Bootstrap_of__observTableFile00 plant year stage reprstr recruitment 2 1987 D 0 4 1987 J 0 5 1987 D 0 31 1987 V 0 36 1987 G 5 37 1987 J 0 41 1987 J 0 43 1987 S 0 46 1987 V 0 2 1988 V 0 4 1988 D 0 5 1988 V 0 9 1988 J 0 RJ 14 1988 J 0 RJ 2012-10-12 12:05:46.851 UTC Table containing demographic data of individuals in two year The input data (a .txt-file) has to have the format of a table containing the demographic data on a series of individuals in two 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, not longer than 5 characters. For all individuals, the number of offspring is specified in a chosen way (in the example, 'repstr' gives the number of flowers/fruits for each plant. In the example, it can be seen that only generative adults (stage=G) had flowers. Individuals without offspring have to be indicated by filling in '0' in this column, which cannot have empty cells. The column 'recruitment' specifies those individuals that are new to the population by means of a code. In the example, 'RS' is a new seedling, and 'RJ' a new juvenile plant. As can be seen in the example, no code is needed in this column for individuals that were already present. 2012-10-12 12:05:58.914 UTC SpeciesName00 Gentiana pneumonanthe 2012-10-19 13:29:46.648 UTC In this input port SpeciesName comes the title of the bar plot that will be generated with the analysis. As an example, it can be the name of the species or the name of the place where the research has been conducted, between others. 2012-11-05 15:01:23.953 UTC Bootstrap_Iterations00 10000 2012-10-18 08:38:58.81 UTC Number of iterations for calculation of bootstrap distributions 2012-10-18 08:39:43.774 UTC Confidence_Interval_CI 95% Confidence interval of Lambda In statistics, a confidence interval (CI) is a type of interval estimate of a population parameter and is used to indicate the reliability of an estimate. It is an observed interval (i.e. it is calculated from the observations), in principle different from sample to sample, that frequently includes the parameter of interest if the experiment is repeated. How frequently the observed interval contains the parameter is determined by the confidence level or confidence coefficient. 2012-10-12 12:24:22.164 UTC 2.5% 97.5% 0.954955 1.468701 2012-10-05 14:22:04.620 UTC histogram Histogram plotting the frecuencies of the lambda values and the 95% confidence intervals resulting from the bootstrap analysis 2012-10-12 11:51:41.883 UTC DisplayConfidenceIntervalinput1output00net.sf.taverna.t2.activitiesrshell-activity1.4net.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-impl1.4net.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.InvokeBootstrap_of__observcensus_data1startYear0stages1recruitedStages1plotTitle0bootstrapIterations0confidence_interval11histogram00net.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.InvokeCensusData_ReadFromFilecensus_data_file0census_data11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity census_data_file 0 false census_data 1 1 false localhost 6311 false false census_data_file TEXT_FILE census_data 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.InvokeSelectYearcensus_data1yearColumnName0initialYear00net.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.InvokeSortAndCategoriseStacensus_data1stageColumnHeader0matrixStages11recruitedStages11net.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.Invokestagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity stage 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.InvokeDisplayConfidenceIntervalinputBootstrap_of__observconfidence_intervalBootstrap_of__observcensus_dataCensusData_ReadFromFilecensus_dataBootstrap_of__observstartYearSelectYearinitialYearBootstrap_of__observstagesSortAndCategoriseStamatrixStagesBootstrap_of__observrecruitedStagesSortAndCategoriseStarecruitedStagesBootstrap_of__observplotTitleSpeciesNameBootstrap_of__observbootstrapIterationsBootstrap_IterationsCensusData_ReadFromFilecensus_data_fileTableFileSelectYearcensus_dataCensusData_ReadFromFilecensus_dataSelectYearyearColumnNameyearvalueSortAndCategoriseStacensus_dataCensusData_ReadFromFilecensus_dataSortAndCategoriseStastageColumnHeaderstagevalueConfidence_Interval_CIDisplayConfidenceIntervaloutputhistogramBootstrap_of__observhistogram b8fe02f6-e147-4416-aeb4-6c4e54589512 2012-06-27 08:19:06.56 UTC 8ab40f79-92fd-40d5-811f-77b34d941a14 2012-10-19 13:24:50.273 UTC 671f03a1-3f9b-49b6-955a-f1f0eda1bc0f 2012-10-19 04:09:44.131 UTC e98a3578-498e-4d02-9059-57c0cdf09e83 2012-06-27 05:56:22.181 UTC aa848d79-a9f7-497e-ba06-ee6feddc1da3 2012-06-27 06:00:45.433 UTC This workflow calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to estimate lambda, because lambda is estimated from imperfect data, such estimation are uncertain. Therefore, when the results have policy implications it is important to quantify that uncertainty. Confidence interval is one of the traditional tools to doing so (see outputs: Bootstrap analysis). A detailed description of resampling methods to estimate confidence intervals for demographic estimates is described Caswell (2001, Chapter 12) ============================================================ Literature Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts. ======================================================= 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 based on Package ‘popbio’ in R. 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 2012-11-02 16:06:49.640 UTC 619e109f-43f3-48b3-ac8d-8deb22b7f014 2012-10-18 15:02:38.208 UTC Maria Paula Balcázar-Vargas, Jonathan Giddy and G. Oostermeijer 2012-11-02 16:02:15.171 UTC f1e75c19-47b2-4a85-a395-d51df8ac03a8 2012-10-18 06:33:19.190 UTC 499c4e20-0bb6-40da-8c3f-9e9582bfcf99 2012-10-19 04:04:47.859 UTC b52aa862-b3ab-4602-a90f-14cf4a02b16f 2012-10-12 11:28:21.258 UTC 3d8f7330-9060-42ea-94bc-f7c2878ce81a 2012-10-12 12:06:43.914 UTC be9d3a0d-f115-4b04-9737-99f2a1dbed3b 2012-10-12 12:24:31.305 UTC e8691fb7-25dd-4b77-9354-d166d4e212de 2012-10-19 03:58:55.240 UTC 1da10601-a701-4542-ac84-b210462a5812 2012-06-27 06:02:05.237 UTC a2241565-aea1-4d78-96f5-2933de945d60 2012-10-18 05:53:58.759 UTC b6490574-28b7-488e-837e-31cb2c2fa5d9 2012-10-12 11:33:07.305 UTC 7f76e2ec-0550-44c2-ac29-00ab2441c50a 2012-06-27 05:33:43.841 UTC 7591e001-5af0-4a55-ad35-d4c1bf998b87 2012-10-19 04:38:51.329 UTC 2ca6a24a-223b-435c-94df-72f7e34d19c0 2012-10-17 13:53:27.500 UTC 4061280c-1210-44a7-85c8-f5af4b65e282 2012-10-19 04:44:49.149 UTC 64b7a30a-283a-420c-a188-4b4f43af31e5 2012-11-05 15:01:26.531 UTC b60b6baa-0ced-481b-8ad5-2a9413a4fa2c 2012-10-12 12:10:41.867 UTC 96776de8-09fd-4460-8184-862440d9756e 2012-10-05 14:13:16.854 UTC 142a1764-0032-4f03-be33-a00089d40ab4 2012-06-27 05:53:46.91 UTC d646dd81-0fc6-46b9-891d-205f2e5a04a6 2012-10-12 11:51:58.883 UTC b46bb259-d69c-45b9-a69c-30d5a0feede5 2012-11-02 16:06:49.984 UTC c59ea476-edf3-4861-9400-197620cb3f2b 2012-10-19 04:44:29.699 UTC c444c1e9-3edc-4516-bae8-7863671fae6b 2012-10-05 14:07:31.729 UTC c85e6aa9-ac00-4bb3-98e5-418a8889c146 2012-10-19 13:29:48.523 UTC 1f58efab-3e46-4669-aadd-23ff3fdd62f4 2012-10-05 14:23:50.167 UTC 9efa79be-1ec8-4e3f-91da-c031c7613816 2012-10-18 08:39:44.4 UTC a01daa2d-e2f8-4615-81cb-606b7c3243fb 2012-06-27 05:57:46.34 UTC 20da6a63-dead-45c4-b790-d0b972cd5e77 2012-10-19 13:26:39.101 UTC b72b3f2b-ccd6-4520-9d21-c5fe7b69b11a 2012-06-27 07:51:21.217 UTC 11cb7b6d-0894-4775-9fae-88c6a282d107 2012-10-18 08:38:44.0 UTC 1d8a9d9c-4e2f-4893-9fc4-de8ad25777fe 2012-10-19 03:55:44.385 UTC Bootstrap of observed census transitions. 2012-10-05 14:10:39.479 UTC a80afc82-32e5-4297-ad9c-ec863cd14fc2 2014-07-21 09:41:38.384 UTC fd4211f0-3d79-4602-8aaf-dc75784ede5a 2012-06-27 08:17:14.444 UTC 19a56ddd-bfdc-4736-8b5c-19a78c1a21a0 2012-10-18 12:50:25.97 UTC fa80c538-bf1e-4c79-8c8a-b1a2b38e6056 2012-10-12 11:51:39.383 UTC d562d031-b108-4006-9cda-73cd1ae7b12e 2012-11-02 16:13:50.312 UTC 7b0b5300-78d0-4580-b69c-7072e9e31fc3 2012-10-19 13:05:13.617 UTC 75353ac2-b7b7-4842-bcd4-309605dac448 2012-10-12 12:01:54.789 UTC bd29b59d-e91a-48ae-8996-df31dd66ba7c 2012-06-27 07:39:46.142 UTC 94f751a0-1f45-40dd-93d1-a9c43590c214 2012-10-19 13:36:58.476 UTC 9f0a72d2-94fb-4dd5-a7dd-95722d7ecef0 2012-10-18 12:36:13.747 UTC 9195bc9b-d72b-4210-88d4-73ae1b6a85fb 2012-10-18 14:56:07.710 UTC 208fcd5f-7e4f-4c74-8014-864e118dac6d 2012-10-12 11:26:23.664 UTC 8b334097-9faa-4020-b1b2-6e37585c8b30 2012-06-27 07:32:37.375 UTC a5bcaeba-4926-4951-894f-4ba13d7a393f 2012-10-18 06:07:59.437 UTC Workflow4census_data11stageColumnHeader00allStagesParseStagescensus_data1stage_column_header0all_stages11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity census_data 1 false stage_column_header 0 false all_stages 1 1 false localhost 6311 false false census_data R_EXP stage_column_header STRING all_stages STRING_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.InvokeParseStagescensus_datacensus_dataParseStagesstage_column_headerstageColumnHeaderallStagesParseStagesall_stages 8af0f726-006f-4a83-9eec-9cdc97dcb9d0 2012-07-06 06:48:37.151 UTC 0e09a93a-32f2-49b8-8a35-7499aa48b3a2 2012-07-11 12:30:56.575 UTC fea78a2d-fde4-46ab-9a54-741b27dc5a90 2012-07-11 12:32:16.405 UTC 90ada9ed-5f4a-4e0a-89a3-1d037e18ba01 2012-10-17 11:15:32.500 UTC e5f31b22-95ac-436a-a9c5-1ae57fe52f5e 2012-07-13 06:18:59.775 UTC 7273a214-8b3e-45b9-9e68-d785a84e8f67 2012-07-11 14:11:47.824 UTC 8a5082d0-529b-4205-b3e2-8e0cd8812239 2012-07-06 06:56:06.356 UTC SortAndCategoriseStacensus_data11stageColumnHeader00matrixStagesrecruitedStagesreproductiveStagesParseStages_FromCensusDatastageColumnHeader0census_data1allStages11net.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.InvokeCategoriseStagesInteractionunsortedStages1recruitedStages11reproductiveStages11sortedStages11net.sf.taverna.t2.activitiesinteraction-activity1.0.4net.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/popmod-20121018/select_stages.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.InvokeParseStages_FromCensusDatastageColumnHeaderstageColumnHeaderParseStages_FromCensusDatacensus_datacensus_dataCategoriseStagesInteractionunsortedStagesParseStages_FromCensusDataallStagesmatrixStagesCategoriseStagesInteractionsortedStagesrecruitedStagesCategoriseStagesInteractionrecruitedStagesreproductiveStagesCategoriseStagesInteractionreproductiveStages f787870d-2e46-4690-ae74-fbbf081fadf8 2012-07-13 06:21:53.243 UTC dc6206c9-7fe9-4d01-aabd-467efd437717 2012-07-13 06:19:12.877 UTC d9512ecc-29c2-4cb3-80e8-448c80c6bc31 2012-07-11 14:15:54.232 UTC e5cadf2e-40f8-473e-898d-a5fd35f0a426 2012-07-13 06:19:48.93 UTC 87e7040d-54ea-4f8b-8638-2945c37877a1 2012-10-07 22:14:35.518 UTC f421171e-a6bf-43d7-86b2-698255bd39f3 2012-07-06 07:07:32.666 UTC 20a399cf-7784-47b3-a40d-93d618f79137 2012-07-11 14:15:34.830 UTC 9ee8406f-b625-4130-a04c-7ef1721c8572 2012-10-17 11:16:07.104 UTC 592b9f2e-fcf1-49f5-952b-faa461b53ba7 2012-10-17 11:27:59.579 UTC 81624fcb-191c-43b4-8009-7007913e2603 2012-07-11 14:08:48.463 UTC f0be6e07-8fa8-4d7c-b86a-438ca0446799 2012-07-11 13:20:57.597 UTC 4ff7f14e-1340-42b8-aee8-5c8bd1bb34c2 2012-07-06 07:00:42.164 UTC SortAndCategoriseStages 2012-10-17 11:05:25.583 UTC 4b28bd15-1c07-4b9b-a98a-b7a0e2fa1f80 2012-07-06 06:58:00.480 UTC 1e6b402b-d71a-4e09-89c8-529b7a4c6ca0 2012-07-11 14:12:08.550 UTC 61b01f4b-0f97-42d1-ad6b-526d7111a154 2012-07-06 07:02:27.552 UTC 7635bc83-f341-40b2-82aa-9e8f960a8e2b 2012-07-11 12:36:11.769 UTC d5ce2f50-4e3f-41a9-8860-bc701d7681a4 2012-10-17 11:06:54.436 UTC 726ce44a-a330-4362-887d-0b718fca8485 2012-10-17 11:06:22.517 UTC 1c93c7b5-4270-48db-9083-a6a7ff1f4887 2012-07-06 07:00:03.815 UTC ParseYears_FromCensucensus_data11yearColumnName00censusYearsParseYearsyear_column_name0census_data1census_years11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity census_data 1 false year_column_name 0 false census_years 1 1 false localhost 6311 false false census_data R_EXP year_column_name STRING census_years STRING_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.InvokeParseYearsyear_column_nameyearColumnNameParseYearscensus_datacensus_datacensusYearsParseYearscensus_years 1e1e8835-e729-4aba-90b7-ba7c653a1f2d 2012-07-13 07:52:51.988 UTC 23762bae-1b51-4606-9a3a-a2a8b04649a1 2012-07-11 13:15:24.271 UTC 8af0f726-006f-4a83-9eec-9cdc97dcb9d0 2012-07-06 06:48:37.151 UTC fea78a2d-fde4-46ab-9a54-741b27dc5a90 2012-07-11 12:32:16.405 UTC cdf75737-30bb-4c7a-9693-2aa928c8569c 2012-10-17 11:46:13.979 UTC 4b236f5e-9a91-4db9-924c-6674c3231133 2012-07-13 07:50:51.370 UTC 450ea8ae-73da-42ed-95c9-02cf53fa556f 2012-10-17 11:43:58.240 UTC ParseYears_FromCensusData 2012-10-17 11:40:35.234 UTC 0e09a93a-32f2-49b8-8a35-7499aa48b3a2 2012-07-11 12:30:56.575 UTC 81324627-fa47-4a0d-8ffe-64698a7ee09d 2012-07-13 06:24:44.255 UTC 5787d50e-f7cc-47e6-b10a-c49b57e36e27 2012-07-11 16:05:30.475 UTC 8a5082d0-529b-4205-b3e2-8e0cd8812239 2012-07-06 06:56:06.356 UTC 2d4260a9-618f-45c7-9cee-2234c370a514 2012-07-11 13:14:26.564 UTC Bootstrap_of__observcensus_data11 Table containing demographic data of individuals in two year The input data (a .txt-file) has to have the format of a table containing the demographic data on a series of individuals in two 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, not longer than 5 characters. For all individuals, the number of offspring is specified in a chosen way (in the example, 'repstr' gives the number of flowers/fruits for each plant. In the example, it can be seen that only generative adults (stage=G) had flowers. Individuals without offspring have to be indicated by filling in '0' in this column, which cannot have empty cells. The column 'recruitment' specifies those individuals that are new to the population by means of a code. In the example, 'RS' is a new seedling, and 'RJ' a new juvenile plant. As can be seen in the example, no code is needed in this column for individuals that were already present. 2012-10-12 12:05:58.914 UTC plant year stage reprstr recruitment 2 1987 D 0 4 1987 J 0 5 1987 D 0 31 1987 V 0 36 1987 G 5 37 1987 J 0 41 1987 J 0 43 1987 S 0 46 1987 V 0 2 1988 V 0 4 1988 D 0 5 1988 V 0 9 1988 J 0 RJ 14 1988 J 0 RJ 2012-10-12 12:05:46.851 UTC stages11 S J V G D 2012-10-12 11:26:02.851 UTC Stage input port: Here come 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. 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 2012-10-12 11:25:20.445 UTC recruitedStages11startYear00plotTitle00bootstrapIterations00projection_matrix Projection matrix Output port: Creates a stage matrix from the input data. 2012-10-12 11:33:07.101 UTC 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 2012-10-12 11:32:28.195 UTC confidence_interval 2.5% 97.5% 0.954955 1.468701 2012-10-05 14:22:04.620 UTC 95% Confidence interval of Lambda In statistics, a confidence interval (CI) is a type of interval estimate of a population parameter and is used to indicate the reliability of an estimate. It is an observed interval (i.e. it is calculated from the observations), in principle different from sample to sample, that frequently includes the parameter of interest if the experiment is repeated. How frequently the observed interval contains the parameter is determined by the confidence level or confidence coefficient. 2012-10-12 12:24:22.164 UTC histogram Histogram plotting the frecuencies of the lambda values and the 95% confidence intervals resulting from the bootstrap analysis 2012-10-12 11:51:41.883 UTC trans1logPreparecensus_data1recruited_stages1stages1start_year0trans111log00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity census_data 1 false stages 1 false recruited_stages 1 false start_year 0 false trans1 1 1 trans 1 1 log 0 0 false localhost 6311 false false census_data R_EXP stages STRING_LIST recruited_stages STRING_LIST start_year INTEGER trans1 R_EXP trans R_EXP log TEXT_FILE 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.InvokeAnalysisstages1trans11projection_matrix11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity trans1 1 false stages 1 false projection_matrix 1 1 false localhost 6311 false false trans1 R_EXP stages STRING_LIST projection_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.InvokePlotHistogramplot_title0a1ci1histogram00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity a 1 false ci 1 false plot_title 0 false ci 1 1 histogram 0 0 false localhost 6311 false false a R_EXP ci R_EXP plot_title STRING ci R_EXP histogram PNG_FILE 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.InvokeConfidenceIntervaltrans11bootstrap_iterations0ci11a11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity trans1 1 false bootstrap_iterations 0 false a 1 1 ci 1 1 false localhost 6311 false false trans1 R_EXP bootstrap_iterations INTEGER a R_EXP ci 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.InvokeDisplayTrans1input1output00net.sf.taverna.t2.activitiesrshell-activity1.4net.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-impl1.4net.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.InvokePreparecensus_datacensus_dataPreparerecruited_stagesrecruitedStagesPreparestagesstagesPreparestart_yearstartYearAnalysisstagesstagesAnalysistrans1Preparetrans1PlotHistogramplot_titleplotTitlePlotHistogramaConfidenceIntervalaPlotHistogramciConfidenceIntervalciConfidenceIntervaltrans1Preparetrans1ConfidenceIntervalbootstrap_iterationsbootstrapIterationsDisplayTrans1inputPreparetrans1projection_matrixAnalysisprojection_matrixconfidence_intervalConfidenceIntervalcihistogramPlotHistogramhistogramtrans1DisplayTrans1outputlogPreparelog This Workflow was created by: Maria Paula Balcázar-Vargas, Jonathan Giddy and G. Oostermeijer 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 based on Package ‘popbio’ in R. 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 2012-10-12 11:04:44.914 UTC ee769dbe-15e6-4f27-bf6f-feb4292a5a47 2012-10-19 04:38:45.215 UTC bd29b59d-e91a-48ae-8996-df31dd66ba7c 2012-06-27 07:39:46.142 UTC fa80c538-bf1e-4c79-8c8a-b1a2b38e6056 2012-10-12 11:51:39.383 UTC 4280c8bb-56c9-4795-b78a-106cdbf36e1a 2012-10-18 06:07:44.858 UTC 75353ac2-b7b7-4842-bcd4-309605dac448 2012-10-12 12:01:54.789 UTC 245ec9d7-9e92-478a-8214-d4f3f8a11e1e 2012-10-18 05:43:24.204 UTC 294ceddd-75cb-4181-b87c-3939b2ee08f4 2012-10-18 12:50:20.12 UTC fd4211f0-3d79-4602-8aaf-dc75784ede5a 2012-06-27 08:17:14.444 UTC d646dd81-0fc6-46b9-891d-205f2e5a04a6 2012-10-12 11:51:58.883 UTC Bootstrap of observed census transitions. 2012-10-05 14:10:39.479 UTC aa848d79-a9f7-497e-ba06-ee6feddc1da3 2012-06-27 06:00:45.433 UTC The goal of a demographic analysis is very often to estimate lambda, because lambda is estimated from imperfect data, such estimation are uncertain. Therefore, when the results have policy implications it is important to quantify that uncertainty. Confidence intervals is one of the traditional tools to doing so (Caswell 2001). This workflow calculate bootstrap distributions of population growth rates (lambda), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. A detailed description of resampling methods to estimate confidence intervals for demographic estimates is described Caswell (2001, Chapter 12). 2012-10-12 12:10:40.351 UTC 1f58efab-3e46-4669-aadd-23ff3fdd62f4 2012-10-05 14:23:50.167 UTC e0a9cd7d-9df2-484d-bfb5-293e3485e692 2012-10-18 05:47:47.58 UTC be9d3a0d-f115-4b04-9737-99f2a1dbed3b 2012-10-12 12:24:31.305 UTC ea499285-044d-4fcf-b361-82e705bce535 2012-10-19 03:58:49.660 UTC 142a1764-0032-4f03-be33-a00089d40ab4 2012-06-27 05:53:46.91 UTC 0a45c68e-bb69-40fc-b695-3d6f8ebda19b 2012-10-18 08:38:21.536 UTC b8fe02f6-e147-4416-aeb4-6c4e54589512 2012-06-27 08:19:06.56 UTC 1da10601-a701-4542-ac84-b210462a5812 2012-06-27 06:02:05.237 UTC b6490574-28b7-488e-837e-31cb2c2fa5d9 2012-10-12 11:33:07.305 UTC a01daa2d-e2f8-4615-81cb-606b7c3243fb 2012-06-27 05:57:46.34 UTC 96776de8-09fd-4460-8184-862440d9756e 2012-10-05 14:13:16.854 UTC b60b6baa-0ced-481b-8ad5-2a9413a4fa2c 2012-10-12 12:10:41.867 UTC 2ca6a24a-223b-435c-94df-72f7e34d19c0 2012-10-17 13:53:27.500 UTC b72b3f2b-ccd6-4520-9d21-c5fe7b69b11a 2012-06-27 07:51:21.217 UTC 105112aa-5a6e-4ace-9437-6421b756a88b 2012-10-19 04:44:24.480 UTC e98a3578-498e-4d02-9059-57c0cdf09e83 2012-06-27 05:56:22.181 UTC aa6cba9d-a378-40a3-aeb7-c42870cdb776 2012-10-19 04:02:43.872 UTC 8b334097-9faa-4020-b1b2-6e37585c8b30 2012-06-27 07:32:37.375 UTC c444c1e9-3edc-4516-bae8-7863671fae6b 2012-10-05 14:07:31.729 UTC 32904aa5-ff7a-4ad8-84a5-199a181f790f 2012-10-18 12:36:09.164 UTC b52aa862-b3ab-4602-a90f-14cf4a02b16f 2012-10-12 11:28:21.258 UTC 7f76e2ec-0550-44c2-ac29-00ab2441c50a 2012-06-27 05:33:43.841 UTC 023bd080-a31d-46d1-a2b6-6f70249bf319 2012-10-18 15:02:35.315 UTC 208fcd5f-7e4f-4c74-8014-864e118dac6d 2012-10-12 11:26:23.664 UTC dc4a1937-f538-413c-ab37-4601c9f40c67 2012-10-18 14:55:56.19 UTC 096ec245-ec16-40b5-bad6-7da6a1d58ce0 2012-10-19 03:55:10.475 UTC 3d8f7330-9060-42ea-94bc-f7c2878ce81a 2012-10-12 12:06:43.914 UTC SelectYearcensus_data11yearColumnName00initialYearSelectYear_Interactionyears1year00net.sf.taverna.t2.activitiesinteraction-activity1.0.4net.sf.taverna.t2.activities.interaction.InteractionActivity years 1 text/plain java.lang.String false year 0 0 http://biovel.googlecode.com/svn/tags/popmod-20121018/select_year.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.InvokeParseYears_FromCensuyearColumnName0census_data1censusYears11net.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.InvokeSelectYear_InteractionyearsParseYears_FromCensucensusYearsParseYears_FromCensuyearColumnNameyearColumnNameParseYears_FromCensucensus_datacensus_datainitialYearSelectYear_Interactionyear 0556bfe7-45af-4fad-ba6a-50b93e7550f8 2012-10-17 11:47:27.572 UTC 001a52e9-fb0b-4c0f-97fc-33bcc3749029 2012-10-17 12:15:53.73 UTC 1066a8b8-63d1-4f5b-aebf-43172f877d3c 2012-09-28 08:44:39.139 UTC b033a199-d1e5-4225-b27b-4b828c693d52 2012-07-11 16:06:33.247 UTC 6f93190c-3845-41bb-ba74-775b9596ae5c 2012-07-11 16:05:56.5 UTC ddf40f01-1f62-4477-a4a4-6467bcc05f25 2012-07-13 07:52:57.834 UTC SelectYear 2012-10-17 11:47:50.307 UTC 3c1aa296-4541-43a3-8b8a-6448e435e600 2012-07-13 07:51:05.500 UTC 7e051801-8211-4f67-bebe-d7fd628d68c6 2012-07-13 06:24:48.987 UTC 7172c953-a063-4d58-b19d-6912223595e7 2012-10-17 11:47:53.180 UTC be02d73d-ace1-46be-9b88-98048dac2d45 2012-07-11 16:03:25.310 UTC ca84a3a5-d487-4aed-acb8-69a077a1e2c8 2012-07-13 06:25:21.195 UTC