Calculate_quasi_extistages11 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 14:00:58.934 UTC [S, J, V, G, D] 2014-04-10 12:11:16.814 UTC graph_title00 Is the main title to be display in the quasiextinction threshold graph. Click in set value and then write the text in the right space. 100 is the quasiextinction threshold value used in this tutorial run. Please do not use a title longer than the suggest it. 2014-07-10 12:46:59.535 UTC Time to reach a quasi-extinction threshold of 100 individuals. 2014-04-10 09:46:15.887 UTC intervals00 This value is the farthest future time horizon (e.g. 25) and therefore the years of axis X of the output graph. 2014-07-10 12:54:01.304 UTC 25 2014-04-10 08:52:23.616 UTC iterations00 5000 2014-04-10 08:52:50.456 UTC The number of realization of population growth to simulate each run or number of iterations. 2014-07-10 12:54:18.836 UTC probabilities11 [0.1, 0.2, 0.2, 0.2, 0.1, 0.2] 2014-08-13 09:48:30.482 UTC Probabilities of choosing each submitted matrix. Note that the value of probabilities must equal to 1. This value can be ignore if the user does want use probabilities [ ]. Use probabilities: Each probability corresponding to each year and each year corresponds to a matrix. Probabilities and years should follow the same order. e.g. In this tutorial, 6 matrices are used, therefore 6 probabilities must be used, the probabilities must follow the same order as the submitted matrices (years). [0.1, 0.2, 0.2, 0.2, 0.1, 0.2]. The probabilities must be settled to 1. The first matrix (year = 1987) has a 0.1% probability to be chosen over 1. The second matrix (year = 1988) has a 0.2% probability to be chosen over 1. etc. Ignore probabilities: When the user wants to ignore the use of probabilities: [ ] 2014-08-14 11:41:51.840 UTC years11 [1987, 1988, 1989, 1990, 1991, 1992] 2014-07-31 11:35:08.83 UTC Eeach year represents a matrix and therefore characterizes a period of transition. The respective years must be filled one by one. In the tutorial, we have 6 matrices (see 5.2.2 Input data) that represent 6 years (e.g.: 1987 =data interval between 1987 and 1988; 1988= data interval between 1988 and 1989). 2014-08-14 11:44:56.843 UTC threshold00 The quasi-extinction threshold, express as a density. The entries in the inicial population vector represent densities, but quasi-extinction thresholds are typically expressed in terms of numbers of individuals (Morris and Doak 2002). Thus when we ask whether the summed densities across all or a subset of the classes has fallen below the quasi-extinction threshold, we first need to be sure that a numerical threshold has been converted to a density. For example, let's assume that the densities in the population vector represent mean numbers of individuals per hectare, that the population occupies 1,000 hectares, and that we have decided to set the quasiextinction threshold at a total of 100 individuals in the reproductive classes. One hundred reproductive individuals in the entire population represents an average density of 0.1 individuals per hectare summed across the reproductive classes, so we would consider the population to have hit the threshold if this sum hits 0.1, not 100. Alternatively, we could multiply the starting densities by 1,000 to arrive at an estimate of total numbers and set the quasiextinction threshold to 100 (Morris and Doak 2002). 2014-04-10 12:21:44.969 UTC 100 2014-04-10 12:21:52.265 UTC max_runs00 50 2014-04-10 08:53:09.999 UTC The number of times to simulate CDF (cumulative distribution function). 2014-07-31 11:54:22.225 UTC sumweight11 Summed density to compare the quasi-extinction threshold. A vector of ones and zeroes used to omit stage classes when checking quasiextinction threshold (0 = omit a stage, 1= include). Use sumweight, ignore stages: In this tutorial, matrices have 5 stages, therefore 5 sumweight data must be used, the sumweight values must follow the same order as the submitted stages. In this example, the zero instruct the workflow to ignore seedlings (S is the first stage, see Stages) when summing the densities across classes to compare to the quasi-extinction threshold (Figure 9). Ignore sumweight: When the user wants to ignore the use of sumweight: [ ] 2014-08-14 11:43:06.189 UTC [0, 1, 1, 1, 1] 2014-04-10 12:21:28.59 UTC quasiextinction_threshold_graph0 Plots the numeric results of the Quasi-extinction threshold numeric results. 2014-07-31 12:39:22.277 UTC quasiextinction_threshold0 This text has been adapted to the Gentiana exampled following Morris and Doak (2002). The Figure 19 and 20 are the numeric and graphic results of 50 separate runs of this workflow, each with 5,000 separate realizations of population growth and a quasi-extinction threshold of 100. Figure 20 shows little variation among the separate runs, indicating that in this example, 5,000 realizations provide a reasonably good estimate of the extinction time CDF (Morris and Doak 2002, advocate increasing the number of realizations per run until separate runs yield very similar estimates for the CDF). Starting with a population density of 344 individual plants, the probability of hitting a threshold density of 50 individual plants reaches a value of 0.1 after only about 7.5 years, and exceeds 0.8 by year 25 (see Morris and Doak 2002). In this tutorial, it is computed the probability that the total density over all classes except seedlings (S) falls below 50. In this example the quasi-extinction threshold is applied to a subset of the stages (J, V, G and D). For this purpose, the sumweights were [0 1 1 1 1 1] (see input ports example Sumweight ignoring seedlings (S) when summing the densities across classes to compare to the quasi-extinction threshold (Morris and Doak 2002). The entries in the Initial population vector (see interactions) represent densities, but quasi-extinction thresholds are typically expressed in terms of numbers of individuals. Thus when it is asked whether the summed densities across all or a subset of the classes has fallen below the quasi-extinction threshold, first it is necessary to be sure that a numerical threshold has been converted to a density. For example, let's assume that the densities in the population vector represent mean numbers of individuals per hectare, that the population occupies 100 hectares, and that we have decided to set the quasiextinction threshold at a total of 50 individuals. One hundred reproductive individuals in the entire population represents an average density of 0.5 individuals per hectare summed across the J, V, G and D stages, so it would be considered the population to have hit the threshold if this sum hits 0.5, not 50. Alternatively, it could be multiplied the starting densities by 100 to arrive at an estimate of total numbers and set the quasiextinction threshold to 50 (Morris and Doak 2002). 2014-07-31 12:39:00.76 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.Invokegraphprobabilities1iterations0intervals0graph_title0stages1abundances1matrices1threshold0max_runs0weight1quasiextinction_plot00x11net.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 threshold 0 false max_runs 0 false weight 1 false quasiextinction_plot 0 0 x 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 threshold INTEGER max_runs INTEGER weight INTEGER_LIST quasiextinction_plot PNG_FILE x 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.Invokefalsevalue00net.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.InvokeInitial_Population_Vectorvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity Set 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.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.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_LyearsRequestStageMatricesmultiplefalsevalueRequestStageMatricesfieldYearvalueRequestStageMatricestitleSelect_a_matrixvalueRequestStageMatricesforceEqualNumberMatricesPerFieldforceEqualNumberMatricesPerFieldvalueRequestStageMatricesminMatricesPerFieldminMatricesPerFieldvalueReadStageMatrixmatrix_fileFlatten_ListoutputlistReadStageMatrixlabels_LstagesFlatten_ListinputlistRequestStageMatricesmatrices_LLConvert_LRn2_to_RLn2list_of_r_expressionsReadStageMatrixmatrix_Rn2graphprobabilitiesprobabilitiesgraphiterationsiterationsgraphintervalsintervalsgraphgraph_titlegraph_titlegraphstagesstagesgraphabundancesAddNamesexprgraphmatricesConvert_LRn2_to_RLn2r_list_of_expressionsgraphthresholdthresholdgraphmax_runsmax_runsgraphweightsumweightAbundance_InteractionstagesstagesAbundance_InteractiontitleInitial_Population_VectorvalueAbundance_InteractionmessageFirstListElementelemAddNameslabelsstagesAddNamesexprAbundance_InteractionabundancesOutputFundamentalMatrix_3inputgraphxFirstListElementlistyearsquasiextinction_threshold_graphgraphquasiextinction_plotquasiextinction_thresholdOutputFundamentalMatrix_3output 9ea12456-f5e0-4a6b-b8df-e5bb15ee6a28 2014-07-31 11:54:06.2 UTC 55f9101d-3ad5-4a52-8d33-aae113558e7d 2014-04-10 12:21:17.469 UTC fbc4d358-ab9f-4863-9cbd-25a25434ab39 2014-01-30 12:20:41.104 UTC cae708bc-8d4e-4509-9e48-8d6ce1350ea7 2014-07-31 12:39:01.109 UTC 098dbce3-6f92-46cc-a6ff-83502f306561 2014-01-30 14:02:39.207 UTC 804c6cc1-dcf1-4308-a565-09fda96b1cb6 2014-04-10 08:52:02.963 UTC e72bc4ea-d7aa-4b82-86bf-b31c783c8324 2014-01-30 12:19:46.292 UTC 2bf51525-de06-4e53-bf0e-f4f10740a33a 2014-05-21 12:26:58.158 UTC 1095a7c2-e074-49e5-afb8-7f4bbb0da7ca 2014-08-14 11:43:31.798 UTC 352a165e-e1b7-4081-a39d-098cc18760d1 2014-01-30 12:25:41.905 UTC 59e1411f-7c58-4230-b459-b9aba461a2c0 2014-07-31 11:54:36.497 UTC f4d466f2-fb11-4666-b6c5-0f653926bddd 2014-07-31 12:39:23.455 UTC 6030d43e-332e-4261-b9cc-c0c1717fda03 2014-08-13 10:06:23.745 UTC 09e513eb-bb94-4685-8188-04162dfbcc26 2014-03-05 12:03:51.758 UTC 4cd83774-63ed-4c4b-a881-33529e3823cd 2014-01-22 14:59:33.446 UTC 16e5aa72-ee8c-4939-9f43-9719ec2f857f 2014-07-10 12:10:34.885 UTC 6399b2c3-c7d2-467e-a0fe-36b1b480deff 2014-01-30 12:31:27.856 UTC 348f209f-f7de-42f1-9a56-9dcb19dc4ec2 2014-01-30 12:52:09.874 UTC 00e69d2e-8f43-4184-9376-af62f7ec8ac5 2014-08-14 11:44:58.518 UTC This workflow estimates by simulation the quasi-extinction probability time cumulative distribution function for a structured population in an independently and identically distributed (iid) stochastic environment. This workflow is based on the popbio package (stoch.quasi.ext - Calculate quasi-extinction threshold, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.5 (Morris and Doak 2002). For more details of the analysis see: Calculating the probability of hitting a quesi-extinction threshold by time t, method: simulating extinction probabilities (Morris and Doak 2002, pag: 241-244 and Caswell 2001, pag: 443-444). This models do not permit extinction, however we can study quasi-extinction (Caswell 2001). A population is quasi-extinct if it shrinks to a specific fraction of its current size (Ginsbur et al 1982 in Caswell 2001). The quasi-extinction threshold can be chosen in the belief that it would pose a significant threat of the real exaction (Caswell 2001). METHOD: SIMULATING EXTINCTION PROBABILITIES Keep track of whether the total population density (or the density summed across a subset of the classes with which we are particularly concerned, such as the reproductive classes) has fallen below the quasiextinction threshold each year. The fraction of realizations that first hit the threshold during or before year t gives the cumulative probability of extinction (Morris and Doak 2002). This workflow performs such a calculation. 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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f50211da-b3dc-4499-9694-05f33ab09887 2014-01-22 15:32:42.979 UTC 957de4e5-a5f6-4245-83a8-367f5741944f 2014-08-04 12:56:47.905 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 472c6bef-15bc-4782-ab72-9e041b46e9d0 2013-10-14 14:28:56.870 UTC Jonathan Giddy 2013-09-04 15:12:34.436 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. 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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 5f4b1899-ccf2-474b-b4fb-01a59e02f264 2013-11-13 15:42:43.559 UTC 9b37bccc-b963-457b-9efc-66985cb5aba7 2014-05-21 12:39:57.735 UTC 4dbc4a0b-5962-4f21-96d2-0fb20185b17a 2014-01-16 11:25:38.561 UTC 379602b6-1644-4b9f-a5bb-8161e03da77d 2013-10-28 16:47:25.115 UTC 47ab6f65-4bec-406a-8560-db17661b13f0 2014-08-13 10:35:20.302 UTC b5e0ea8e-2e1a-409c-aec7-3f4c72ed167a 2013-11-13 15:32:49.843 UTC f5456cef-7975-4376-a757-68764ae30f0e 2014-08-13 10:35:34.505 UTC 08912d22-d766-4700-9394-77b1ef8e3a09 2013-10-28 16:49:51.515 UTC 3682addc-6be9-4f7c-a61c-756ce05a2fdf 2013-11-13 15:33:56.716 UTC 4a0bbebd-3357-48c7-ad1e-b5bcb7b6ec5c 2013-11-13 13:50:35.668 UTC 9973b049-ee79-4fd7-8a87-8cf191d9509f 2013-10-28 15:04:57.615 UTC 1791ddd6-09f3-4609-83f3-1910f5d7d37f 2014-05-01 11:02:46.628 UTC e04e4d3f-c7c9-438c-bc0c-c9740084e902 2013-11-13 13:50:47.718 UTC 249fb6a7-886e-4835-8b18-8bc293a6d77e 2013-10-28 16:45:55.371 UTC 9b0bff5f-8571-46ca-932e-0804b8324dda 2014-08-13 10:37:16.35 UTC