Life_Table_Response_years11Years: All years which start a period of transition. This should indicate two consecutive study periods. In the following example, we have six years (e.g.: 1988 =data interval between 1988 and 1989 and 1989= data interval between 1989 and 1990).2014-04-17 09:47:02.55 UTC[1987, 1988, 1989, 1990, 1991, 1992]2014-04-02 11:50:44.473 UTCstages11[S, J, V, G, D]2014-04-02 11:50:23.417 UTCStages: the names of the stages or categories of the input matrix. In the following example, the matrix has 5 stages or categories. The respective name stages must be filled one by one. First click Add Value, enter a stage name (not longer than 8 characters) and press Enter; then click Add Value and enter the next stage name, repeat the action until you have entered all the stage names.
In the following example, the matrix has 5 stages or categories:
The stages of this matrix are called:
1) Seedlings S
2) Juveniles J
3) Vegetative V
4) Reproductive individuals G
5) Dormant plants D2014-04-17 09:46:02.872 UTCPooled_matrix_file00Pooled_matrix_file: Weighted main Matrix in a .txt file format what popbio (R package) calls pooled matrix (to see more details: Horvitz, Schemske and Caswell 1997; Horvitz, and Schemske 1995). Click in Set file location, a window dialog appears and the user selects the file (e.g. MT_pooled data.txt) and then clicks the Open button. Then the link to the file will appear on the Taverna window. 2014-04-17 09:45:33.331 UTC0.0074 0 0 6.0510 0
0.1953 0.0092 0 5.9154 0
0.3167 0.6710 0.6999 0.4621 0.7636
0 0.0258 0.0663 0.4818 0.1287
0 0.0214 0.0473 0.0561 0.10772014-03-28 13:35:49.687 UTCplot_title00Plot_Title: Descriptive main title for labelling generated outputs (graphs). Click Add Value, enter a title and press Enter.2014-04-17 09:45:05.223 UTCLTRE, Gentiana pneumonanthe2014-03-28 13:45:47.950 UTCLTRE_Analysis0$`1987`
S J V G D
S -0,000427437 0 0 0,017977128 0
J -0,018948429 0,000125413 0 0,063000672 0
V 0,02217648 0,027240295 0,08050301 -0,005123488 0,001407312
G 0 0,02999793 -0,28293633 0,04915813 -0,002225181
D 0 0,002716886 -0,02162583 -0,003004855 -0,002262304
$`1988`
S J V G D
S -6,95E-05 0 0 -0,015389513 0
J 4,96E-03 -0,000558645 0 0,01926612 0
V -7,30E-03 0,020735759 0,04387892 -0,019217928 -0,001781114
G 0,00E+00 -0,017338168 0,09869957 0,16998346 0,011994002
D 0,00E+00 -0,006333278 -0,01669189 -0,004617703 0,000357214
$`1989`
S J V G D
S 4,81E-05 0,00E+00 0 -0,079033122 0
J -1,37E-02 -1,11E-03 0 -0,137816922 0
V -1,63E-02 -2,39E-02 -0,004376839 0,002379802 -0,001615473
G 0,00E+00 -1,11E-02 -0,190435466 -0,039096363 0,003208923
D 0,00E+00 -6,95E-05 0,004850583 0,000120345 0,002089625
$`1990`
S J V G D
S -0,000269809 0 0 -0,063011581 0
J -0,013011246 0,000303558 0 -0,160845614 0
V -0,046430953 -0,046785723 -0,006004358 0,008516046 0,002694165
G 0 -0,024276849 -0,169262225 -0,054201685 -0,020216428
D 0 -0,002132282 -0,020610214 -0,003466185 0,001150681
$`1991`
S J V G D
S -0,000324936 0 0 -0,082567502 0
J -0,019091282 -0,001030737 0 -0,168009967 0
V -0,030504132 -0,052268343 -0,07184465 0,007067617 0,003212066
G 0 -0,028415235 -0,16602744 -0,05199214 -0,007222026
D 0 -0,006109288 -0,03369773 -0,004342381 -0,003520319
$`1992`
S J V G D
S -0,000189651 0 0 -0,051219954 0
J -0,017605964 -0,001154529 0 -0,119286554 0
V -0,033613991 0,019059924 -0,03514813 0,006108974 0,008998567
G 0 -0,028684697 -0,2645677 -0,055151583 -0,03686409
D 0 -0,004550707 0,01982567 0,001756256 -0,005900316
2014-03-28 13:55:01.421 UTCLTRE_Analysis:
Intermediary results showing the matrices calculated on the LTRE analysis per year. After this step the workflow sums up all the values per matrix giving us the final result: LTRE_ Results.2014-04-02 11:30:16.422 UTCLTRE_Results0LTRE_ Results:
The results of the LTRE per year. These are the generated values of the plotted LTRE graph.2014-04-02 11:30:36.167 UTC1987 1988 1989 1990 1991 1992
-0.0422506 0.2805752 -0.5058927 -0.6178607 -0.7166884 -0.59818852014-03-28 13:59:24.93 UTCLTRE_Graph0LTRE_Graph:
Creates a histogram to display the LTRE_Results. The year effect is shown in the Figure. In this example: The year 1988 had the largest positive effect on lambda, and the other years had a negative effect. 2014-04-02 11:30:23.231 UTCReadStageMatrixmatrix_file0xlabels1ylabels1matrix11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivityxlabels1falseylabels1falsematrix_file0falsematrix11falselocalhost6311falsefalsexlabelsSTRING_LISTylabelsSTRING_LISTmatrix_fileTEXT_FILEmatrixR_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.InvokeReadPooledMatrixmatrix_file0xlabels1ylabels1matrix11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivityxlabels1falseylabels1falsematrix_file0falsematrix11falselocalhost6311falsefalsexlabelsSTRING_LISTylabelsSTRING_LISTmatrix_fileTEXT_FILEmatrixR_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.InvokeAddNameslabels1expr1expr11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivityexpr1falselabels1falseexpr11falselocalhost6311falsefalseexprR_EXPlabelsSTRING_LISTexprR_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.InvokeCalculateYearEffectmatrices1pooled_matrix1xlabel0xticks1ylabel0plot_colour0plot_title0LTRE_Analysis11LTRE_Results_RLn11graph00net.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.InvokeListRtoRListlist_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.Invokexlabelvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivityYearsnet.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.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the user the introduction of stage matrices 2014-08-13 09:40:21.490 UTCnet.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_fileReadStageMatrixxlabelsReadStageMatrixylabelsReadPooledMatrixmatrix_fileReadPooledMatrixxlabelsReadPooledMatrixylabelsAddNameslabelsAddNamesexprCalculateYearEffectmatricesCalculateYearEffectpooled_matrixCalculateYearEffectxlabelCalculateYearEffectxticksCalculateYearEffectylabelCalculateYearEffectplot_colourCalculateYearEffectplot_titleListRtoRListlist_of_r_expressionsPrintAnalysisrexprPrintResultsrexprRequestStageMatricesvaluesLTRE_AnalysisLTRE_ResultsLTRE_Graph95c803bc-8325-408a-bd8c-10d5f6ada6a22014-04-02 11:50:44.640 UTC18c4eeb8-867b-4c95-88ea-e05b8595cc002014-01-09 10:38:48.222 UTCThe Life Table Response Experiments Effect of Years in One Place workflow provides an environment to analyse two or more matrices from different years in one location. The objective of this workflow is to determine the effects of the research years (2 or more) in one place on λ. This workflow performs a fixed LTRE, one way design (Caswell 2001).
LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on λ under two or more sets of environmental conditions (in this case 2 or more years in one location) (Horvitz, Schemske and Caswell 1997). The goal of the analysis is to quantify the contribution of each of the vital rates to the variability in λ. (Caswell 1989, 1996, 2001 in Horvitz, Schemske and Caswell 1997).
Fixed Treatments: Decomposing Years Treatment Effects in one location or place
A fixed-effect analysis treats the matrices as representative of particular conditions, either experimental or natural (high vs. low nutrients in a one-way model, for example, or year and spatial location in a two-way model). The goal is to determine how much a treatment level (in this case year) on λ is contributed by each of the vital rates. The analysis uses a linear approximation in which the sensitivities appear as slopes. The effect of a treatment on λ depends on its effect on each matrix entry and on the sensitivity of λ to that entry. (Horvitz, Schemske and Caswell 1997).
For more details of the analysis see: Retrospective Analyses: Fixed Treatments (page 262 in Horvitz, Schemske and Caswell 1997) and Chapter 10 Life Table Response Experiments (page 258 in Caswell 2001).
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. 1989. The analysis of life table response experiments. I. Decomposition of treatment effects on population growth rate. Ecological Modelling 46: 221-237.
Caswell, H. 1996. Demography meets ecotoxicology: Untangling the population level effects of toxic substances. Pp. 255-292 in M. C. Newman and C. H. Jagoe, eds., Ecotoxicology: A Hierarchical Treatment. Lewis, Boca Raton, Fla.
Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.
Horvitz, C.C. and D.W. Schemske. 1995. Spatiotemporal Variation in Demographic Transitions of a Tropical Understory Herb: Projection Matrix Analysis. Ecological Monographs, 65:155-192
Horvitz, C., D.W. Schemske, and Hal Caswell. 1997. The relative "importance" of life-history stages to population growth: Prospective and retrospective analyses. In S. Tuljapurkar and H. Caswell. Structured population models in terrestrial and freshwater systems. Chapman and Hall, New York.
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
2014-04-17 09:44:37.246 UTCMaria Paula Balcázar-Vargas, Jonathan Giddy, Francisco Quevedo and Gerard Oostermeijer2014-08-13 15:06:53.953 UTCcf5d4da2-05ba-4d0a-9be6-6394a5b3479f2014-03-28 14:59:48.772 UTC912c941a-280a-462e-b2d7-5d677e5470ea2014-03-28 13:24:34.661 UTC42b0b3cc-f24a-45f0-9c70-7ee6b642c6db2014-03-28 13:48:51.759 UTCbb2abaa0-6770-4154-8fe7-f73253f9cf492014-04-17 09:47:04.603 UTC0f74d343-dea2-4b8e-ba47-78035b22525d2014-08-13 15:06:55.504 UTC37d391e2-3f0f-4582-8865-3e60c8539c1c2014-01-09 10:37:15.381 UTC95a33542-c8d6-498d-b246-8e85697055e12014-08-13 10:30:26.487 UTC19d711bf-10e6-4cc3-aff6-949fe866e46e2014-04-02 11:30:37.237 UTC2de008d8-f612-4e55-9aae-bcbe99767a582014-08-11 10:55:37.675 UTCea1a70de-8996-4713-99ba-222ae76a32f82014-01-09 10:34:46.590 UTCe5145e38-9a49-42ed-a93d-4059e934f2102014-01-09 10:38:14.641 UTC04551d66-4d11-4071-8f90-3dc44ff4c27c2014-01-09 10:39:28.414 UTCf6f707d4-2315-4b39-84c8-8e06eb7320092014-08-13 09:46:47.128 UTCLife Table Response Experiment Year Effect in One Location or Place2014-04-02 11:23:31.382 UTCa185a5b8-f620-4553-8da5-79c80b888aa92014-04-17 09:44:39.189 UTCd6c4e74a-c2b5-4328-b178-669b1508bbef2014-03-28 13:59:24.276 UTC3b27b1f8-f1d7-47be-94d4-d0646e9d24e92014-03-28 14:55:32.14 UTC4c2bae6b-69c6-4e9f-9f8e-431051560b0f2014-03-28 13:45:45.608 UTC66c08fd8-d1cf-4b84-8a1c-c2b99d8f3b382014-04-17 09:44:06.366 UTC69113e1e-6ee6-45eb-94cf-f44aec06abef2014-03-28 13:46:49.704 UTCea8ef35f-341c-4bd7-858d-594854efdb062014-03-28 13:35:49.846 UTC3c786ca1-5d23-4907-9a83-43c9622ba3062014-08-13 10:06:24.805 UTC89b9d79d-225c-4e44-b652-ce0efedf0aa02014-04-02 11:30:35.317 UTC067e249a-3afe-4cb1-8787-1b5d5d440ecc2014-04-17 09:45:59.652 UTC63c96824-2e52-4c18-8e7e-55edcaa26b472014-08-11 10:51:13.778 UTCe4d115e7-82d2-42db-b46f-c8b38e989e7f2014-03-28 13:55:16.499 UTCd88716c4-8891-4e0a-964e-d43a400be9fc2014-03-28 13:50:11.912 UTCfb0ff3e3-4525-4bcf-9a5a-ce62c620f9112014-03-28 13:57:13.223 UTCLife_Table_Response_matrices11pooled_matrix11xticks11xlabel00plot_colour00plot_title00ylabel00LTRE_Analysis1graph0LTRE_Results1LTRE_Results_RLn1LTREmatrices1pooled_matrix1LTRE_Analysis11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivitymatrices1falsepooled_matrix1falseLTRE_Analysis11falselocalhost6311falsefalsematricesR_EXPpooled_matrixR_EXPLTRE_AnalysisR_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.InvokePlotLTRELTRE_Analysis1xticks1xlabel0plot_colour0plot_title0ylabel0graph00LTRE_Results11LTRE_Results_RLn11net.sf.taverna.t2.activitiesrshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.rshell.RshellActivityplot_colour0falseLTRE_Analysis1falsexticks1falsexlabel0falseylabel0falseplot_title0falseLTRE_Results11LTRE_Results_RLn11graph00falselocalhost6311falsefalseplot_colourSTRINGLTRE_AnalysisR_EXPxticksSTRING_LISTxlabelSTRINGylabelSTRINGplot_titleSTRINGLTRE_ResultsDOUBLE_LISTLTRE_Results_RLnR_EXPgraphPNG_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.InvokeLTREmatricesLTREpooled_matrixPlotLTRELTRE_AnalysisPlotLTRExticksPlotLTRExlabelPlotLTREplot_colourPlotLTREplot_titlePlotLTREylabelLTRE_AnalysisgraphLTRE_ResultsLTRE_Results_RLn627ddba7-2980-423b-b333-6988e033c3102014-01-09 10:34:46.784 UTCLife Table Response Experiment2013-11-27 14:27:50.10 UTCRequestStageMatricesvalues11matrices1RequestStageMatricestitle0field0values1message0minMatricesPerField0multiple0forceEqualNumberMatricesPerField0matrices22net.sf.taverna.t2.activitiesinteraction-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.interaction.InteractionActivityfield0text/plainjava.lang.Stringfalsetitle0text/plainjava.lang.Stringfalsevalues1text/plainjava.lang.Stringfalsemultiple0text/plainjava.lang.Stringfalsemessage0text/plainjava.lang.StringfalseminMatricesPerField0text/plainjava.lang.StringfalseforceEqualNumberMatricesPerField0text/plainjava.lang.Stringfalsematrices22http://biovel.googlecode.com/svn/tags/mpm-20140811/select_matrices.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.Invokefieldvalue00Name of the field to introduce the stage matrices2014-08-13 09:46:27.925 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivityYearnet.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.InvokeforceEqualNumberMatricesPerFieldvalue00Boolean to force or not that the user introduces the same number of matrices in each field.
Possible values:
true => all elements should have the same number of matrices
false => the elements can have different number of matrices from one to anot2014-08-13 09:40:42.463 UTCnet.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.Invokemessagevalue00Message to show to the user the action s/he needs to perform in the interaction page2014-08-13 09:40:51.74 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect matrix files, then click Confirmnet.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.InvokeminMatricesPerFieldvalue00Minimum number of matrices per field2014-08-13 09:41:01.365 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity1net.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.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.Invoketitlevalue00Title to be shown in the interaction page2014-08-13 09:41:34.771 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivitySelect a stage matrix for each yearnet.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.InvokeFlattenListinputlist2outputlist11net.sf.taverna.t2.activitiesbeanshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityinputlist2text/plainjava.lang.Stringtrueoutputlist11workflownet.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.InvokeRequestStageMatricestitleRequestStageMatricesfieldRequestStageMatricesvaluesRequestStageMatricesmessageRequestStageMatricesminMatricesPerFieldRequestStageMatricesmultipleRequestStageMatricesforceEqualNumberMatricesPerFieldFlattenListinputlistmatrices1629a676-0820-432d-a5e0-c2b63dfe216a2014-08-11 10:37:09.774 UTCeb7ff995-6def-43c9-9248-422a828fb6d22014-08-11 10:48:09.842 UTC53df2b6d-fc40-46f1-9ccc-f72c7011dd572014-08-13 10:30:16.788 UTCRequestStageMatrices2014-08-11 10:35:59.628 UTCb5df8a82-43c1-4126-afda-73a7a47ee6372014-08-11 10:55:22.947 UTC2b747eb4-5df4-455e-b118-82b57c02d1942014-08-13 09:46:46.757 UTCConvert_Taverna_listlist_of_r_expressions22r_list_of_expressions1RExpressionToStringstringlist1concatenated00net.sf.taverna.t2.activitiesbeanshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivityseperator0text/plainjava.lang.Stringtruestringlist1text/plainjava.lang.Stringtrueconcatenated00workflownet.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.InvokeJoinListOfStringsIntoRListstringlist1output11net.sf.taverna.t2.activitiesbeanshell-activity1.5-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitystringlist1text/plainjava.lang.Stringtrueoutput11workflownet.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.InvokeRExpressionToStringstringlistJoinListOfStringsIntoRListstringlistr_list_of_expressionse138fe4e-acf6-4e88-a83f-f7dd8b7d45112014-01-09 10:34:46.821 UTCConvert Taverna list of RExpr to R list2013-11-27 14:27:50.10 UTCJonathan Giddy2013-11-27 14:27:50.10 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.
Version 1: initial implementation
Version 2: reduce number of BeanShells
2013-11-27 14:27:50.10 UTC