Calculate_quasi_extistages11the 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 D2014-07-31 14:00:58.934 UTC[S, J, V, G, D]2014-04-10 12:11:16.814 UTCgraph_title00Is 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 UTCTime to reach a quasi-extinction threshold of 100 individuals.
2014-04-10 09:46:15.887 UTCintervals00This 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 UTC252014-04-10 08:52:23.616 UTCiterations0050002014-04-10 08:52:50.456 UTCThe number of realization of population growth to simulate each run or number of iterations.2014-07-10 12:54:18.836 UTCprobabilities11[0.1, 0.2, 0.2, 0.2, 0.1, 0.2] 2014-08-13 09:48:30.482 UTCProbabilities 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 UTCyears11[1987, 1988, 1989, 1990, 1991, 1992]2014-07-31 11:35:08.83 UTCEeach 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 UTCthreshold00The 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 UTC1002014-04-10 12:21:52.265 UTCmax_runs00502014-04-10 08:53:09.999 UTCThe number of times to simulate CDF (cumulative distribution function).2014-07-31 11:54:22.225 UTCsumweight11Summed 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 UTCquasiextinction_threshold_graph0Plots the numeric results of the Quasi-extinction threshold numeric results.2014-07-31 12:39:22.277 UTCquasiextinction_threshold0This 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 UTCRequestStageMatricesvalues_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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Loopnet.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.Retry1.0100050000net.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.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.RshellActivitystages1falseabundances1falsematrices1falsegraph_title0falseintervals0falseiterations0falseprobabilities1falsethreshold0falsemax_runs0falseweight1falsequasiextinction_plot00x11falselocalhost6311falsefalsestagesSTRING_LISTabundancesR_EXPmatricesR_EXPgraph_titleSTRINGintervalsINTEGERiterationsINTEGERprobabilitiesDOUBLE_LISTthresholdINTEGERmax_runsINTEGERweightINTEGER_LISTquasiextinction_plotPNG_FILExR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.01002000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAbundance_Interactionstages1title0message0abundances11Abundance 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 UTCnet.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.interaction.InteractionActivitystages1text/plainjava.lang.Stringfalsemessage0text/plainjava.lang.Stringfalsetitle0text/plainjava.lang.Stringfalseabundances11http://biovel.googlecode.com/svn/tags/mpm-20140521/set_abundance.htmlLocallyPresentedHtmlfalsenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityfalsenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityYearnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.RshellActivityexpr1falselabels1falseexpr11falselocalhost6311falsefalseexprINTEGER_LISTlabelsSTRING_LISTexprR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivitySet initial population vectornet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivitylist1text/plainjava.lang.Stringtrueelem00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivitySelect a matrixnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeforceEqualNumberMatricesPerFieldvalue00Boolean 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 anot2014-08-13 09:40:42.463 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivityfalsenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeminMatricesPerFieldvalue00Minimum number of matrices per field2014-08-13 09:39:20.174 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity1net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricesvalues_LRequestStageMatricesmultipleRequestStageMatricesfieldRequestStageMatricestitleRequestStageMatricesforceEqualNumberMatricesPerFieldRequestStageMatricesminMatricesPerFieldReadStageMatrixmatrix_fileReadStageMatrixlabels_LFlatten_ListinputlistConvert_LRn2_to_RLn2list_of_r_expressionsgraphprobabilitiesgraphiterationsgraphintervalsgraphgraph_titlegraphstagesgraphabundancesgraphmatricesgraphthresholdgraphmax_runsgraphweightAbundance_InteractionstagesAbundance_InteractiontitleAbundance_InteractionmessageAddNameslabelsAddNamesexprOutputFundamentalMatrix_3inputFirstListElementlistquasiextinction_threshold_graphquasiextinction_threshold9ea12456-f5e0-4a6b-b8df-e5bb15ee6a282014-07-31 11:54:06.2 UTC55f9101d-3ad5-4a52-8d33-aae113558e7d2014-04-10 12:21:17.469 UTCfbc4d358-ab9f-4863-9cbd-25a25434ab392014-01-30 12:20:41.104 UTCcae708bc-8d4e-4509-9e48-8d6ce1350ea72014-07-31 12:39:01.109 UTC098dbce3-6f92-46cc-a6ff-83502f3065612014-01-30 14:02:39.207 UTC804c6cc1-dcf1-4308-a565-09fda96b1cb62014-04-10 08:52:02.963 UTCe72bc4ea-d7aa-4b82-86bf-b31c783c83242014-01-30 12:19:46.292 UTC2bf51525-de06-4e53-bf0e-f4f10740a33a2014-05-21 12:26:58.158 UTC1095a7c2-e074-49e5-afb8-7f4bbb0da7ca2014-08-14 11:43:31.798 UTC352a165e-e1b7-4081-a39d-098cc18760d12014-01-30 12:25:41.905 UTC59e1411f-7c58-4230-b459-b9aba461a2c02014-07-31 11:54:36.497 UTCf4d466f2-fb11-4666-b6c5-0f653926bddd2014-07-31 12:39:23.455 UTC6030d43e-332e-4261-b9cc-c0c1717fda032014-08-13 10:06:23.745 UTC09e513eb-bb94-4685-8188-04162dfbcc262014-03-05 12:03:51.758 UTC4cd83774-63ed-4c4b-a881-33529e3823cd2014-01-22 14:59:33.446 UTC16e5aa72-ee8c-4939-9f43-9719ec2f857f2014-07-10 12:10:34.885 UTC6399b2c3-c7d2-467e-a0fe-36b1b480deff2014-01-30 12:31:27.856 UTC348f209f-f7de-42f1-9a56-9dcb19dc4ec22014-01-30 12:52:09.874 UTC00e69d2e-8f43-4184-9376-af62f7ec8ac52014-08-14 11:44:58.518 UTCThis 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. Version 2.3.1
2014-08-14 11:39:09.782 UTC9b80b070-a717-4de8-ad28-f6aecba0ed4a2014-01-22 15:36:19.385 UTC8dd07f91-9134-4529-a9b0-5cb77ac7ac3a2014-04-10 08:58:51.686 UTCe22c8fc0-897d-4851-821a-b52c19f082282014-01-30 13:04:03.827 UTC0babaaa0-8442-4064-9607-96994e0078932014-01-30 12:41:59.713 UTC4c03c322-f6b1-47d6-a859-7bdb3baf39222014-05-02 10:01:36.73 UTCb727bda2-3e1a-4f51-991d-26c4ff3565442014-03-05 11:47:37.258 UTC50390b9d-cb62-445c-9ede-a7357ad4c0212014-05-21 12:25:01.833 UTCc397f693-3a09-4b1b-8212-fc8ac92a80ca2014-04-10 12:20:27.168 UTC3ac23716-4b4c-4b53-bb1d-e3e4fa3bd9e22014-07-31 14:01:00.135 UTCbd0ca9a0-da0b-42f0-99a1-289898da2c682014-07-31 11:35:08.473 UTCaf1ed12c-fb04-490c-9cd8-c9d37050acf32014-01-22 15:30:51.591 UTCa0da9b64-8fa4-4c9a-9ff0-1e15ea21431f2014-05-02 09:39:01.647 UTCf4b2c9ca-1cc2-4c24-a7fc-084d7d253b312014-01-30 12:32:54.963 UTC597fe0cc-cfeb-4fd0-83b2-492be45faa102014-08-14 09:31:37.248 UTC84672eae-1670-4d63-9f5b-a7f689fe13d92014-05-21 12:29:20.323 UTCMaria Paula Balcazar-Vargas, Mikolaj Krzyzanowski, Jonathan Giddy, Francisco Quevedo and Gerard Oostermijer .2014-08-14 09:02:05.78 UTCf692eb9a-8365-4992-8df2-f35ea8a16f242014-08-14 09:02:06.534 UTC4e549d4f-b1dc-417b-99f6-cf4d09c3296f2014-07-31 12:41:24.964 UTCd69cab4f-c25c-4626-93b8-cfccd68b86c92014-05-21 12:30:45.690 UTC89a93c3f-dfdd-49d1-93b0-e9fab1577e2f2014-02-19 15:05:32.759 UTC12c02214-db07-4511-8f8b-0038c4054e382014-08-13 10:45:22.416 UTC217d4dcf-1d99-4b1a-8d24-9c16ae5f69382014-01-30 13:26:10.134 UTC785491ad-b0cd-4cc9-949b-d6277ea759272014-01-30 12:14:17.602 UTC7858ebd2-e7ef-4d9f-9399-5238f390a4732014-01-30 13:52:14.782 UTC19920aef-bdc0-4c4c-916a-3ae020cc77f92014-01-22 15:37:40.706 UTCdd1497ee-2af8-442e-9749-bcdbaeb3693b2014-04-10 12:20:16.435 UTCc7fc79f1-1545-48da-a748-a2104f1714642014-01-30 12:41:13.191 UTC6f78ab7c-498a-47df-b4d4-734203b129de2014-01-30 12:44:46.92 UTC5cad32e9-3dff-4f10-becb-2138b5494d9f2014-01-30 14:16:24.425 UTC8cd7b65a-9970-4368-beff-3cd665e7fca12014-07-10 14:42:27.316 UTCb52b5c17-9c4f-414d-997f-8c8a18702f552014-04-10 11:07:13.229 UTC4b09c6e5-5def-4c9a-8a1b-7dbff06e99652014-01-30 12:29:36.252 UTC4fe26cb9-e5f3-4eff-9fa4-9ce697308ad12014-07-31 13:58:17.464 UTC02b22ece-2aff-4d2e-a47c-7c617995ca422014-02-19 14:56:57.596 UTCac80823a-6112-469c-9ed6-4f0d797d77652014-01-30 12:18:16.259 UTCb925170a-0f46-4fc0-9dfd-b2abd93c28c92014-01-30 12:23:36.905 UTCeafd9d19-c984-468f-8c6d-8d3e015e67b42014-01-22 15:33:59.286 UTC0a14a306-a7a5-42fe-935a-5d3111bb1efe2014-04-10 12:21:52.472 UTC59b59c5c-1f95-47d8-89a9-47dc2a92dfa62014-01-30 13:06:46.694 UTC6fc10a03-a298-4faf-8841-00e3d4b26dee2014-01-30 12:43:53.718 UTC9872b138-0076-4688-91b2-aa0159c9c45b2014-02-19 14:51:46.366 UTC491e2e66-1ed0-486e-b5e2-e7af7d363fa72014-04-10 07:54:32.467 UTC3660a11a-23e6-4ae8-86c2-45652e978e502014-01-22 15:34:57.108 UTC7fe5f0b8-9227-41be-8fc0-28fc6043dc692014-04-10 08:38:24.244 UTCaad0a94d-7b8f-4456-b05b-692305e3a8a32014-07-31 13:58:45.148 UTC56019124-40d5-460a-9ee9-19768098cbcb2014-08-14 11:39:11.455 UTCCalculate quasi-extinction threshold.2014-04-10 07:46:09.732 UTC16bbba14-f0c8-4834-9a20-69b6b00d2e742014-05-21 12:35:35.546 UTC097fa23b-db71-4e2b-b914-964f837a66952014-04-10 12:19:45.723 UTC4d6c2248-e9b5-4e71-99f1-450feb1bfefe2014-03-05 11:49:42.586 UTC44c45cf1-929f-45b9-899b-38e8d35cdb672014-04-10 12:19:10.96 UTC04b45320-02de-4863-9d91-eaeea171ae602014-03-05 12:00:23.575 UTC39b26aeb-2d36-494a-b1e4-f8c7b93cc38b2014-04-10 12:11:17.258 UTC6a9ba498-545a-443d-aa37-51f5de0d8d292014-04-10 12:21:29.324 UTCdf50d7f7-8e37-4649-bbfe-2f179541ea7d2014-01-30 12:26:33.170 UTC07502403-4448-42e3-8bb7-892f791f7f4d2014-04-10 09:48:53.111 UTCdaa4c78f-91b1-4654-9c17-d6f1a8f7908e2014-02-19 14:58:26.219 UTC7b7e7a13-78c5-4ab4-9596-a46a98f0e40e2014-02-19 15:03:52.411 UTC1dd5ce4f-4c1d-45d8-b4e1-81b41659f19e2014-01-30 14:22:33.751 UTCc63606c5-b094-44df-87e3-312f7b68154b2014-05-21 12:33:28.357 UTC6a52d51e-7ea6-4764-a6a0-e4f56fcc2d4f2014-04-10 09:00:08.196 UTC975cd586-3894-44b0-86b3-fbeecd2719622014-01-30 12:28:04.777 UTC55862f7b-a4a1-457b-b412-bd794151d42e2014-03-05 11:58:11.169 UTCf081ac8e-6319-4878-a68c-f0a1b89baece2014-01-30 12:34:40.860 UTC3925f682-1af0-4b0b-ab44-0e5cd9fad4ed2014-04-10 12:18:50.617 UTC4a1a32c9-8ba1-4986-9829-b08bfd97cece2014-01-22 15:40:58.43 UTCc8b38a30-24e4-48ca-9c6e-11bbee667d582014-03-05 11:55:16.836 UTC64c3bd8f-c595-4271-95ad-cfe39c15da202014-02-19 15:00:26.49 UTC085e1cfd-9e6d-461b-be83-97958fd74c302014-01-30 14:06:28.387 UTC51991b5b-acac-4955-9247-1904c44052f82014-04-10 08:59:37.870 UTC19959a83-9e2c-44ca-83f2-674860c6bfa22014-07-10 12:28:05.51 UTCecf02b3d-a2d0-437e-b3e0-d9af2c6f7f0e2014-04-10 12:20:53.823 UTC431627d6-4dde-4fa9-af3b-11794cc8a8e92014-03-05 11:48:28.179 UTC3b116d0c-6e9c-4977-8c84-ba965de76b152014-07-10 12:47:00.475 UTCf50211da-b3dc-4499-9694-05f33ab098872014-01-22 15:32:42.979 UTC957de4e5-a5f6-4245-83a8-367f5741944f2014-08-04 12:56:47.905 UTCConvert_Taverna_listlist_of_r_expressions22r_list_of_expressions1FlattenListOfStringsToStringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueconcatenated00workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergeUserNameHere2013-10-14 14:22:51.151 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueoutput11workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergeUserNameHere2013-10-14 14:21:14.818 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlattenListOfStringsToStringstringlistCombineListOfStringsIntoRListstringlistr_list_of_expressions472c6bef-15bc-4782-ab72-9e041b46e9d02013-10-14 14:28:56.870 UTCJonathan Giddy2013-09-04 15:12:34.436 UTCThis 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 UTCConvert Taverna list of RExpr to R list2013-09-04 15:13:12.850 UTC1ff54110-840d-474e-95a4-877c8f2c5b5e2013-09-04 15:26:02.821 UTC13112099-3efd-42a7-bf18-a93c89de52dd2013-09-04 15:30:31.850 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15:33:20.159 UTCa6ec62ed-cbc2-4705-812f-9fb8b80101692013-10-14 14:12:24.533 UTCReadStageMatrix2013-10-14 14:13:34.18 UTC6b5b9009-65c6-45a2-941f-188268b27c592013-10-14 14:13:35.986 UTC19c3521a-2d42-4f77-8dd2-10ab64286ef22013-10-15 13:59:10.98 UTCWorkflow188input11output0PrettyPrintRinput1output00net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivityinput1falseoutput00falselocalhost6311falsefalseinputR_EXPoutputTEXT_FILEnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrettyPrintRinputoutputdeb0863c-b567-4755-af9c-b8b74d5e08e52013-06-21 14:31:25.529 UTC1c210d9a-059f-4c52-8df7-0310db5e211f2013-06-21 14:30:38.141 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