Workflow13stage_matrix11text/rdf+n3<>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#carriesInputType>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#StageMatrix> .
2013-03-14 13:20:11.793 UTCcolumns_fecundity11text/rdf+n3<>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#carriesInputType>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#FecundityColumns> .
2013-03-14 13:20:03.572 UTCrows_fecundity11text/rdf+n3<>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#carriesInputType>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#FecundityRows> .
2013-03-14 13:20:08.652 UTCresulttext/rdf+n3<>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#carriesResultType>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#FundamentalMatrix> .
2013-03-14 13:20:26.650 UTCDisplayFundamentalMatrixinput1output00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityinput1falseoutput00falsespringer.grid.cf.ac.uk6311falsefalseinputR_EXPoutputTEXT_FILEnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFundamental_matrixstage_matrix1columns_fecundity1rows_fecundity1fundamental_matrix11Age specific survival or fundamental analysis.
This workflow gives the basic information on age-specific survival, this includes the fundamental matrix (N): is the mean of the time spent in each stage class, the Variance (var): is the variance in the amount of time spent in each stage class, the Coefficient of variation (cv): is the coefficient of variation of the time spent in each class (sd/mean- the ratio of the standard deviation to the mean), Meaneta: is the mean of time to death, of life expectancy of each stage and Vareta: is the variance of time to death. (see outputs: Age specific survival).2012-11-01 10:11:32.593 UTCnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshellnet.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflownet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDisplayFundamentalMatrixinputFundamental_matrixstage_matrixFundamental_matrixcolumns_fecundityFundamental_matrixrows_fecundityresulttext/rdf+n3<>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#performsTask>
<http://www.semanticweb.org/ontologies/2012/11/popmod.owl#FundamentalMatrixCalculation> .
2013-03-14 13:19:57.223 UTC625fbbc6-032a-431f-b1e5-9e3c0882e7532013-03-14 13:20:49.391 UTC804c1e9c-8059-49eb-88cf-f5a62213d9d42013-03-14 13:19:21.374 UTCe09fd098-df50-4fa5-82f3-e5fdfd0869552013-03-14 16:46:08.870 UTCFundamental_matrixstage_matrix110.0000 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
2012-10-03 14:34:31.812 UTCThe stage matrix file input port:
Here comes the stage matrix without the stage names (as you see in the example). It should be provied as a txt-file.
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): 153-166.2012-10-10 12:44:04.359 UTCrows_fecundity111
22012-10-10 12:36:41.765 UTCTo perform the fundamental matrix analysis N, 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 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 12:34:12.781 UTCcolumns_fecundity1142012-10-10 12:36:25.328 UTCTo perform the fundamental matrix analysis N, 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
2012-10-10 12:38:41.968 UTCfundamental_matrix$N
S J V G D
S 1.00000000 0.0000000 0.0000000 0.0000000 0.0000000
J 0.05848485 1.0101010 0.0000000 0.0000000 0.0000000
V 6.88603853 11.9918695 13.3528343 10.0128734 12.9527790
G 0.20805087 0.4661775 0.3904662 2.9174703 0.6909984
D 0.12868882 0.2520032 0.2460596 0.1845124 1.2624386
$var
S J V G D
S 0.00000000 0.00000000 0.0000000 0.0000000 0.0000000
J 0.05624588 0.01020304 0.0000000 0.0000000 0.0000000
V 129.59269836 164.45409019 164.9453506 157.1299726 165.1853617
G 0.96262845 2.03661916 1.7354172 5.5941629 2.8634574
D 0.17967383 0.32076827 0.3146653 0.2473139 0.3313126
$cv
S J V G D
S 0.000000 NaN NaN NaN NaN
J 4.055104 0.100000 NaN NaN NaN
V 1.653183 1.069388 0.9618261 1.2519033 0.9922539
G 4.715848 3.061284 3.3737933 0.8107017 2.4488847
D 3.293833 2.247448 2.2797338 2.6952479 0.4559411
$meaneta
S J V G D
8.281263 13.720151 13.989360 13.114856 14.906216
$vareta
S J V G D
143.2630 181.0125 181.4811 177.0582 181.0617
2012-10-10 12:56:28.203 UTCThe fundamental matrix workflow gives the basic information on age-specific survival, this includes the mean, variance and coefficient of variation (cv) of the time spent in each stage class and the mean and variance of the time to death.
Fundamental matrix (N): is the mean of the time spent in each stage class
E.g.:For our Gentiana example means a J plants will spends, on average, about 1 year as a Juvenile, 11 as vegetative plant, less than a year a reproductive and dormant plant.
Variance (var): is the variance in the amount of time spent in each stage class.
Coefficient of variation (cv): is the coefficient of variation of the time spent in each class (sd/mean- the ratio of the standart deviation to the mean).
Meaneta: is the mean of time to death, of life expectancy of each stage.
E.g.:The mean age at death is the life expectancy; the life expectancty of a new individual seedling is 8 years.
Vareta: is the variance of time to death
For further information please see
Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.
2012-10-10 12:59:24.859 UTCfundamental_matrixcolumns1rows1stage_matrix1a11net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivitystage_matrix1falserows1falsecolumns1falsea11falsespringer.grid.cf.ac.uk6311falsefalsestage_matrixR_EXProwsDOUBLE_LISTcolumnsDOUBLE_LISTaR_EXPnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefundamental_matrixcolumnsfundamental_matrixrowsfundamental_matrixstage_matrixfundamental_matrix5d52fc73-4937-4ab4-a7fb-ff38d0384a112012-10-30 07:01:53.978 UTC3da39227-d90d-44b6-93e6-a5c6c6635c282012-03-30 15:42:09.674 UTC068f4c47-ac93-41d1-928b-e5313ddf7dc92012-03-30 15:27:01.885 UTC252c40b1-ea29-47e7-bf0f-3af7aab03d0c2012-10-10 12:47:26.968 UTC7bb65b13-5427-4b64-bf88-b97ba2bd87c82012-10-11 11:57:47.796 UTC1d18264c-9c31-446e-b5fe-faf419d8697b2012-10-03 14:35:35.765 UTC5ddec6d6-2ef8-4a1b-8905-4ebc313e8a5f2012-03-30 15:53:45.576 UTC514adf8d-61fa-467f-9395-f5979832478d2012-10-10 12:42:45.593 UTCMaria Paula Balcázar-Vargas, Jonathan Giddy and Gerard Oostermeijer2012-10-10 12:20:09.765 UTCThe fundamental matrix workflow gives the basic information on age-specific survival, this includes the mean, variance and coefficient of variation (cv) of the time spent in each stage class and the mean and variance of the time to death.
Fundamental matrix (N): is the mean of the time spent in each stage class
Variance (var): is the variance in the amount of time spent in each stage class.
Coefficient of variation (cv): is the coefficient of variation of the time spent in each class (sd/mean- the ratio of the standart deviation to the mean)
Meaneta: is the mean of time to death, of life expectancy of each stage.
Vareta: is the variance of time to death
For more information see:
Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts (pag 118-120)2012-10-10 12:35:37.812 UTC482df01a-aece-421a-87e6-87c6fed3098c2012-04-27 06:16:05.128 UTC64fd75c1-1560-485f-9e95-f556f284ea0a2012-10-03 14:35:02.156 UTC028669ad-d798-4123-bf4a-b99951b64e182012-10-11 11:46:36.203 UTC573c3e8c-5192-4dcd-a1b1-4c69d93185d82012-10-03 13:17:26.78 UTCdb524ca2-dc25-4036-b866-fb6f2449f18b2012-09-28 15:07:54.812 UTCae90fa83-15d4-42a1-b5fc-75f5b05405552012-09-26 14:28:58.906 UTCFundamental matrix2012-09-26 14:05:47.140 UTC5ad8da23-95d6-4f62-b1fc-82689c17ffd72012-03-30 15:52:40.327 UTC88ba65a7-98b4-4f47-89d6-836e7c1fa9c12012-09-26 14:26:56.765 UTC8237763e-e3d3-4a89-8154-c0e7ebe6ac992012-03-30 15:58:10.751 UTCe4416b66-0517-4982-9ffc-07d9225b4cb42012-04-27 10:20:27.369 UTC85e5205a-e20f-42a5-85b6-857a1bcf67512012-04-27 10:04:31.201 UTC29186c39-3022-4d52-90d0-8f7fd7bcef272012-03-30 15:47:32.455 UTC553eb85d-393a-488a-84ae-6190b23e80cc2012-03-30 15:56:49.708 UTC67f6d5fc-c41e-4a15-aa70-06a91d869ca32012-09-26 14:09:13.187 UTC09f91d33-9f50-4983-96c9-1335ed1f92b42012-04-27 06:19:38.161 UTC03f85255-cd88-4d89-b6b6-40c5c6eae7f52012-10-10 12:59:26.406 UTCfae44800-e1c6-41e0-9784-aa2a44d757512012-09-28 12:28:31.62 UTC5af80ab8-1db1-4552-a538-92256862e14e2012-09-26 14:20:30.218 UTC73569abf-949f-48f6-92cf-9d91b9b9fc5b2012-10-10 12:59:04.609 UTCe1d1c2a5-29c1-4939-b4b2-0980a2dceaea2012-10-10 12:30:26.453 UTC26a58a12-7058-4ecc-8626-8f4208df050d2012-04-27 06:37:14.879 UTC348192ff-7a44-4a75-a3b4-af3adf25ea2b2012-04-27 06:08:00.914 UTC4953ee13-f5cd-4472-9bc9-19401eef9af42012-10-11 12:39:20.734 UTC554ae0b3-6ab6-4242-9607-94afd162770d2012-10-03 13:28:40.515 UTC6a5c611c-cfcf-4964-9c89-f254b5521e152012-04-26 16:16:27.814 UTC044bc39f-c00c-4683-aec3-9b467473c8942012-10-10 12:44:06.562 UTC02ba332a-4054-4142-88ef-9d17ab76aa382012-10-10 12:43:36.218 UTC808d955e-b242-463f-9ab0-3e5526d243912012-10-30 07:03:42.367 UTC1e66a160-d9a3-485d-b31e-cac2c674a2962012-03-30 15:59:19.350 UTCf4dfa9b1-5f6a-46a6-a7ab-5a660a1735eb2012-04-27 06:33:44.26 UTCe4172fb8-fbf4-4a13-aad8-b4ea9a55fcaa2012-09-28 15:08:43.718 UTC