Elasticity_and_Sensimatrix_file00 The input data must be a .csv-file, with its fields separated by ";" and has to have the format of a table containing a decomposed matrix. Decimal numbers must be separated by a period e.g.: 0.578. This table has 4 initial columns with information about: 1. Name of the species (species), 2. Classes (classOrganized) a. "veg": photosynthetically active but not sexually reproductive (and not dormant). b. "rep": photosynthetically active and sexually reproductive (including classes of which only a part of the individual is sexually reproductive) c. "dorm": dormant. d. "seed": bank seeds, etc. 3. Name of the stages (classAuthor), the stage codes can be chosen by the user. 4. Class Number: numerical order of the stages The survival/growth/shrink matrix starts in the column number 5 (matrix U), after this matrix comes fecundity matrix (matrix F) and finally the vegetative reproduction matrix (matrix C). An example decomposed matrix is found: http://www.myexperiment.org/files/1268.html 2014-08-29 11:35:56.684 UTC species;classOrganized;classAuthor;classNumber;U1;U2;U3;U4;U5;F1;F2;F3;F4;F5;C1.1;C1.2;C1.3;C1.4;C1.5 Gentiana pneumonanthe;veg;S;1;0;0;0;0;0;0;0;0;7.666;0;0;0;0;0;0 Gentiana pneumonanthe;veg;J;2;0.0579;0.01;0;0;0;0;0;0;8.523;0;0;0;0;0;0 Gentiana pneumonanthe;veg;V;3;0.4637;0.83;0.9009;0.2857;0.8604;0;0;0;0;0;0;0;0;0;0 Gentiana pneumonanthe;rep;G;4;0;0.04;0.009;0.619;0.1162;0;0;0;0;0;0;0;0;0;0 Gentiana pneumonanthe;dorm;D;5;0;0.03;0.018;0;0.0232;0;0;0;0;0;0;0;0;0;0 2014-08-29 11:36:01.734 UTC matrix_dimensions00 5 2014-08-28 09:29:09.679 UTC It is the number of categories that the matrix contains. First press add value, fill a number and press enter. 2014-08-29 09:27:09.678 UTC Vital_Rates_Elasticities0 Sur Sur Sur Sur Sur GrowShrink veg 0 0 0 0,021274786 0 0 veg 0,011536481 0,00133395 0 0,158060708 0 0,006612559 veg 0,053880709 0,064568244 0,273239013 0,00308989 0,005094827 0,030287938 rep 0 0,091655275 0,080401698 0,197187815 0,020267107 0 dorm 0 0,009050726 0,021171904 0 0,000532768 0 2014-08-29 09:25:44.474 UTC Elasticities of the vital rates Only the first 7 columns are shown. 2014-08-29 09:26:19.265 UTC Vital_Rates_Sensitivities0 Sur Sur Sur Sur Sur GrowShrink veg 0 0 0 0,05047776 0 0 veg 0,015689331 0,001814139 0 0,214958679 0 0,073722666 veg 0,071862873 0,08611727 0,364429886 0,004121111 0,006795176 0,042164082 rep 0 0,125379152 0,109984905 0,269741604 0,027724239 0 dorm 0 0,011203217 0,026207117 0 0,000659474 0 2014-08-29 09:26:36.616 UTC Sensitivities of the vital rates Only the first 7 columns are shown. 2014-08-29 09:26:24.870 UTC Vital_rate_sensitivities_and_elasticities_analysisdimensions0matrix_file0sens00elas00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity matrix_file 0 false dimensions 0 false elas 0 0 sens 0 0 false localhost 6311 false false matrix_file TEXT_FILE dimensions INTEGER elas TEXT_FILE sens TEXT_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeVital_rate_sensitivities_and_elasticities_analysisdimensionsmatrix_dimensionsVital_rate_sensitivities_and_elasticities_analysismatrix_filematrix_fileVital_Rates_ElasticitiesVital_rate_sensitivities_and_elasticities_analysiselasVital_Rates_SensitivitiesVital_rate_sensitivities_and_elasticities_analysissens 2fcaf7e5-e3b1-4e0c-97ac-df4da3519e6a 2014-03-20 12:40:16.329 UTC 37600523-120e-4c94-a1b2-a26d57c2ff06 2014-05-14 13:57:15.454 UTC 6ba89ca3-dae6-4dc4-b781-dc490195ac40 2014-08-27 13:54:50.839 UTC 1d05210a-b815-436c-a1b7-f3a1609b9891 2014-08-27 13:46:03.835 UTC d95a0339-350f-47d3-818e-fee6528edb27 2014-03-20 12:50:41.182 UTC 82f1b7b0-2a6e-4a0a-ba7e-6f82abad08b4 2014-08-27 13:47:10.138 UTC a4709ccd-6cc8-4a8b-850e-a2abd6c397b3 2014-08-29 08:54:00.335 UTC cc0c7f09-c8ff-4d34-8ed2-fefc5d12f228 2014-03-20 13:08:33.533 UTC 0f5c27dc-634a-4a76-93a9-ec20a5274e4a 2014-03-20 13:09:41.953 UTC c9321bfc-fb6b-4dab-a5d3-22da90cc8c95 2014-03-20 13:22:34.454 UTC cc0cd1a9-bb7b-4844-815f-4b69dae22c71 2014-03-20 13:05:46.23 UTC a4c524fb-ff1a-4f61-9fb7-5c40fb8e7eaa 2014-03-20 13:20:20.180 UTC d46ed938-f6e4-4bb3-a94e-f36a990ee295 2014-06-20 11:38:42.998 UTC 30152064-c17d-408d-8a94-6600950c21b6 2014-06-20 11:32:12.101 UTC b93f829a-17c6-4d81-a8fd-748df57cfbde 2014-08-29 09:23:19.334 UTC e8f7da2d-6e35-49bd-8521-9691f6f6b9b6 2014-08-28 11:34:20.138 UTC 5713ced9-a967-47a4-b5ae-7d297dc756a7 2014-03-20 12:40:57.980 UTC ba95920c-1dec-4e0f-b48d-aea6c0d20256 2014-03-20 13:03:45.247 UTC 622a3dfe-9ac9-4b6c-ba6f-f1f5edd0f9d9 2014-06-20 11:35:41.427 UTC 1250ba61-6d9d-486e-993b-b42c72262603 2014-08-28 11:33:48.132 UTC 0896599b-82f9-478d-aceb-a4846a5a3497 2014-08-29 09:28:49.221 UTC 5b417c8f-d40f-400b-be84-243312208d55 2014-06-20 11:39:06.18 UTC 956eb7ae-a9b8-4b0b-9147-ae73e6ce0a9a 2014-08-27 13:44:34.75 UTC Elasticity and Sensitivity of the Vital rates 2014-08-28 07:44:20.253 UTC 10366b80-eea2-46fa-bc16-4bbde53c3635 2014-03-20 13:15:55.741 UTC 9875d75a-4381-4369-88bd-7f7cc89ec34a 2014-08-29 09:26:36.816 UTC 3e3afe2b-66c7-4768-8674-ade814893354 2014-08-28 11:30:10.702 UTC a1af34f0-b6fc-4c4b-ab2c-741fee487d56 2014-06-20 11:36:05.86 UTC 410953cc-8bbc-4ba3-a191-72d938129a48 2014-06-20 11:40:02.427 UTC 05f3e2fd-d250-452b-9bd6-488e3c45fec8 2014-03-20 12:45:47.30 UTC 829023b2-edda-42c9-931f-0b9094f64468 2014-03-20 12:41:58.25 UTC 3e9671eb-99a7-4256-bece-fbc4b1655450 2014-08-29 09:07:10.744 UTC bb3930a2-6778-4fee-8ef5-cea6be6f2e13 2014-03-20 13:13:08.682 UTC 46e9aa05-e286-4d77-b5a9-f820d0c7b7c0 2014-08-28 09:08:44.459 UTC 2981243f-6bc2-4cf9-a899-c654c86a4553 2014-03-20 13:06:26.439 UTC 9cf7f782-a36c-4834-afe2-db62d1dad270 2014-08-28 11:54:01.369 UTC f3997244-e51a-4b7a-945f-abca50bdfa64 2014-03-20 13:12:33.453 UTC 4d10b021-946f-4b07-a893-f7a25d8403b1 2014-03-20 13:05:11.24 UTC e0ef2984-045f-4577-8552-afd32bcf1a19 2014-03-28 17:31:17.729 UTC 3b643b7f-e0a8-4a88-9c3c-05fa119a93b2 2014-03-20 12:42:38.457 UTC 0ccab983-5988-4cfe-8388-aabee018efc6 2014-08-27 13:29:13.595 UTC 177bf69b-5628-41e7-8089-aae2064405c0 2014-08-28 11:23:17.550 UTC b22633f7-bb64-4aab-b9c1-1affab53f7f3 2014-08-27 13:57:52.325 UTC ec27e4fb-99e1-481f-9db0-d6477a43a2eb 2014-08-28 09:24:16.312 UTC dd5e840e-869c-4651-b145-3f514197f0b3 2014-03-20 13:12:14.823 UTC ba6242e4-2e70-45db-8168-0c4b530759b8 2014-08-28 09:24:31.800 UTC 2c91ae71-c704-4899-bf25-9ef2156010e0 2014-08-27 14:09:32.112 UTC 9756acef-ca3b-42b6-ba3d-1a792b6910ff 2014-03-20 12:44:44.235 UTC 3abb2f08-d5d2-497a-9eb1-d01b477f6efc 2014-08-29 11:36:07.776 UTC c16ca6b0-5796-41a1-8a47-0dafdaf8d1f1 2014-08-28 09:29:13.992 UTC 5cd247da-7955-42a6-a3af-6b3bab31d7d9 2014-08-29 11:07:00.355 UTC cad9c80d-7cdb-4b25-9321-8ca4bdb15ee2 2014-03-20 13:17:54.921 UTC This workflow calculates the Elasticity and Sensitivity of population growth rate with respect to various vital rates. The goal in both cases is to determine which vital rates has/ve the most influence on population growth rate (λ). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses. a) The sensitivity matrix: The sensitivity describes the effect on λ of changes in vital rates of the matrix. The derivative tells what would happened to λ if aij was to change, not whether, or in what direction, or how much, aij actually change (Caswell 2001). b) The Elasticity matrix: The elasticities of λ with respect to the vital rate are often interpreted as the “relative contributions” of each of the vital rates to λ (de Kroon et al 1986). For further information see: de Kroon, et al., 1986. and Caswell 2001. This Rscript extract sensitivities and elansticities of the vital rates from a decomposed matrix. This code was developed by R. Salguero-Gomez (Max Planck Institute) modified after E. Jongejans (Nijmegen University). Last modified: Mar 29th, 2012, Modified for Taverna by Maria Paula Balcazar-Vargas. 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. -------------------------------------------------------------------------------------------------------------------------------------- For further details see: Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts. 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 2014-08-29 09:31:55.316 UTC e4df70f1-d8b9-4603-b727-0d844a967041 2014-08-29 09:31:55.436 UTC 3f6cf3fc-7571-4694-8e85-f6c3544d152e 2014-08-27 14:13:40.303 UTC dea749ef-7dfa-44ed-b06b-9c23ad0ac7ba 2014-03-20 13:15:30.723 UTC dee3b4e4-34ed-48ad-9ebd-af7bf378f44b 2014-08-29 09:24:46.34 UTC 061f9e8d-da14-4ba0-a775-fea26ca0893d 2014-08-27 14:21:05.892 UTC cd8f0f60-2bd3-4187-bec7-3876ff7e3f26 2014-08-27 14:05:59.866 UTC ea842604-6bd1-423d-943f-32d33aa61569 2014-08-29 09:25:05.919 UTC 5aef2b60-9bc0-4111-a2ad-1d70bb40b9c9 2014-03-20 13:11:35.746 UTC 8945daa4-47a3-4b42-a8ca-faac4b1d2595 2014-03-20 13:10:46.628 UTC 4f9661bb-cdc2-4d95-bdcd-bbfbdb216ca1 2014-08-27 13:47:42.169 UTC 2537bc1e-d720-4663-b1c6-481e4e4defdc 2014-06-27 09:30:23.7 UTC fe6d1bae-7724-45dd-80dd-7505c8e93649 2014-03-20 12:17:49.708 UTC 6fe5e846-6be2-4c88-941b-bbf8e11e711a 2014-08-29 08:54:29.320 UTC 5dfa2901-e0ad-4de7-8b40-1fbb1c449b92 2014-08-27 13:59:28.333 UTC 172c94d3-c09f-4e48-a6f9-2d77a502b07b 2014-03-20 12:41:27.681 UTC 83b461d3-c353-4158-bc64-e2a363eea48b 2014-08-27 14:12:41.407 UTC Maria Paula Balcazar-Vargas, Jonathan Giddy and Gerard Oostermijer 2014-08-29 09:29:25.295 UTC 4c434384-9e67-4631-8ddb-00abd6a14f74 2014-08-28 09:22:20.228 UTC