Log_log_plots_of_varstages11[S, J, V, G, D]2014-08-13 10:58:38.493 UTCThe names of the stages or categories of the input matrix. In the following example, the matrix has 5 stages.
The stages of this matrix are called:
1) Seedlings S
2) Juveniles J
3) Vegetative V
4) Reproductive individuals G
5) Dormant plants D2014-08-13 11:00:43.617 UTCyears11[1987, 1988, 1989, 1990, 1991, 1992]2014-08-13 10:59:02.855 UTCEach year represents a matrix and therefore characterizes a period of transition.
In this tutorial, we have 6 matrices (see Input data) that represent 6 years
e.g.: 1987 =data interval between 1987 - 1988 and
1988= data interval between 1988 - 1989 etc.2014-08-14 12:58:31.269 UTCpfister_graph0Graph plotting CV vs. Elasticity in matrix elements, showing the regression line (red line) and the Spearman correlation value (ρ) between these two values.2014-08-14 12:58:38.518 UTCspearman_rank0Spearman correlation results of the CV vs. Elasticity in matrix elements 2014-08-13 12:59:24.274 UTC"Spearman's rank correlation rho"
data: vr1$cv and vr1$elas
S = 1488, p-value = 0.02377
alternative hypothesis: true rho is not equal to 0
sample estimates:
rho
-0.5356037
2014-08-13 12:36:53.4 UTCpfister_plot0Graphs of the calculated values of Sensitivity vs. Variance and CV vs. Elasticity in matrix elements.2014-08-13 12:37:16.812 UTCpfister_plot_table0A table of calculated values of mean, variance, CV, sensitivity and elasticity of the matrix elements.2014-08-13 12:37:34.494 UTC mean var cv sens elas
a11 0,002459698 1,26E-05 144,05386 0,021023792 5,47E-05
a21 0,067350239 6,32E-03 118,07172 0,066912895 4,77E-03
a31 0,173736086 2,66E-02 93,93399 0,088205265 1,62E-02
a22 0,004605797 2,48E-05 108,22858 0,099776711 4,86E-04
a32 0,609529672 3,73E-02 31,68504 0,131526685 8,48E-02
a42 0,012105466 2,09E-04 119,40443 0,919475709 1,18E-02
a52 0,011466467 1,23E-04 96,55131 0,226904442 2,75E-03
a33 0,715390128 1,28E-02 15,84439 0,576723463 4,36E-01
a43 0,025026248 1,17E-03 136,89433 4,031753836 1,07E-01
a53 0,032102959 5,30E-04 71,69679 0,994939665 3,38E-02
a14 2,227331845 9,11E+00 135,51451 0,008903495 2,10E-02
a24 3,154680462 9,60E+00 98,19777 0,028337352 9,45E-02
a34 0,466249338 4,43E-02 45,12835 0,037354589 1,84E-02
a44 0,454649217 5,63E-02 52,20394 0,261138165 1,26E-01
a54 0,0247669 1,32E-03 146,62524 0,064442605 1,69E-03
a35 0,831731875 1,60E-02 15,20576 0,023961774 2,11E-02
a45 0,09676079 7,56E-03 89,85414 0,167511778 1,71E-02
a55 0,071507318 4,15E-03 90,12403 0,041337869 3,13E-03
2014-08-13 12:37:51.667 UTCRequestStageMatricesvalues_L1multiple0field0title0matrices_LL22net.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.InvokeReadStageMatrixmatrix_file0labels_L1matrix_Rn211net.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.Loopnet.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.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.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.InvokeConvert_LRn2_to_RLn2list_of_r_expressions2r_list_of_expressions11net.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.Invokegraph20bmatrices1fec_xy1pfister_plot200spr11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivitymatrices1falsefec_xy1falsepfister_plot200spr11falselocalhost6311falsefalsematricesR_EXPfec_xySTRING_LISTpfister_plot2PNG_FILEsprR_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.Retry1.01002000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemultiplevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivityfalsenet.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.InvokeYearvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-S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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 UTCnet.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.interaction.InteractionActivitystages1text/plainjava.lang.Stringfalsemessage0text/plainjava.lang.Stringfalsetitle0text/plainjava.lang.StringfalsefecundityIndices11//biovel.googlecode.com/svn/tags/mpm-20140626/select_fecundity_matrix.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.Invokegraph20amatrices1pfister_plot00tab11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivitymatrices1falsepfister_plot00tab11falselocalhost6311falsefalsematricesR_EXPpfister_plotPNG_FILEtabR_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.Retry1.01002000net.sf.taverna.t2.coreworkflowmodel-impl1.5-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeOutputFundamentalMatrix_3_2input1output00net.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.Invokemessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect fecundity stage transitions, then click the Confirm button.net.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.InvokeSelect_stagesvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect fecundity transitionsnet.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.InvokeSelect_a_matrixvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect a matrixnet.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.InvokeRequestStageMatricesvalues_LRequestStageMatricesmultipleRequestStageMatricesfieldRequestStageMatricestitleReadStageMatrixmatrix_fileReadStageMatrixlabels_LFlatten_ListinputlistConvert_LRn2_to_RLn2list_of_r_expressionsgraph20bmatricesgraph20bfec_xyOutputFundamentalMatrix_3inputCategoriseStages_InteractionmessageCategoriseStages_InteractiontitleCategoriseStages_Interactionstagesgraph20amatricesOutputFundamentalMatrix_3_2inputpfister_graphspearman_rankpfister_plotpfister_plot_table23ac88cc-a1ca-4307-b37e-81bb4ffb977a2014-08-13 12:35:25.67 UTC2bfb4912-f75b-409a-b8f0-e401d1aa288e2014-06-09 11:30:39.493 UTC026c2803-8198-4b45-ac58-286c58bb73d12014-01-30 15:06:30.379 UTCd9df7dc7-ff05-420d-8552-9d8d93c107852014-01-30 15:15:14.703 UTC6399b2c3-c7d2-467e-a0fe-36b1b480deff2014-01-30 12:31:27.856 UTC6f78ab7c-498a-47df-b4d4-734203b129de2014-01-30 12:44:46.92 UTC217d4dcf-1d99-4b1a-8d24-9c16ae5f69382014-01-30 13:26:10.134 UTC287c70cb-a73c-4762-a645-2f03bba953872014-08-19 08:50:16.336 UTC7a79e657-35a3-42d8-979d-4878384fd1122014-05-01 11:10:26.483 UTCc968ca36-13de-4606-8bcf-455186a2ed622014-01-30 15:16:28.95 UTC67369ce6-3783-41ed-9d1a-09edd0615d982014-03-12 13:56:21.508 UTC514ceb09-013e-444d-8f7a-5e50e7608e432014-06-09 10:48:28.347 UTC0babaaa0-8442-4064-9607-96994e0078932014-01-30 12:41:59.713 UTCaa94cc1e-117a-48f8-a3ee-9c4b3fa8615d2014-03-12 14:24:14.586 UTCfbc4d358-ab9f-4863-9cbd-25a25434ab392014-01-30 12:20:41.104 UTCba7b6ae2-1a23-4049-8ae7-031ea06668b92014-06-09 12:29:07.138 UTC616b6248-a39e-4724-a0d5-186d0e0840122014-08-13 12:36:53.134 UTC156c2607-3107-4265-b7a3-c9bff4be75b52014-06-09 12:15:46.613 UTC498d9ea4-ddd2-4036-845e-d9da698cffd22014-02-19 13:28:23.718 UTC0f434d33-5836-4460-9074-9f0e808f51642014-06-09 12:23:40.12 UTCe0b5af5a-ec95-4cd9-8ed5-fc666c425fc62014-06-09 12:30:55.275 UTC098dbce3-6f92-46cc-a6ff-83502f3065612014-01-30 14:02:39.207 UTC1dd5ce4f-4c1d-45d8-b4e1-81b41659f19e2014-01-30 14:22:33.751 UTCe22c8fc0-897d-4851-821a-b52c19f082282014-01-30 13:04:03.827 UTCe72bc4ea-d7aa-4b82-86bf-b31c783c83242014-01-30 12:19:46.292 UTC37a3d6c0-367e-4df6-bba4-1cfe17034daa2014-07-02 12:33:19.933 UTC9b80b070-a717-4de8-ad28-f6aecba0ed4a2014-01-22 15:36:19.385 UTC785491ad-b0cd-4cc9-949b-d6277ea759272014-01-30 12:14:17.602 UTC480620c4-5a62-4d77-b32e-523bbea340b52014-05-30 08:32:01.943 UTC44642922-7ed1-45e5-9bf4-6d0b087d4ad12014-03-12 14:26:47.907 UTC0ffe2b8c-307c-4604-924a-d9a6d23aba7c2014-03-12 14:09:41.930 UTC59b59c5c-1f95-47d8-89a9-47dc2a92dfa62014-01-30 13:06:46.694 UTC975cd586-3894-44b0-86b3-fbeecd2719622014-01-30 12:28:04.777 UTC19920aef-bdc0-4c4c-916a-3ae020cc77f92014-01-22 15:37:40.706 UTC02f9be04-9ad9-4f7c-a42e-35ee0bc50aff2014-05-21 12:46:15.738 UTCe167e277-3b91-4339-a2a6-66e65a7b385a2014-08-19 08:49:36.438 UTC3660a11a-23e6-4ae8-86c2-45652e978e502014-01-22 15:34:57.108 UTCaa234bcf-72bf-4e4d-a2d1-f3f434e161a12014-08-21 08:52:40.347 UTC5cad32e9-3dff-4f10-becb-2138b5494d9f2014-01-30 14:16:24.425 UTCc5a0629e-47de-4574-84b8-15d21f43edc02014-02-04 11:18:29.32 UTCbcaaa4a0-0663-4d39-b61b-2bae44ce940a2014-02-19 13:32:24.458 UTCc3b208b7-bef2-4582-a3a1-82174e4ba8fb2014-06-09 12:24:22.521 UTCbba5fbd2-997b-4b0d-b8d4-12c530301ff62014-06-09 11:19:11.929 UTC6fc10a03-a298-4faf-8841-00e3d4b26dee2014-01-30 12:43:53.718 UTC1f6d5764-6e50-4994-a068-350a28bfdc322014-08-13 12:37:51.797 UTCThis workflow creates log-log plots of both variance vs. sensitivity and CV vs. elasticity in matrix elements. Plots are based on Figure 2 in Pfister (1998). This workflow calculates as well the summary mean, variance, CV, sensitivities and elasticities of each matrix element of the submitted matrices.
Please if you want to know more about this analyses please refer to: Pfister, C.A. 1998. Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications. Proc. Natl. Acad. Sci. USA, 95: 213–218.
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.
Pfister, C.A. 1998. Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications. Proc. Natl. Acad. Sci. USA, 95: 213–218.
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Stubben, C., B. Milligan, P. Nantel. 2011. Package ‘popbio’. Construction and analysis of matrix population models. 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UTCnet.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.InvokeFlattenListOfStringsToStringstringlistCombineListOfStringsIntoRListstringlistr_list_of_expressionsJonathan Giddy2013-09-04 15:12:34.436 UTCConvert Taverna list of RExpr to R list2013-09-04 15:13:12.850 UTC13112099-3efd-42a7-bf18-a93c89de52dd2013-09-04 15:30:31.850 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.
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