Calculate_and_Plot_acensus_data_file00 The input data file must have the format of a table (a .csv-file) containing the demographic data on a series of individuals over several years. Each individual has a table row for each year and is identified by a number (plant column in example). For the year specified in the column 'year', each individual has a certain life stage ('stage'). The stage codes can be chosen by the user, but they have to be specified with a string and cannot be longer than 8 characters. When an individual died after a year or later the stage will be: dead. First, click in Set file location, a window dialog appears and the user selects the file (e.g. Data_Gentiana.csv) and then clicks the Open button. Then the link to the file will appear on the Taverna window. 2014-08-22 13:27:39.870 UTC plant year stage 2 1987 D 4 1987 J 5 1987 D 31 1987 V 36 1987 G 37 1987 J 41 1987 J 43 1987 S 46 1987 V 2 1988 V 4 1988 D 5 1988 V 9 1988 J 14 1988 J 2014-08-22 09:44:27.173 UTC graph_title00 Gentiana pneumonanthe 2014-08-22 09:49:08.203 UTC Main title of the plots. As example, it can be the name of the species or the name of the place where the research has been conducted. 2014-08-22 13:28:02.504 UTC last_year00 this value is used to calculate and plot the abundances of the submitted data. For example, data from 1987 to 1993 (Data_Gentiana.csv). If the year 1993 is submitted, the abundances will be calculated and graphed from 1987-1993. 2014-08-22 13:16:49.17 UTC 1993 2014-08-22 11:11:28.383 UTC number_individuals_per_stage_per_year_graph0 Graph showing the abundance per stage per year. 2014-08-22 13:05:25.791 UTC proportion_individuals_per_stage_per_year_graph0 Graph showing the proportion of individuals per stage per year. 2014-08-22 13:06:14.474 UTC number_individuals_per_stage_per_year0 A table with numerical results of abundance per stage per year (.csv or txt files). 2014-08-22 13:29:04.573 UTC 1987 1988 1989 1990 1991 1992 1993 S 69 161 117 17 9 0 0 J 100 179 189 83 11 5 21 V 111 258 398 428 369 232 161 G 21 23 52 26 13 11 3 D 43 8 7 29 14 3 18 2014-08-22 13:04:37.131 UTC graphnumber_individuals1stages1last_year0sv1graph_title0proportion_individuals_graph00number_individuals_graph00number_individuals11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity number_individuals 1 false graph_title 0 false stages 1 false sv 1 false last_year 0 false number_individuals_graph 0 0 proportion_individuals_graph 0 0 number_individuals 1 1 false localhost 6311 false false number_individuals R_EXP graph_title STRING stages STRING_LIST sv R_EXP last_year INTEGER number_individuals_graph PNG_FILE proportion_individuals_graph PNG_FILE number_individuals 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.InvokeCategoriseStages_InteractionunsortedStages1sortedStages11 With this dialogue automatically appears the names of the stages or categories of the census data file. When the dialogue appears, the stages are in disorder, so the user drags and organizes the stages according to the order in the life cycle. Then, the author chooses if the stage belongs to the recruited, reproductive category or it should be excluded. Recruited means that new individuals can be recruited to this (these) stage(s). Reproductive stages are those that reproduce (produce offspring) (in this example the stage G). In the census data file Dt1.txt, x is use to denote when a plant has died in the second year, so the user must selected in the excluded column. Then the user clicks in confirm and you will read stages submitted. In the following example, the life cycle of Gentiana pneumonanthe has 5 stages or categories: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D 2012-11-01 14:53:35.21 UTC net.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.interaction.InteractionActivity unsortedStages 1 text/plain java.lang.String false sortedStages 1 1 recruitedStages 1 1 reproductiveStages 1 1 http://biovel.googlecode.com/svn/tags/mpm-20130805/select_stages.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.Invoketablecensus_data_file0stages11number_individuals11sv11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivity census_data_file 0 false number_individuals 1 1 stages 1 1 sv 1 1 false localhost 6311 false false census_data_file TEXT_FILE number_individuals R_EXP stages STRING_LIST sv 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.Invokegraphnumber_individualstablenumber_individualsgraphstagesCategoriseStages_InteractionsortedStagesgraphlast_yearlast_yeargraphsvtablesvgraphgraph_titlegraph_titleOutputFundamentalMatrix_3inputgraphnumber_individualsCategoriseStages_InteractionunsortedStagestablestagestablecensus_data_filecensus_data_filenumber_individuals_per_stage_per_year_graphgraphnumber_individuals_graphproportion_individuals_per_stage_per_year_graphgraphproportion_individuals_graphnumber_individuals_per_stage_per_yearOutputFundamentalMatrix_3output ad69cb62-f545-4cfb-9b21-88b7f9861659 2014-02-04 12:02:04.488 UTC 83ab0223-236b-450f-ba2a-295d993993f3 2014-08-22 09:49:10.433 UTC 0d90eb97-1147-461a-89f2-6870c84d2985 2014-03-12 13:25:57.350 UTC 71b07b3a-895a-4671-ad1f-fa5ab23fa71e 2014-03-12 12:25:12.373 UTC d5bdee58-41a9-48b7-a0db-747f073011ae 2014-03-12 12:18:43.926 UTC d5357b00-1991-467a-a453-5105a4857bac 2014-03-12 13:05:51.29 UTC 274b5f04-287e-401d-8e2c-3adba78d9924 2014-03-12 13:27:04.835 UTC This workflow calculates and plots the abundance per stage per year. 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. 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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