Stages_vectors_plotsstages11 The names of the stages or categories of the input matrix. It is very important that the stages names are not longer than 8 characters. The name of the stages must be added one by one as list. The respective name stages must be filled one by one. First press add value, 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: S J V G D S 0.0000 0.0000 0.0000 7.6660 0.0000 J 0.0579 0.0100 0.0000 8.5238 0.0000 V 0.4637 0.8300 0.9009 0.2857 0.8604 G 0.0000 0.0400 0.0090 0.6190 0.1162 D 0.0000 0.0300 0.0180 0.0000 0.0232 The stages of this matrix are called: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D 2014-07-02 14:53:12.797 UTC [S, J, V, G, D] 2014-01-16 12:10:18.628 UTC surv_graph_title00 Gentiana pneumonanthe survival curves 2014-01-24 13:58:36.365 UTC Is the main title to be display in the Survival Rates Graph. e.g.: Gentiana pneumonanthe survival curves (Gentiana pneumonanthe: species name). 2014-07-02 14:53:19.139 UTC years11 Years the data was collected in. The respective years must be filled one by one. First press add value, fill a 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. 1) 1987 or 2) 1987-1988 2014-07-02 14:53:47.603 UTC [1987-1988, 1988-1989, 1989-1990, 1990-1991, 1991-1992, 1992-1993] 2014-07-22 11:55:41.468 UTC growth_graph_title00 Is the main title to be display in the Growth rate graph. e.g.: Gentiana pneumonanthe growth rates (Gentiana pneumonanthe: species name). 2014-07-02 14:52:59.386 UTC Gentiana pneumonanthe growth rates 2014-01-24 13:30:44.101 UTC stage_graph_title00 Is the main title to be display in the Stage Vectors Graph. (Note: will appear as Title - Year) The year will automatically be incorporate base on the year of the matix. e.g.: Gentiana pneumonanthe stage vectors - 1987 2014-07-02 14:53:05.766 UTC Gentiana pneumonanthe stage vectors 2014-01-24 13:37:42.303 UTC iterations00 10 2014-01-22 14:18:41.941 UTC This value will be use to plot a output graph that shows a simulation of the number of individuals per stage a few years after the study (e.g. 10). This value represents the years of axis X of the output graph: Stage_Vector_Graph. 2014-01-24 13:32:58.360 UTC Growth_Rates_Graph Growth Rates Graph: Plots the population growth rate or lambda values (eigen analyses) of each submitted matrix. 2014-04-02 14:18:38.702 UTC Survival_Rates_Graph Survival Rates Graph: The graph shows the changes of the survival values per stages across the years. 2014-04-02 11:46:34.384 UTC Stage_Vectors_Graph Stage Vector Graph: Plots short-term dynamics and convergence to stage distribution. It is a plot that charts the number of individuals per stage vs. years in the short-term (e.g. 5, 10 years). 2014-04-02 14:23:34.163 UTC Population_Projection $lambda [1] 1,233262 $stable.stage S J V G D 0,14257959 0,16213323 0,6585692 0,02289356 0,01382442 $stage.vectors 0 1 2 3 4 5 S 1 7,6666667 6,0132402 6,5785668 7,4579422 8,8300772 J 1 8,35368531 7,0267626 7,5286166 8,5167886 10,0605771 V 1 3,34084844 13,7843123 21,5532895 29,3963464 37,8777932 G 1 0,78433568 0,8580739 0,9727751 1,1517492 1,3911717 D 1 0,07127383 0,3124636 0,4664355 0,6250534 0,7997037 $pop.sizes [1] 5 20,21681 27,99485 37,09968 47,14788 58,95932 $pop.changes [1] 4,043362 1,384731 1,325232 1,270843 1,250519 1,24087 2014-04-02 14:16:53.747 UTC Eigen Analysis Calculates the population growth rate and stable stage distribution by repeated projections of the equation n(t+1)=An(t). a) Lambda or dominant eigenvalue: This value describes the population growth rate of a stage matrix. The population will be stable, grow or decrease at a rate given by lambda: e.g.: λ = 1 (population is stable), λ > 1 (population is growing) and finally λ < 1 (population is decreasing). b) The stable stage distribution (w): It is the proportion of the number of individuals per stage. It is given analytically by the right eigenvector (another property of the transition matrix) that corresponds to the dominant eigenvalue c) Stage.vector: A matrix with the number of projected individuals in each stage class. d) Pop.sizes: Total number of projected individuals. e) Pop.changes: Proportional change in population size. 2014-04-02 14:15:09.376 UTC Survival_Rates_Values Survival Rates Values: It is a table showing the survival rates values per stage per year, these values are plotted in the Survival Rates Graph. 2014-04-02 11:46:42.20 UTC 1987-1988 1988-1989 1989-1990 1990-1991 1991-1992 S 0.52174 0.52174 0.24786 0.058824 0.11111 J 0.91000 0.78212 0.56085 0.409639 0.36364 V 0.92793 0.93798 0.75377 0.724299 0.58424 G 0.90476 1.00000 0.92308 0.923077 0.92308 D 1.00000 1.00000 1.00000 1.000000 1.00000 2014-01-24 14:31:19.957 UTC Growth_Rates_Values Growth Rates Values: It is a table showing the population growth rate or lambda values (eigen analyses) of each submitted matrix. 2014-04-02 14:20:53.595 UTC 1987-1988 1988-1989 1989-1990 1990-1991 1991-1992 1.23234 1.59471 0.82632 0.74448 0.61868 2014-01-24 14:22:04.975 UTC survival_ratesmatrices1graph_title0rows1columns1survival_curves_plot00sc11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity matrices 1 false graph_title 0 false rows 1 false columns 1 false survival_curves_plot 0 0 sc 1 1 false localhost 6311 false false matrices R_EXP graph_title STRING rows INTEGER_LIST columns INTEGER_LIST survival_curves_plot PNG_FILE sc R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokegrowth_ratesyears1matrices1graph_title0growth_rates_plot00gr11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity matrices 1 false years 1 false graph_title 0 false growth_rates_plot 0 0 gr 1 1 false localhost 6311 false false matrices R_EXP years STRING_LIST graph_title STRING growth_rates_plot PNG_FILE gr R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRequestStageMatricesmultiple0values_L1field0title0matrices_LL22net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.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-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeReadStageMatrixmatrix_file0labels_L1matrix_Rn211net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFalsevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConvert_LRn2_to_RLn2list_of_r_expressions2r_list_of_expressions11net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeYearvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Year net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAddNamesexpr1labels1expr11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity expr 1 false labels 1 false expr 1 1 false localhost 6311 false false expr R_EXP labels STRING_LIST expr R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSelect_matrix_filesvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select matrix files net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokestage_vectorsstages1graph_title0iterations0year0stage_matrix1growth_rates_plot00projection11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity stage_matrix 1 false stages 1 false year 0 false graph_title 0 false iterations 0 false growth_rates_plot 0 0 projection 1 1 false localhost 6311 false false stage_matrix R_EXP stages STRING_LIST year STRING graph_title STRING iterations INTEGER growth_rates_plot PNG_FILE projection R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCategoriseStages_InteractionunsortedStages1message0title0sortedStages11reproductiveStages11recruitedStages11 With this dialogue automatically appears the names of the stages or categories of the census data file. When the dialogue appears, the stages are in disorder, so the user drags and organizes the stages according to the order in the life cycle. Then, the author chooses if the stage belongs to the recruited, reproductive category or it should be excluded. Recruited means that new individuals can be recruited to this (these) stage(s). Reproductive stages are those that reproduce (produce offspring) (in this example the stage G). In the census data file Dt1.txt, x is use to denote when a plant has died in the second year, so the user must selected in the excluded column. Then the user clicks in confirm and you will read stages submitted. In the following example, the life cycle of Gentiana pneumonanthe has 5 stages or categories: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D 2012-11-01 14:53:35.21 UTC net.sf.taverna.t2.activitiesinteraction-activity1.0.4net.sf.taverna.t2.activities.interaction.InteractionActivity unsortedStages 1 text/plain java.lang.String false message 0 text/plain java.lang.String false title 0 text/plain java.lang.String false sortedStages 1 1 recruitedStages 1 1 reproductiveStages 1 1 http://biovel.googlecode.com/svn/tags/mpm-20140521/select_fecundity.html LocallyPresentedHtml false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFecundityCols_FromReproductiveStagesall_values1some_values1indices11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity some_values 1 false all_values 1 false indices 1 1 false localhost 6311 false false some_values STRING_LIST all_values STRING_LIST indices INTEGER_LIST net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFecundityRows_FromRecruitedStagesall_values1some_values1indices11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity some_values 1 false all_values 1 false indices 1 1 false localhost 6311 false false some_values STRING_LIST all_values STRING_LIST indices INTEGER_LIST net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeOutputFundamentalMatrixinput1output00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeOutputFundamentalMatrix_2input1output00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeOutputFundamentalMatrix_3input1output00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select recruited and reproductive stages, then click the Confirm button. net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSelect_stagesvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select stages net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 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2014-01-22 13:25:39.859 UTC 17d13d72-7e8f-4bc3-89e7-b64939515b50 2014-01-24 13:55:14.445 UTC f250e52e-8361-48c8-95d4-3b1b599d1bb8 2014-05-21 11:15:53.485 UTC e5a58b4e-4fdb-4407-ae95-8d6db054d519 2014-01-16 12:19:38.627 UTC 00a687d1-ea72-40c8-bdef-5dcb1fc9c746 2014-01-24 13:19:24.523 UTC 175baf82-c01b-417b-9fac-798fb1978976 2014-01-08 01:52:42.927 UTC 9e9a631c-3785-456b-909c-fb3955888999 2014-01-08 01:44:47.624 UTC 432a2951-4f5a-47f7-b540-26620a4bc582 2014-01-16 13:25:24.403 UTC 28e83f49-7e33-4fcc-9816-a85824199c18 2014-01-24 13:58:36.514 UTC 82b368d4-c996-41c1-a526-8f4c5138a27e 2014-01-24 15:50:47.109 UTC 48740cd7-2b4a-4963-bc0e-4e58c2306d82 2014-01-08 13:09:34.496 UTC 413d3699-1aa4-4a8b-a335-c4c347e8f138 2014-01-16 12:18:00.419 UTC 1a7d1842-d979-424f-be21-c7e33200c315 2014-01-08 13:26:07.123 UTC 513bef37-bb5a-4448-b5b0-0723520e6fc0 2014-01-16 13:05:25.49 UTC 77329c73-24a1-4e49-83e7-1c53d73a6c9b 2014-05-21 11:14:38.966 UTC 01573bd6-0712-4fe4-9719-7c88225ce819 2014-01-22 12:35:56.271 UTC ad4ddea0-c53c-41ec-9a40-c06e5a8526a1 2014-01-22 13:40:49.417 UTC 71cb5b4e-06c5-448d-95ce-c86cbb44e747 2014-01-22 13:02:02.125 UTC 8c8fb537-bd6a-482e-a032-2317ebc281ea 2014-01-22 13:23:15.914 UTC fb546a59-21ce-4728-ad96-860556e683c8 2014-01-24 14:02:12.462 UTC The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices: - Survival values calculations per stage per year and its respective plot; - Growth rates (lambda) calculations per year and its respective plot; - Stage Vectors calculations and their respective plots. ====================================================== This workflow requires an instance of Rserve on localhost 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 uses the R pack ‘popbio’ (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). References: Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts. Jongejans E. & H. de Kroon. 2012. Matrix models. Chapter in Encyclopaedia of Theoretical Ecology (eds. Hastings A & Gross L) University of California, p415-423 Oostermeijer J.G.B., M.L. Brugman; E.R. de Boer; H.C.M. Den Nijs. 1996. Temporal and Spatial Variation in the Demography of Gentiana pneumonanthe, a Rare Perennial Herb. The Journal of Ecology, Vol. 84(2): 153-166. Stubben, C & B. Milligan. 2007. Estimating and Analysing Demographic Models Using the popbio Package in R. Journal of Statistical Software 22 (11): 1-23 Stubben, C., B. Milligan, P. Nantel. 2011. Package ‘popbio’. Construction and analysis of matrix population models. 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net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Select a matrix for each year, then click the Confirm button. net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSelectMatricesInteractionvaluesvalues_LSelectMatricesInteractionmultiplemultipleSelectMatricesInteractionfieldfieldSelectMatricesInteractiontitletitleSelectMatricesInteractionmessagemessagevaluematrices_LLSelectMatricesInteractionmatrices 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 0d79c056-ce74-4602-9cbd-60c90307105f 2014-05-01 10:33:23.704 UTC 5f4b1899-ccf2-474b-b4fb-01a59e02f264 2013-11-13 15:42:43.559 UTC 9973b049-ee79-4fd7-8a87-8cf191d9509f 2013-10-28 15:04:57.615 UTC 3cd4cf73-e925-449c-895d-318bf4964ede 2014-05-01 10:43:19.183 UTC 379602b6-1644-4b9f-a5bb-8161e03da77d 2013-10-28 16:47:25.115 UTC 4dbc4a0b-5962-4f21-96d2-0fb20185b17a 2014-01-16 11:25:38.561 UTC 08912d22-d766-4700-9394-77b1ef8e3a09 2013-10-28 16:49:51.515 UTC 843dddc5-5f13-47f3-986b-aadbb69b939e 2014-05-21 11:15:50.752 UTC 48a16a67-9f67-4ab2-9f60-29e450086912 2014-07-22 11:50:04.801 UTC 3682addc-6be9-4f7c-a61c-756ce05a2fdf 2013-11-13 15:33:56.716 UTC 249fb6a7-886e-4835-8b18-8bc293a6d77e 2013-10-28 16:45:55.371 UTC 4a0bbebd-3357-48c7-ad1e-b5bcb7b6ec5c 2013-11-13 13:50:35.668 UTC Convert_Taverna_listlist_of_r_expressions22r_list_of_expressionsFlattenListOfStringsToStringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.4net.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-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCombineListOfStringsIntoRListstringlist1output11net.sf.taverna.t2.activitieslocalworker-activity1.4net.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-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlattenListOfStringsToStringstringlistlist_of_r_expressionsCombineListOfStringsIntoRListstringlistFlattenListOfStringsToStringconcatenatedr_list_of_expressionsCombineListOfStringsIntoRListoutput Jonathan Giddy 2013-09-04 15:12:34.436 UTC 472c6bef-15bc-4782-ab72-9e041b46e9d0 2013-10-14 14:28:56.870 UTC 13112099-3efd-42a7-bf18-a93c89de52dd 2013-09-04 15:30:31.850 UTC 1ff54110-840d-474e-95a4-877c8f2c5b5e 2013-09-04 15:26:02.821 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 ReadStageMatrixlabels_L11matrix_file00matrix_Rn2Matrix_ReadFromFilematrix_file0labels1read_matrix11net.sf.taverna.t2.activitiesrshell-activity1.4net.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-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMatrix_ReadFromFilematrix_filematrix_fileMatrix_ReadFromFilelabelslabels_Lmatrix_Rn2Matrix_ReadFromFileread_matrix 19c3521a-2d42-4f77-8dd2-10ab64286ef2 2013-10-15 13:59:10.98 UTC c8cf946f-3771-4321-870a-26408be164c7 2013-10-14 15:33:20.159 UTC a6ec62ed-cbc2-4705-812f-9fb8b8010169 2013-10-14 14:12:24.533 UTC ReadStageMatrix 2013-10-14 14:13:34.18 UTC 6b5b9009-65c6-45a2-941f-188268b27c59 2013-10-14 14:13:35.986 UTC