Calculate_and_Plot_acensus_data_file00The 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 UTCplant 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 UTCgraph_title00Gentiana pneumonanthe2014-08-22 09:49:08.203 UTCMain 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 UTClast_year00this 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 UTC19932014-08-22 11:11:28.383 UTCnumber_individuals_per_stage_per_year_graph0Graph showing the abundance per stage per year.2014-08-22 13:05:25.791 UTCproportion_individuals_per_stage_per_year_graph0Graph showing the proportion of individuals per stage per year.2014-08-22 13:06:14.474 UTCnumber_individuals_per_stage_per_year0A 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 UTCgraphnumber_individuals1stages1last_year0sv1graph_title0proportion_individuals_graph00number_individuals_graph00number_individuals11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivitynumber_individuals1falsegraph_title0falsestages1falsesv1falselast_year0falsenumber_individuals_graph00proportion_individuals_graph00number_individuals11falselocalhost6311falsefalsenumber_individualsR_EXPgraph_titleSTRINGstagesSTRING_LISTsvR_EXPlast_yearINTEGERnumber_individuals_graphPNG_FILEproportion_individuals_graphPNG_FILEnumber_individualsR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCategoriseStages_InteractionunsortedStages1sortedStages11With 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 D2012-11-01 14:53:35.21 UTCnet.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.interaction.InteractionActivityunsortedStages1text/plainjava.lang.StringfalsesortedStages11recruitedStages11reproductiveStages11http://biovel.googlecode.com/svn/tags/mpm-20130805/select_stages.htmlLocallyPresentedHtmlfalsenet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.RshellActivitycensus_data_file0falsenumber_individuals11stages11sv11falselocalhost6311falsefalsecensus_data_fileTEXT_FILEnumber_individualsR_EXPstagesSTRING_LISTsvR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokegraphnumber_individualsgraphstagesgraphlast_yeargraphsvgraphgraph_titleOutputFundamentalMatrix_3inputCategoriseStages_InteractionunsortedStagestablecensus_data_filenumber_individuals_per_stage_per_year_graphproportion_individuals_per_stage_per_year_graphnumber_individuals_per_stage_per_yearad69cb62-f545-4cfb-9b21-88b7f98616592014-02-04 12:02:04.488 UTC83ab0223-236b-450f-ba2a-295d993993f32014-08-22 09:49:10.433 UTC0d90eb97-1147-461a-89f2-6870c84d29852014-03-12 13:25:57.350 UTC71b07b3a-895a-4671-ad1f-fa5ab23fa71e2014-03-12 12:25:12.373 UTCd5bdee58-41a9-48b7-a0db-747f073011ae2014-03-12 12:18:43.926 UTCd5357b00-1991-467a-a453-5105a4857bac2014-03-12 13:05:51.29 UTC274b5f04-287e-401d-8e2c-3adba78d99242014-03-12 13:27:04.835 UTCThis 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. Version 2.3.12014-08-22 09:22:34.163 UTCc78f02c5-cfec-4f52-94d8-4036d9cd1c2a2014-08-22 09:44:27.533 UTC2f59e405-e2c1-4359-923d-afc3ea991dc72014-03-12 12:38:19.629 UTC629957e1-f769-4ebc-9ae9-fc127ca707702014-03-12 12:11:29.293 UTC6092b41e-64aa-4c77-8283-5df2efde582e2014-03-12 13:04:28.821 UTCc6b4835b-45d3-4423-8c74-138257b6c9dd2014-02-04 12:04:09.248 UTCdfed9d85-7cb6-49d9-9ac0-1095ce4e662a2014-02-26 14:45:46.505 UTC397d9144-57bf-4aa8-8256-12742b5e0e092014-03-12 12:49:41.780 UTCe05f1c87-b042-4ccc-8887-74b9e451c6622014-02-04 11:59:43.291 UTC1a0fd6d7-259c-448d-9b65-f2f8e02f948c2014-02-04 12:08:24.992 UTC3eabdbda-b1f9-4d7c-8df9-d29a4fffda312014-03-12 12:43:47.478 UTCCalculate and Plot abundance over the years2014-08-22 09:20:01.406 UTCd0f6f663-4263-4b4d-b47e-a883f1d199c92014-03-05 11:34:12.491 UTCb5c6fb46-754e-4790-8107-c593c9fda4c82014-02-21 11:00:51.269 UTC92aeb90f-3954-4c8f-a958-38c7bcb3c62a2014-08-22 13:28:22.517 UTC49e328ac-96b0-4d89-8f07-1895e7e5f5202014-08-22 13:04:37.261 UTC57ff886d-c0d6-4b27-9102-37d1f573cf8d2014-03-05 11:41:13.820 UTC7c992da0-79bc-4f17-a7cc-551384cc6faa2014-03-05 11:39:21.773 UTC028854a0-c987-4710-93a7-9773508c55e92014-02-04 12:04:28.600 UTCa2f197c6-db18-4902-a72b-09622ab57da52014-03-12 12:19:45.375 UTC6e3faa2f-4f12-48a4-abfc-a0ab8caaeb202014-03-12 12:12:30.723 UTC8163cfea-c64a-44d2-b19d-8e4bf9dd0e4c2014-03-12 12:29:29.333 UTC7ce0b0d5-b7d4-441d-b629-9d66734a29b72014-03-12 12:22:58.20 UTCbd72edcf-03e1-4d48-ad36-78d186668ce92014-03-12 12:31:09.544 UTC21a5090e-be62-46b7-854f-67d327f71b2e2014-08-22 11:11:28.523 UTCMaria Paula Balcázar-Vargas, Mikołaj Krzyżanowski, Jonathan Giddy, Gerard Oostermeijer.
2014-08-22 09:19:28.560 UTCed8c8605-c74a-4086-aff5-c0f84c1b71f22014-03-12 12:13:07.196 UTC7d909bac-a7df-4097-a493-85a38b1ed6bd2014-03-12 12:44:26.681 UTC27d098d4-24e0-49f4-b92f-533b73b97e042014-03-05 11:35:38.315 UTC21b07b46-aabf-479b-a8b9-80aedd1b161a2014-08-22 09:33:55.665 UTC44c6eadf-ce22-4603-9ec0-de4bf0c4239c2014-02-26 14:49:27.256 UTC2cdbb52b-8d67-4578-88e9-c1e5ef2c8ea12014-03-12 12:57:22.847 UTCb8af9fb2-6f17-4ca1-9433-d6088bd40ae72014-08-22 13:06:14.674 UTC4a5de42a-acdf-452b-ae7e-05d06fdf12d72014-03-12 13:00:35.256 UTCaeb08cdf-d022-469f-8e06-73a79ad643f22014-03-12 13:40:49.28 UTC5e7974c5-9476-413a-9d83-4f30c5f467dd2014-02-04 12:07:38.133 UTCb39d4add-da4b-4125-b061-0483d91aa2792014-03-12 13:32:19.281 UTCe3b5311d-0f6e-48cd-84ab-d2bdf22e77252014-02-04 12:23:51.500 UTCb6af795f-3518-46c5-9bb2-38cf1f0100072014-03-20 12:08:25.484 UTC894e793b-77fd-404f-abbd-42843517e7ac2014-03-12 12:40:06.462 UTC4125c9c4-52df-4884-b3f8-31e840ae7dd82014-08-22 13:16:49.197 UTCcebddf61-8458-49c7-81ee-6292f37ec7bc2014-08-22 10:37:57.344 UTC1b0529ab-b8d3-4931-a8c0-d8974160330e2014-03-12 12:48:36.966 UTC9c35b884-0ad4-4a1f-8a49-7ccd263a8ea22014-03-12 12:37:25.552 UTC7444860d-30c5-484d-8c50-ad3f2245ad082014-03-12 12:44:47.152 UTC87e7a92a-4c6f-4a9b-b73b-093342fc1a9c2014-08-22 09:20:16.911 UTCba6e2da1-e12d-4c90-b153-50dd9c941de62014-03-12 13:25:04.152 UTCaeacb777-d66b-4ab2-83cb-4763a582ca012014-08-22 13:29:06.103 UTC7c437604-40ec-4bab-b673-1956acdf5bac2014-03-12 12:14:54.653 UTCde6e763b-def3-4a05-ad14-d6629f61f3412014-03-12 12:41:12.725 UTC1dc8a6c1-79fa-452e-926d-4feeda02e9e92014-02-04 11:54:12.376 UTC1afebf5c-1ceb-4639-a203-db4c28a0d5ef2014-03-12 12:50:41.403 UTC7bb09953-8702-4336-b50b-448929fca3aa2014-03-12 12:51:45.965 UTC0f0156cb-7d2b-471f-898b-b3d6db60cf772014-02-26 14:38:55.703 UTC335649dd-e6de-490f-a98e-bc63a6ca9afb2014-02-04 12:15:05.87 UTC075a95eb-ad37-471f-b280-e620c43962e22014-02-04 11:59:29.517 UTCf80ebc32-4011-46dc-8dd3-95c7fdb6e9222014-08-22 13:20:16.613 UTCf5a8ff0c-c4f5-4970-8d99-7ca429a986442014-02-04 11:54:54.991 UTC4787b2e6-f1c0-416f-9050-b5411ff327532014-03-12 13:28:26.262 UTC94528594-e0d3-4353-801d-4d9b710949e42014-08-22 13:27:41.291 UTC494211b4-0729-4c91-be40-36a84febb9e82014-03-05 11:34:37.29 UTC97bec3a5-9498-48a2-80df-7f26757a080a2014-02-04 12:03:55.999 UTCb7298a49-fbca-4315-93cc-e687d82bc4df2014-03-12 12:54:22.752 UTC8d6cd893-d8ee-47e5-bc29-61257e23b3972014-02-26 14:46:39.948 UTC7bc41436-17bb-4d13-bf2d-740d1be7e4932014-03-12 13:23:44.690 UTCd361ad61-f417-4cbe-8a26-4bed21cf70e82014-03-05 11:42:49.164 UTC156f5a83-a102-4035-9adc-357046413ed62014-03-12 12:55:05.679 UTC9ef07849-4a5f-49f3-83ce-21e72da7fe4e2014-03-12 12:46:51.819 UTC2ddd7435-0d22-45da-8a94-0352fce45f502014-02-14 12:34:07.270 UTCd2ed2191-71ff-4a83-bfac-4c1fdcedfb732014-03-12 13:38:05.656 UTC12737b7b-92ef-4360-ba3c-9e0ffe56be8b2014-02-04 12:03:13.195 UTCb6e2e727-ad0d-494b-b1d4-211d9203c8d22014-03-12 12:42:36.889 UTC935d3f0f-6108-4c44-bebf-d191c852c75e2014-03-12 13:07:16.711 UTC41bcb12b-b3a4-43d1-aaa6-4cabc4464efa2014-03-05 11:44:26.760 UTCWorkflow188input11output0PrettyPrintRinput1output00net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivityinput1falseoutput00falselocalhost6311falsefalseinputR_EXPoutputTEXT_FILEnet.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrettyPrintRinputoutput1c210d9a-059f-4c52-8df7-0310db5e211f2013-06-21 14:30:38.141 UTC3da1a855-6b93-4760-9496-19703d7ec3962014-01-22 14:29:59.616 UTCdeb0863c-b567-4755-af9c-b8b74d5e08e52013-06-21 14:31:25.529 UTC