Stages_vectors_plotsstages11The 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 as list.
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
2014-07-02 14:53:12.797 UTC[S, J, V, G, D]2014-01-16 12:10:18.628 UTCsurv_graph_title00Gentiana pneumonanthe survival curves2014-01-24 13:58:36.365 UTCIs the main title to be display in the Survival Rates Graph.
e.g.: Gentiana pneumonanthe survival curves (Gentiana pneumonanthe: species name).2014-07-02 14:53:19.139 UTCyears11Years the data was collected in.
The respective years must be filled one by one. First press add value, fill a year and press enter, then press add value and fill once again the next year, repeat the action until you have fill all the years.
The years can be display as follow:
e.g.
1) 1987
or
2) 1987-19882014-07-02 14:53:47.603 UTC[1987-1988, 1988-1989, 1989-1990, 1990-1991, 1991-1992, 1992-1993]2014-07-22 11:55:41.468 UTCgrowth_graph_title00Is the main title to be display in the Growth rate graph.
e.g.: Gentiana pneumonanthe growth rates (Gentiana pneumonanthe: species name).2014-07-02 14:52:59.386 UTCGentiana pneumonanthe growth rates2014-01-24 13:30:44.101 UTCstage_graph_title00Is the main title to be display in the Stage Vectors Graph.
(Note: will appear as Title - Year)
The year will automatically be incorporate base on the year of the matix.
e.g.: Gentiana pneumonanthe stage vectors - 1987 2014-07-02 14:53:05.766 UTCGentiana pneumonanthe stage vectors2014-01-24 13:37:42.303 UTCiterations00102014-01-22 14:18:41.941 UTCThis value will be use to plot a output graph that shows a simulation of the number of individuals per stage a few years after the study (e.g. 10). This value represents the years of axis X of the output graph: Stage_Vector_Graph.
2014-01-24 13:32:58.360 UTCGrowth_Rates_GraphGrowth Rates Graph:
Plots the population growth rate or lambda values (eigen analyses) of each submitted matrix. 2014-04-02 14:18:38.702 UTCSurvival_Rates_GraphSurvival Rates Graph:
The graph shows the changes of the survival values per stages across the years. 2014-04-02 11:46:34.384 UTCStage_Vectors_GraphStage Vector Graph:
Plots short-term dynamics and convergence to stage distribution. It is a plot that charts the number of individuals per stage vs. years in the short-term (e.g. 5, 10 years).2014-04-02 14:23:34.163 UTCPopulation_Projection$lambda
[1] 1,233262
$stable.stage
S J V G D
0,14257959 0,16213323 0,6585692 0,02289356 0,01382442
$stage.vectors
0 1 2 3 4 5
S 1 7,6666667 6,0132402 6,5785668 7,4579422 8,8300772
J 1 8,35368531 7,0267626 7,5286166 8,5167886 10,0605771
V 1 3,34084844 13,7843123 21,5532895 29,3963464 37,8777932
G 1 0,78433568 0,8580739 0,9727751 1,1517492 1,3911717
D 1 0,07127383 0,3124636 0,4664355 0,6250534 0,7997037
$pop.sizes
[1] 5 20,21681 27,99485 37,09968 47,14788 58,95932
$pop.changes
[1] 4,043362 1,384731 1,325232 1,270843 1,250519 1,24087
2014-04-02 14:16:53.747 UTCEigen Analysis
Calculates the population growth rate and stable stage distribution by repeated projections of the
equation n(t+1)=An(t).
a) Lambda or dominant eigenvalue: This value describes the population growth rate of a stage matrix. The population will be stable, grow or decrease at a rate given by lambda: e.g.: λ = 1 (population is stable), λ > 1 (population is growing) and finally λ < 1 (population is decreasing).
b) The stable stage distribution (w): It is the proportion of the number of individuals per stage. It is given analytically by the right eigenvector (another property of the transition matrix) that corresponds to the dominant eigenvalue
c) Stage.vector: A matrix with the number of projected individuals in each stage class.
d) Pop.sizes: Total number of projected individuals.
e) Pop.changes: Proportional change in population size.
2014-04-02 14:15:09.376 UTCSurvival_Rates_ValuesSurvival Rates Values:
It is a table showing the survival rates values per stage per year, these values are plotted in the Survival Rates Graph.2014-04-02 11:46:42.20 UTC 1987-1988 1988-1989 1989-1990 1990-1991 1991-1992
S 0.52174 0.52174 0.24786 0.058824 0.11111
J 0.91000 0.78212 0.56085 0.409639 0.36364
V 0.92793 0.93798 0.75377 0.724299 0.58424
G 0.90476 1.00000 0.92308 0.923077 0.92308
D 1.00000 1.00000 1.00000 1.000000 1.00000
2014-01-24 14:31:19.957 UTCGrowth_Rates_ValuesGrowth Rates Values:
It is a table showing the population growth rate or lambda values (eigen analyses) of each submitted matrix.
2014-04-02 14:20:53.595 UTC1987-1988 1988-1989 1989-1990 1990-1991 1991-1992
1.23234 1.59471 0.82632 0.74448 0.61868
2014-01-24 14:22:04.975 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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 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14:31:57.752 UTC8853d0a2-2b00-46e4-8276-8b74341029042014-01-08 13:40:53.820 UTC51b62446-ba9d-41d4-8934-a8dc6a12556b2014-01-16 11:55:26.624 UTCe9e65c52-6fd0-474d-b149-a34b7d6af44f2014-01-08 13:22:40.690 UTC3f237f1f-fe25-415e-8d61-55a72dde84482014-01-08 13:35:37.947 UTCfec8e991-b6c5-44b9-af3a-cbda7e7b4b232014-01-08 13:17:12.954 UTC6ba8c161-711a-4eef-81bc-aece93fac8ca2014-01-08 13:39:09.444 UTC85155c5a-3fae-4a06-99cf-50218fb340ab2014-04-02 14:24:56.694 UTC25d3f77f-16fa-4423-8e96-77d18703a84c2014-01-16 13:13:56.771 UTCc6d4cb8f-868e-47cb-ae5f-dd3c5479d7062014-01-16 13:24:03.494 UTCa35c5588-4cc4-44ab-b086-738aa63910112014-07-22 11:59:49.7 UTC4c491160-b4a6-4b52-8b5a-87690d72f7482014-01-22 13:43:59.245 UTC3c3bdfc2-7d6d-4624-9b11-70505faaf1ca2014-01-16 13:11:34.587 UTC5ea8ec94-04b7-4c7f-ace1-914c20ca45262014-01-16 12:58:01.982 UTCf17cd15f-b496-4854-a684-23dac5f3d4882014-01-16 11:54:02.819 UTC5f4343fe-e0c3-4424-ab52-660654936f6f2014-01-24 14:20:43.461 UTC1045b34c-a81f-4d94-bcae-0c6e474b05772014-07-22 11:50:30.327 UTC5caa950c-f1e1-46d2-b5e0-7b20296773452014-01-22 13:28:34.425 UTC3b2e27e7-abd7-4777-ad57-e056d8bce8372014-01-22 13:04:54.282 UTC33dcd649-1237-421d-be06-42d08c6a2a2d2014-01-08 13:48:36.876 UTC1590bc55-96a0-4c4d-a5e1-b28051bbdbd22014-01-16 11:58:41.136 UTC2b9be697-57a1-42db-9994-c9ef8ccc307c2014-01-23 14:42:55.646 UTC0dde5479-1912-49a7-aec4-bade00a9c8442014-01-22 13:59:50.433 UTCStages vectors plots, Survival and Growth rate curves2014-01-24 14:57:58.220 UTC83ac6ad8-2a35-4795-855b-0e3373b018142014-01-16 12:56:20.54 UTC4a54da54-1145-4cd7-95c7-936037e98f3c2014-01-16 13:02:22.27 UTC6d260a63-d7df-4911-855e-449cb6ce31fb2014-01-16 11:51:15.337 UTCe569126d-1a19-4124-a31b-ddd2a58153502014-01-24 14:03:08.668 UTC01a4cbaf-0319-400f-aa39-709396922a3c2014-01-23 14:09:34.383 UTC9b410a14-62b0-401a-af7f-ab5cb42e6acf2014-01-16 12:45:14.217 UTC8a0a6c57-b557-4906-9e13-4c64635d05822014-01-16 12:00:50.557 UTC66a6f93f-2e52-46ea-b45b-f8675a1c82332014-01-22 14:05:42.52 UTC800dec9a-d6d6-4614-8473-00391fe7be022014-01-08 01:53:50.78 UTC2df37c4a-2131-465e-a2af-446bd51458a52014-01-24 10:08:53.943 UTC04501273-3028-45f6-88d0-cd56a7e7d69b2014-01-23 15:24:46.486 UTCMaria Paula Balcazar-Vargas, Mikolaj Krzyzanowski, Jonathan Giddy, Gerard Oostermijer.2014-01-24 15:50:45.836 UTCd567dc57-4a87-4711-9d16-08333070bde62014-04-02 14:16:53.940 UTC58da4d94-8c36-441c-bce2-7f3eee3cc3302014-01-16 12:47:23.97 UTC6adbf0a7-1303-46fe-8afd-6019116dfea52014-01-24 14:32:30.550 UTC53092889-739b-481b-b740-dbab3bd1bb572014-01-16 12:52:36.645 UTCe1deed45-2357-47e6-bfe9-83079e0a57792014-01-08 14:02:26.396 UTC6691ecd3-0979-4902-9dd3-5f399fb8dc702014-01-08 01:48:10.531 UTC5b717f5a-2671-40b5-8100-b80a52804e482014-07-02 14:53:49.973 UTCf19da1c8-a5b3-430f-bc66-2513d2be4a932014-01-22 13:27:17.352 UTC7113a059-2edb-45c5-9e56-839864098bb82014-01-22 13:25:39.859 UTC17d13d72-7e8f-4bc3-89e7-b64939515b502014-01-24 13:55:14.445 UTCf250e52e-8361-48c8-95d4-3b1b599d1bb82014-05-21 11:15:53.485 UTCe5a58b4e-4fdb-4407-ae95-8d6db054d5192014-01-16 12:19:38.627 UTC00a687d1-ea72-40c8-bdef-5dcb1fc9c7462014-01-24 13:19:24.523 UTC175baf82-c01b-417b-9fac-798fb19789762014-01-08 01:52:42.927 UTC9e9a631c-3785-456b-909c-fb39558889992014-01-08 01:44:47.624 UTC432a2951-4f5a-47f7-b540-26620a4bc5822014-01-16 13:25:24.403 UTC28e83f49-7e33-4fcc-9816-a85824199c182014-01-24 13:58:36.514 UTC82b368d4-c996-41c1-a526-8f4c5138a27e2014-01-24 15:50:47.109 UTC48740cd7-2b4a-4963-bc0e-4e58c2306d822014-01-08 13:09:34.496 UTC413d3699-1aa4-4a8b-a335-c4c347e8f1382014-01-16 12:18:00.419 UTC1a7d1842-d979-424f-be21-c7e33200c3152014-01-08 13:26:07.123 UTC513bef37-bb5a-4448-b5b0-0723520e6fc02014-01-16 13:05:25.49 UTC77329c73-24a1-4e49-83e7-1c53d73a6c9b2014-05-21 11:14:38.966 UTC01573bd6-0712-4fe4-9719-7c88225ce8192014-01-22 12:35:56.271 UTCad4ddea0-c53c-41ec-9a40-c06e5a8526a12014-01-22 13:40:49.417 UTC71cb5b4e-06c5-448d-95ce-c86cbb44e7472014-01-22 13:02:02.125 UTC8c8fb537-bd6a-482e-a032-2317ebc281ea2014-01-22 13:23:15.914 UTCfb546a59-21ce-4728-ad96-860556e683c82014-01-24 14:02:12.462 UTCThe Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:
- Survival values calculations per stage per year and its respective plot;
- Growth rates (lambda) calculations per year and its respective plot;
- Stage Vectors calculations and their respective plots.
======================================================
This workflow requires an instance of Rserve on localhost
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 uses the R pack ‘popbio’ (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011).
References:
Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.
Jongejans E. & H. de Kroon. 2012. Matrix models. Chapter in Encyclopaedia of Theoretical Ecology (eds. Hastings A & Gross L) University of California, p415-423
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 2.3.1
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UTCWorkflow3values_L11multiple00field00title00matrices_LLSelectMatricesInteractionvalues1multiple0field0title0message0matrices22net.sf.taverna.t2.activitiesinteraction-activity1.0.4net.sf.taverna.t2.activities.interaction.InteractionActivityfield0text/plainjava.lang.Stringfalsevalues1text/plainjava.lang.Stringfalsemultiple0text/plainjava.lang.Stringfalsetitle0text/plainjava.lang.Stringfalsemessage0text/plainjava.lang.Stringfalsematrices22http://biovel.googlecode.com/svn/tags/mpm-20140521/select_matrices.htmlLocallyPresentedHtmlfalsenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect a matrix for each year, then click the Confirm button.net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSelectMatricesInteractionvaluesSelectMatricesInteractionmultipleSelectMatricesInteractionfieldSelectMatricesInteractiontitleSelectMatricesInteractionmessagematrices_LLe04e4d3f-c7c9-438c-bc0c-c9740084e9022013-11-13 13:50:47.718 UTCb5e0ea8e-2e1a-409c-aec7-3f4c72ed167a2013-11-13 15:32:49.843 UTC0d79c056-ce74-4602-9cbd-60c90307105f2014-05-01 10:33:23.704 UTC5f4b1899-ccf2-474b-b4fb-01a59e02f2642013-11-13 15:42:43.559 UTC9973b049-ee79-4fd7-8a87-8cf191d9509f2013-10-28 15:04:57.615 UTC3cd4cf73-e925-449c-895d-318bf4964ede2014-05-01 10:43:19.183 UTC379602b6-1644-4b9f-a5bb-8161e03da77d2013-10-28 16:47:25.115 UTC4dbc4a0b-5962-4f21-96d2-0fb20185b17a2014-01-16 11:25:38.561 UTC08912d22-d766-4700-9394-77b1ef8e3a092013-10-28 16:49:51.515 UTC843dddc5-5f13-47f3-986b-aadbb69b939e2014-05-21 11:15:50.752 UTC48a16a67-9f67-4ab2-9f60-29e4500869122014-07-22 11:50:04.801 UTC3682addc-6be9-4f7c-a61c-756ce05a2fdf2013-11-13 15:33:56.716 UTC249fb6a7-886e-4835-8b18-8bc293a6d77e2013-10-28 16:45:55.371 UTC4a0bbebd-3357-48c7-ad1e-b5bcb7b6ec5c2013-11-13 13:50:35.668 UTCConvert_Taverna_listlist_of_r_expressions22r_list_of_expressionsFlattenListOfStringsToStringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueconcatenated00workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergeUserNameHere2013-10-14 14:22:51.151 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCombineListOfStringsIntoRListstringlist1output11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueoutput11workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergeUserNameHere2013-10-14 14:21:14.818 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlattenListOfStringsToStringstringlistCombineListOfStringsIntoRListstringlistr_list_of_expressionsJonathan Giddy2013-09-04 15:12:34.436 UTC472c6bef-15bc-4782-ab72-9e041b46e9d02013-10-14 14:28:56.870 UTC13112099-3efd-42a7-bf18-a93c89de52dd2013-09-04 15:30:31.850 UTC1ff54110-840d-474e-95a4-877c8f2c5b5e2013-09-04 15:26:02.821 UTCThis workflow accepts a Taverna list of arbitrary R expressions and returns a single R expression representing an R list containing the original expressions.
This workflow relies on the current Taverna behaviour of an R expression being represented by a list of strings containing the deparsed expression. If this changes, this workflow will likely break.
The first BeanShell converts each R expression (actually a list of strings) to a single string. This uses implicit iteration to do this for each R expression, so input port depth is 2 but the BeanShell input depth is 1.
The second Beanshell creates a comma-separated list of the deparsed R expressions and wraps the string with the R list() function. So now we have a single string s that can be turned into an R list using eval(parse(text=s)).
But RShell already does that parsing for us, so we just need to ensure the string looks like an R expression by turning it into a list of strings. So we actually output a 1-element list containing the string.
2013-10-14 14:28:55.280 UTCConvert Taverna list of RExpr to R list2013-09-04 15:13:12.850 UTCReadStageMatrixlabels_L11matrix_file00matrix_Rn2Matrix_ReadFromFilematrix_file0labels1read_matrix11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivitymatrix_file0falselabels1falseread_matrix11falselocalhost6311falsefalsematrix_fileTEXT_FILElabelsSTRING_LISTread_matrixR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMatrix_ReadFromFilematrix_fileMatrix_ReadFromFilelabelsmatrix_Rn219c3521a-2d42-4f77-8dd2-10ab64286ef22013-10-15 13:59:10.98 UTCc8cf946f-3771-4321-870a-26408be164c72013-10-14 15:33:20.159 UTCa6ec62ed-cbc2-4705-812f-9fb8b80101692013-10-14 14:12:24.533 UTCReadStageMatrix2013-10-14 14:13:34.18 UTC6b5b9009-65c6-45a2-941f-188268b27c592013-10-14 14:13:35.986 UTC