Generation_time__T_stage_matrix_file00 A stage matrix In this import port a stage-matrix should be add. The input data (a .txt-file) has to be a point delimited (see example). In the pop-up ‘run workflow’ window, click-on ‘set a location’ and seach in your computer the txt-file of your matrix. Example from: J. Gerard B. Oostermeijer; 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. 2012-10-11 11:35:59.0 UTC 0.0000 0.0000 0.0000 7.6660 0.0000 0.0579 0.0100 0.0000 8.5238 0.0000 0.4637 0.8300 0.9009 0.2857 0.8604 0.0000 0.0400 0.0090 0.6190 0.1162 0.0000 0.0300 0.0180 0.0000 0.0232 2012-10-05 11:35:18.26 UTC stages11 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 2012-10-11 12:39:57.187 UTC [S,J,V,G,D] 2014-07-22 09:27:55.159 UTC Rows_fecundity11 To perform the generation time (T), the row(s) the row(s) in which the recruitment values are found, should be selected. In the example of the Gentiana species (Oostermeijer et al. 1996. The Journal of Ecology): Selected lines are S and J (seedlings and juveniles, these stages receive recruits each year from the stage G): therefore, the numbers 1 and 2 are used to identify these rows (S and J). 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 2012-10-11 12:42:20.515 UTC [1,2] 2014-07-22 09:28:10.892 UTC Columns_fecundity11 4 2012-10-11 11:58:22.562 UTC To perform the generation time (T), the column(s) in which the fecundity values are found, should be selected. In the example of the Gentiana species (Oostermeijer et al. 1996. The Journal of Ecology): The selected column is G (reproductive individuals): therefore number 4 will be used to identify the fecundity column (G). 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 2012-10-11 12:42:12.468 UTC generation_time Generation time (T): The time T required for the population to increase by a factor of Ro (net reproductive rate) e.g.: If Ro (net reproductive rate) = 5.56 and T (generation time) = 8.055 The average plant of the species Gentiana pneumonanthe in Terschelling in the year 1987 replaced itself with almost six new plants and took approximately 8.05 years to do so. 2012-10-11 12:03:38.359 UTC 8.055 2012-10-17 13:36:56.312 UTC Generation_time_analysismat1columns1rows1result00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity mat 1 false rows 1 false columns 1 false result 0 0 false localhost 6311 false false mat R_EXP rows DOUBLE_LIST columns DOUBLE_LIST result DOUBLE 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.Invokeread_matrixstages1filename0mat11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity filename 0 false stages 1 false mat 1 1 false localhost 6311 false false filename TEXT_FILE stages STRING_LIST mat 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.InvokeGeneration_time_analysismatread_matrixmatGeneration_time_analysiscolumnsColumns_fecundityGeneration_time_analysisrowsRows_fecundityread_matrixstagesstagesread_matrixfilenamestage_matrix_filegeneration_timeGeneration_time_analysisresult 04064c96-4b8d-4065-80e5-dfcabcb597de 2012-10-11 11:30:15.656 UTC 19bbf243-d943-409c-9004-bb9df6c33349 2012-06-15 06:40:07.359 UTC 6cefb97d-5207-40ec-847d-6b62cabd12cb 2012-06-15 06:56:38.363 UTC 74dedf92-5055-45bd-995b-5b9df0a480a8 2012-10-05 11:40:27.651 UTC a6d860df-36bb-423a-a7e6-586818fccfc8 2012-09-28 08:06:19.732 UTC 98ee462f-3718-4938-a959-6a042ad29aff 2012-10-05 11:35:18.229 UTC 45f7861f-9c3c-492a-924c-34b896fefa32 2012-10-05 11:35:49.386 UTC 96405b62-f038-4c52-a831-1787aa510bf0 2012-10-11 12:40:08.593 UTC f29cd8ec-6fe8-4962-9bbc-7c99ef58365d 2012-10-11 11:52:57.562 UTC c65932e5-9f7b-4ec2-b218-152de68c3263 2012-10-05 11:48:11.370 UTC e2a9d92c-412f-47fc-a567-39a56abe723e 2012-06-15 06:52:47.83 UTC f3629da2-038d-47c2-b494-15ce65b7df82 2012-10-11 12:02:50.281 UTC c7b6d5dd-ddc3-4388-9f28-647b74d4f5f4 2012-06-15 06:54:00.692 UTC 88440626-1691-4815-909b-c08836952d2a 2012-10-11 11:45:15.453 UTC 227252e7-ff41-47fd-af0c-39907febdc42 2012-09-28 08:07:38.560 UTC c6fd9af5-b7a7-460d-83c8-8122aa11253e 2012-09-28 08:43:02.498 UTC 3b27b30c-4431-409c-97fd-26b37a8823fb 2012-09-28 08:09:20.60 UTC 6e3a57e1-23a5-4883-84d6-bf7a14a9b104 2012-06-21 14:06:12.125 UTC 6ed83074-6a5a-445c-bc2e-d0b4df878369 2012-10-11 11:35:56.890 UTC 18aac4ef-4208-458c-9dbb-9a2e5ee2f3f9 2012-06-21 14:24:41.784 UTC c55402cf-b409-47b3-b079-4cfb1234f6ce 2012-10-05 11:30:55.729 UTC e38e9ac0-3bb8-427d-91c6-a40324275e42 2012-10-11 11:57:10.312 UTC a67ab916-ab83-4d04-acc1-750adbebbea4 2012-10-11 12:03:39.671 UTC 724a9578-a6b6-44b9-9c02-fcf83e375a67 2012-09-28 08:40:05.123 UTC f92df37a-086b-4bbe-b7c2-42bc8660915e 2012-06-15 06:42:22.376 UTC e6545437-85f0-42a0-b54f-066b165d7ec6 2012-10-05 11:51:02.854 UTC d9758ade-7727-44a4-aa75-d0fac485df0d 2012-10-17 13:37:14.171 UTC f589ea15-b89d-415f-b16b-71d6b6abcc59 2012-09-28 08:41:41.388 UTC Generation time (T) 2012-10-05 11:22:20.526 UTC 3979d4bd-1668-4e90-913b-06b22e1229c6 2012-06-22 08:39:22.770 UTC aabd83c8-3016-47ec-a1e2-e6d909289dfa 2012-06-22 08:38:17.934 UTC 00e1ecf7-7f9c-4ee5-baea-9403570f30a4 2012-10-11 12:43:04.531 UTC The time T required for the population to increase by a factor of Ro (net reproductive rate) e.g.: If Ro (net reproductive rate) = 5.56 and T (generation time) = 8.055 The average plant of the species Gentiana pneumonanthe in Terschelling in the year 1987 replaced itself with almost six new plants and took approximately 8.05 years to do so. ========================================================= 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, 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 15:00:50.937 UTC 4ca61c34-e295-4604-9a05-26ddabb217cd 2014-07-22 09:28:27.273 UTC 138bd86c-fd0b-4db2-8092-1e9071940e2a 2012-09-28 08:45:04.951 UTC e7b6d547-d809-4376-b8eb-f1208f5c07be 2012-10-11 12:06:45.921 UTC d175cac8-5f8c-46ea-bb34-cd41954a2c5e 2012-10-11 11:59:17.375 UTC Maria Paula Balcázar-Vargas, Jonathan Giddy and G. Oostermeijer 2012-11-02 15:00:09.343 UTC 3a07650e-1a12-4746-bcb2-1201ee4fe84f 2012-11-02 15:01:05.734 UTC 81787775-16fe-4c13-90dd-0a48678146ee 2012-09-28 08:10:30.76 UTC b5ec6e6b-d9bd-43b3-86d4-f33bd5640243 2012-10-05 11:37:41.839 UTC c4bce93c-e05f-433c-9f0f-36cb69f249e7 2012-10-05 11:49:57.167 UTC c4dc3143-373c-4d4e-adc3-8d8d84dd4a1e 2012-10-05 11:50:33.307 UTC