must sum up 1. First, press add value (see arrow in Fig.), fill a probability number and press enter; then press add value and fill once again the next probability, repeat the action until you have filled the probabilities for all matrices. The order of the probabilities must follow the order of the years input. Each year represent a matrix. e.g. 0.1, 0.1, 0.1, 0.1, 0.2, 0.4 (all the probabilities must sum up 1) 2014-07-25 13:55:07.547 UTC years11 [1987, 1988, 1989, 1990, 1991, 1992] 2014-05-21 14:40:11.539 UTC Years in which the data of the matrices were collected. The years must be added one by one as list. First click in add value, fill the first year and press enter, then press add value and fill once again the next year, repeat the action until you have fill all the years. The years can be display as follow: e.g. • 1987 or • 1987-1988 2014-07-11 13:19:05.871 UTC sumweight11 A vector of ones and zeroes used to omit stage classes when checking density. threshold. The respective sumweights must be filled one by one, the values must be 1 if the stage is included or 0 if is absent. First, press add value (see arrow in Fig.), fill a sumweights number and press enter; then press add value and fill once again the next sumweight, repeat the action until you have filled the sumweights for all stages. The order of the sumweights must follow the order of the stage input. e.g. 1, 1, 1, 1, 1 (all the stages are included) e.g. 1, 1, 1, 0, 1 (stage G is omit) 2014-07-11 13:18:04.174 UTC [1, 1, 1, 1, 1] 2014-07-11 13:19:50.432 UTC nmax11 [] 2014-07-28 14:01:46.564 UTC It is a maximum number of individuals beyond which population projections cannot exceed. No density dependence: If the user wants to use no density dependence, this is established by: First, click in add value, then in the left window a List is added with a "Some input data goes here" element in the right window. Delete that text. After deletion the "List" have no elements in the right window. When running the workflow, Rshell script will assign NULL to the input. (this is when you are running the wf in Taverna workbench). Density dependence: If the user wants to introduce a density dependence: Click in add value and write the number in the right space. e.g. 500 2014-07-11 14:29:27.987 UTC stochastic_projection0equal_selection0unequal_selection0RequestStageMatricesvalues_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.Invokegraphprobabilities1iterations0intervals0graph_title0stages1abundances1matrices1weight1n_max1stochastic_growth_plot00eq11uneq11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity stages 1 false abundances 1 false matrices 1 false graph_title 0 false intervals 0 false iterations 0 false probabilities 1 false weight 1 false n_max 1 false stochastic_growth_plot 0 0 eq 1 1 uneq 1 1 false localhost 6311 false false stages STRING_LIST abundances R_EXP matrices R_EXP graph_title STRING intervals INTEGER iterations INTEGER probabilities DOUBLE_LIST weight INTEGER_LIST n_max INTEGER_LIST stochastic_growth_plot PNG_FILE eq R_EXP uneq 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.InvokeAbundance_Interactionstages1title0message0abundances11 Abundance iteraction: Initial abundance: In this dialogue authomatically appears the fields to fill out the initial abundance per stage observed in the field (see data below). After fill out the abundances, the user confirms the numbers. As a example Gentiana pneumonanthe has 5 stages with its respective abundance: stage abundance 1) S (seedlings) 69 2) J (Juveniles) 100 3) V (vegetative) 111 4) G (reproductive individuals) 21 5) D (dormant plants) 43 2012-11-01 11:56:16.812 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 abundances 1 1 http://biovel.googlecode.com/svn/tags/mpm-20140521/set_abundance.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.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.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 INTEGER_LIST 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.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.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.InvokeInitial_Population_Vectorvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select initial population vector 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_matrix_filesvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select matrix files 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.InvokeFirstListElementlist1elem00net.sf.taverna.t2.activitiesbeanshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity list 1 text/plain java.lang.String true elem 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.InvokeRequestStageMatricesvalues_LyearsRequestStageMatricesmultiplemultiplevalueRequestStageMatricesfieldYearvalueRequestStageMatricestitleSelect_matrix_filesvalueReadStageMatrixmatrix_fileFlatten_ListoutputlistReadStageMatrixlabels_LstagesFlatten_ListinputlistRequestStageMatricesmatrices_LLConvert_LRn2_to_RLn2list_of_r_expressionsReadStageMatrixmatrix_Rn2graphprobabilitiesprobabilitiesgraphiterationsiterationsgraphintervalsintervalsgraphgraph_titlegraph_titlegraphstagesstagesgraphabundancesAddNamesexprgraphmatricesConvert_LRn2_to_RLn2r_list_of_expressionsgraphweightsumweightgraphn_maxnmaxAbundance_InteractionstagesstagesAbundance_InteractiontitleInitial_Population_VectorvalueAbundance_InteractionmessageFirstListElementelemAddNameslabelsstagesAddNamesexprAbundance_InteractionabundancesOutputFundamentalMatrix_3inputgrapheqOutputFundamentalMatrix_3_2inputgraphuneqFirstListElementlistyearsstochastic_projectiongraphstochastic_growth_plotequal_selectionOutputFundamentalMatrix_3outputunequal_selectionOutputFundamentalMatrix_3_2output Maria Paula Balcazar-Vargas, Mikolaj Krzyzanowski, Jonathan Giddy, Francisco Quevedo and Gerard Oostermijer . 2014-07-30 12:22:31.930 UTC 69cdff57-e566-4b9b-98a9-45b0b98819b7 2014-03-05 15:49:04.215 UTC 37c2bda2-fd8e-4c9a-94f4-2e17dd3f8118 2014-07-28 16:54:27.695 UTC 033579c5-1a8a-4b9f-8c74-63a87aee03ba 2014-07-10 12:33:14.480 UTC 352a165e-e1b7-4081-a39d-098cc18760d1 2014-01-30 12:25:41.905 UTC c7fc79f1-1545-48da-a748-a2104f171464 2014-01-30 12:41:13.191 UTC f2ef7c08-49ac-436b-a4ae-9a2b19f85c24 2014-07-10 14:42:24.666 UTC 4b09c6e5-5def-4c9a-8a1b-7dbff06e9965 2014-01-30 12:29:36.252 UTC e22c8fc0-897d-4851-821a-b52c19f08228 2014-01-30 13:04:03.827 UTC ce2001d5-a3e7-41b1-af9a-8f3c528a2deb 2014-02-05 13:22:11.360 UTC 752811f1-6468-4f64-9f11-49d0cda7a85f 2014-07-10 12:57:06.319 UTC e72bc4ea-d7aa-4b82-86bf-b31c783c8324 2014-01-30 12:19:46.292 UTC f7a6e74d-dc66-491b-b0d2-f9abbeae7683 2014-07-10 12:42:48.656 UTC 3660a11a-23e6-4ae8-86c2-45652e978e50 2014-01-22 15:34:57.108 UTC dfc14de5-0609-498c-b6b9-0231d9c5445c 2014-07-25 13:31:46.932 UTC af1ed12c-fb04-490c-9cd8-c9d37050acf3 2014-01-22 15:30:51.591 UTC df50d7f7-8e37-4649-bbfe-2f179541ea7d 2014-01-30 12:26:33.170 UTC 8d809279-8d16-421e-b03b-17b65fc2a745 2014-03-05 14:35:39.929 UTC 72cac1e2-9029-4603-8f97-67aca3e76b99 2014-07-11 14:29:29.258 UTC 975cd586-3894-44b0-86b3-fbeecd271962 2014-01-30 12:28:04.777 UTC b925170a-0f46-4fc0-9dfd-b2abd93c28c9 2014-01-30 12:23:36.905 UTC f1edc485-4c4b-44ba-971d-8fe7606fa067 2014-03-05 13:13:52.949 UTC 217d4dcf-1d99-4b1a-8d24-9c16ae5f6938 2014-01-30 13:26:10.134 UTC 138a43e6-a2a4-43d6-a834-ba27c0b5b168 2014-05-21 14:41:29.549 UTC 5f54285a-3376-4822-8d53-ed98f87f6dbb 2014-03-05 12:12:20.893 UTC fbc4d358-ab9f-4863-9cbd-25a25434ab39 2014-01-30 12:20:41.104 UTC 074d93e2-58ed-46f4-b6da-84c9bbff07f7 2014-03-05 15:59:49.623 UTC 9b80b070-a717-4de8-ad28-f6aecba0ed4a 2014-01-22 15:36:19.385 UTC 59b59c5c-1f95-47d8-89a9-47dc2a92dfa6 2014-01-30 13:06:46.694 UTC Simulate stochastic growth from a sequence of matrices 2014-07-10 12:28:35.864 UTC c3f6066d-838f-49e2-bc95-be6888a88775 2014-07-28 13:53:36.852 UTC 6f78ab7c-498a-47df-b4d4-734203b129de 2014-01-30 12:44:46.92 UTC 17189ca3-7ecb-4f6e-af1a-37864bde0526 2014-03-05 13:14:59.234 UTC 4c1611b0-f95c-49cc-a56f-d7b6e14fff54 2014-07-11 13:19:56.104 UTC 38e4998b-9253-4469-b9ff-b3b8dce7d283 2014-03-05 15:55:07.4 UTC 5c4367a4-766b-41ad-8e11-09e270bc7c0e 2014-03-05 15:50:48.886 UTC c57c0a13-3ab8-4c3f-884f-c7f761ca8d18 2014-03-05 16:02:29.984 UTC 10f8bebd-8324-4144-a1f8-5ccf55927c9b 2014-07-30 12:22:33.562 UTC 19920aef-bdc0-4c4c-916a-3ae020cc77f9 2014-01-22 15:37:40.706 UTC 3de0f13c-49e9-47a8-a8e5-30ad02cf9c41 2014-07-10 12:46:39.601 UTC c75a5a9e-2bc1-475a-b91b-7dcb4330e446 2014-07-10 13:19:23.326 UTC 037d672c-8377-4684-bf3f-e9fef2a6ed5e 2014-05-21 14:34:58.347 UTC 6435d6da-e85e-4c82-b050-032bd48fcdc6 2014-07-28 14:02:00.358 UTC f3a7d64a-1db0-45c1-9c11-016743aaf83d 2014-03-05 15:51:41.811 UTC 90ff69d6-f86e-4209-a0a7-663b17c3c128 2014-05-21 14:37:48.906 UTC 348f209f-f7de-42f1-9a56-9dcb19dc4ec2 2014-01-30 12:52:09.874 UTC cf79b137-b2e4-4a8b-8030-25ac8be5b040 2014-03-05 13:22:14.121 UTC 16628918-ef09-43ec-92ef-7f0ff47c03f2 2014-03-05 13:12:23.822 UTC The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices. This workflow is based on the popbio package (script: stoch.projection - Simulate stochastic growth from a sequence of matrices, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.3 (Morris and Doak 2002). For more details of the analysis see: Exploring population growth in a variable environment with computer simulations (Morris and Doak 2002, pag: 229-233 and Caswell 2001, Chapter 14). Outputs: • Equal selection data • Stochastic projection • Unequal selection data We use Gentiana pneumonanthe only as example how to run this workflow. 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. Morris, W. F., and D. F. Doak. 2002. Quantitative conservation biology: Theory and practice of population viability analysis. Sinauer, Sunderland, Massachusetts, USA. 480 pages 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. 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12:10:38.478 UTC 995361fa-7a38-4e01-b02f-e460edd8704b 2014-07-25 13:55:14.133 UTC e42a1f86-f7b7-4749-934d-18cb319e3d98 2014-03-05 15:47:28.521 UTC 4a1a32c9-8ba1-4986-9829-b08bfd97cece 2014-01-22 15:40:58.43 UTC 76275a5c-b71a-45c8-9105-aac827128a1d 2014-05-21 14:48:44.879 UTC 065be1b6-1f9c-45bc-91b4-e1a533ea1da2 2014-05-21 14:47:12.579 UTC b958e6a7-c09b-43cb-97d9-3972c3a4ec08 2014-02-05 13:20:03.472 UTC 0530bf3c-64ff-4778-85d0-aa3eaa51df37 2014-05-01 10:53:53.919 UTC fc5ee224-e78e-4836-a52b-898437b662ba 2014-05-21 14:54:00.553 UTC 44146ce2-20f8-46e7-8b7e-8ca37e3ea896 2014-05-02 10:00:51.295 UTC f50211da-b3dc-4499-9694-05f33ab09887 2014-01-22 15:32:42.979 UTC 785491ad-b0cd-4cc9-949b-d6277ea75927 2014-01-30 12:14:17.602 UTC 79981e3c-bf7d-4896-bb43-5ebc0ab65ea0 2014-03-05 13:19:29.801 UTC a3023b00-20c0-4f2b-ab4b-e231d6c66d8f 2014-05-21 14:33:35.629 UTC 57b4d3e1-1cc1-411a-aafe-8715172632a7 2014-05-21 14:42:06.55 UTC 4cd83774-63ed-4c4b-a881-33529e3823cd 2014-01-22 14:59:33.446 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 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 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 2a72e54d-1d2f-4db8-bb43-e791bb565727 2014-07-28 16:54:23.544 UTC deb0863c-b567-4755-af9c-b8b74d5e08e5 2013-06-21 14:31:25.529 UTC 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 0bc8db78-b17c-46a6-83ac-ecff2e6aef20 2014-07-28 16:35:57.718 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 6b5b9009-65c6-45a2-941f-188268b27c59 2013-10-14 14:13:35.986 UTC a6ec62ed-cbc2-4705-812f-9fb8b8010169 2013-10-14 14:12:24.533 UTC ReadStageMatrix 2013-10-14 14:13:34.18 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 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-20140521/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_LSelectMatricesInteractionmultiplemultipleSelectMatricesInteractionfieldfieldSelectMatricesInteractiontitletitleSelectMatricesInteractionmessagemessagevaluematrices_LLSelectMatricesInteractionmatrices 3682addc-6be9-4f7c-a61c-756ce05a2fdf 2013-11-13 15:33:56.716 UTC 840d5ee4-61c8-414d-8b30-3cf98429e575 2014-05-01 10:53:42.303 UTC 379602b6-1644-4b9f-a5bb-8161e03da77d 2013-10-28 16:47:25.115 UTC 08912d22-d766-4700-9394-77b1ef8e3a09 2013-10-28 16:49:51.515 UTC 5f4b1899-ccf2-474b-b4fb-01a59e02f264 2013-11-13 15:42:43.559 UTC 4a0bbebd-3357-48c7-ad1e-b5bcb7b6ec5c 2013-11-13 13:50:35.668 UTC e04e4d3f-c7c9-438c-bc0c-c9740084e902 2013-11-13 13:50:47.718 UTC b5e0ea8e-2e1a-409c-aec7-3f4c72ed167a 2013-11-13 15:32:49.843 UTC 64a0c8ba-e643-4c02-8bbf-24224bd6de90 2014-05-21 14:34:13.326 UTC 9973b049-ee79-4fd7-8a87-8cf191d9509f 2013-10-28 15:04:57.615 UTC 4dbc4a0b-5962-4f21-96d2-0fb20185b17a 2014-01-16 11:25:38.561 UTC 249fb6a7-886e-4835-8b18-8bc293a6d77e 2013-10-28 16:45:55.371 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 13112099-3efd-42a7-bf18-a93c89de52dd 2013-09-04 15:30:31.850 UTC Jonathan Giddy 2013-09-04 15:12:34.436 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 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 Convert Taverna list of RExpr to R list 2013-09-04 15:13:12.850 UTC