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3377?size=60x60 Gb Jon Giddy
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Blob Demographic data Gentiana pneumonanthe 1987-1988 fro...

Created: 2012-11-02 10:59:24 | Last updated: 2012-11-07 08:56:00

Credits: User Jon Giddy User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Small example file to allow users to run population modelling workflow  

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Demographic data Gentiana pneumonanthe 1987-1991 fr...

Created: 2012-11-02 12:37:19 | Last updated: 2014-07-04 12:31:17

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Matrix Population Model construction and analysis v20

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This is a .txt file of four years demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysis v...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Demographic data Gentiana pneumonanthe 1987-1988 fro...

Created: 2012-11-05 09:47:37 | Last updated: 2013-08-13 12:06:34

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Matrix Population Model construction and analysis v20

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of one year demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysi...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Created: 2013-08-13 12:17:28

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model analysis v12

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Matrix Population Model analysis v10 (http://www.myexperiment.org/workflows/3686.html) If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 1996. Temporal and Spatial Varia...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Dwingeloo 1 88-89

Created: 2014-01-29 11:22:20

Credits: User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Life Table Response Experiments (LTRE) Fixed design Place effects 1 (http://www.myexperiment.org/packs/574.html) If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 1...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Lochem 89-90

Created: 2014-01-29 11:42:38

Credits: User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Life Table Response Experiments (LTRE) Fixed design Place effects V1 (http://www.myexperiment.org/packs/574.html). If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den ...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Terschelling 88-89

Created: 2014-01-29 11:44:47 | Last updated: 2014-03-28 14:18:17

Credits: User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflows:Life Table Response Experiments (LTRE) Fixed design Place effects V1 (http://www.myexperiment.org/packs/574.html) and Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperi...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Terschelling 89-90

Created: 2014-01-29 11:46:02 | Last updated: 2014-03-28 14:18:57

Credits: User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflows:Life Table Response Experiments (LTRE) Fixed design Place effects V1 (http://www.myexperiment.org/packs/574.html) and Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperi...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Pooled_matrix_file_Gentiana_LTRE

Created: 2014-03-27 10:37:46 | Last updated: 2014-08-29 13:23:06

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pooled_matrix_file or weighted main Matrix - what popbio (R package) calls pooled matrix (to see more details: Horvitz, Schemske and Caswell 1997; Horvitz, and Schemske 1995). This is a matrix in a .txt format, all decimal numbers in each matrix must be indicated by dots e.g.: 0.578.To understand how to calculate a pooled matrix or a weighted main Matrix, please see: Choice of a reference matrix (pag: 253, in Horvitz, Schemske and Caswell 1997). This list of matrices will be used to perf...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Terschelling 87-88

Created: 2014-03-28 14:22:32

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow: Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperiment.org/packs/590.html)If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 19...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Terschelling 90-91

Created: 2014-03-28 14:24:33

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow: Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperiment.org/packs/590.html)If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 19...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Terschelling 91-92

Created: 2014-03-28 14:30:15

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow: Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperiment.org/packs/590.html)If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 19...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Terschelling 92-93

Created: 2014-03-28 14:31:44

Credits: User Maria Paula Balcazar-Vargas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow: Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperiment.org/packs/590.html)If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 19...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Terschelling pooled data or weighted main matrix

Created: 2014-03-28 14:38:43

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow: Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperiment.org/packs/590.html)If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 19...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Cohen’s cumulative distance documentation

Created: 2014-07-24 08:20:42

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Cohen’s cumulative distance

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Cohen’s cumulative distance Workflow provides an environment to calculate the Cohen’s cumulative distance. The Cohen’s cumulative distance measures the difference between observed and expected vectors along the matrix path that the population would take to reach the expected population vector. It is a function of both the observed stage distribution (n...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Keyfitz’s delta documentation

Created: 2014-07-24 08:25:05

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Keyfitz delta

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with the same name.The Keyfitz’s delta Workflow provides an environment to calculate the Keyfitz delta value. Keyfitz’s delta is a measure of the distance between any two probability vectors (Keyfitz 1968). In this case is a measure of the distance between n (Observed Stage Distribution) and w (Stable Stage Distribution). The maximum value is 1 and the minimum value is 0 (w...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Age-specific survival documentation

Created: 2014-07-24 11:48:40

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Age specific analysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with the same name.The age-specific survival analysis workflow gives the basic information of the mean, variance and coefficient of variation (CV) of the time spent in each stage class and the mean and variance of the time of death.AnalysesFundamental matrix (N)Variance(var)Coefficient of variation (CV)MeanetaVareta

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Parametric Bootstrap or Resample a projection matrix...

Created: 2014-07-25 09:41:10

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Parametric Bootstrap or Resample a projection matrix Workflow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants surveyed. The projection matrix A is first split into separate transition and ...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Bootstrap of observed census transitions documentation

Created: 2014-07-25 10:37:03

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Bootstrap of observed census transitions (confidence intervals of λ) workflow for local execution calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to est...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Population Models construction and analyses d...

Created: 2014-07-25 10:48:13 | Last updated: 2014-07-25 10:50:17

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Matrix Population Models construction and analyses Workflow provides an environment for create a stage-matrix with no density dependence and perform several analyses on it.Analyses:Eigen analysis.Age specific survival.Generation time (T).Net reproductive rate (Ro).Transient Dynamics.Bootstrap of observed census transitions (Confidence intervals of λ).Survival cur...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix Population Models analysis documentation

Created: 2014-07-25 10:55:42

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model analysis v12

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Matrix Population Models analysis Workflow provides an environment to perform several analyses on a stage-matrix with no density dependence.Analyses:Eigen analysis.Age specific survival.Generation time (T).Net reproductive rate (Ro).Transient Dynamics.Resample a projection matrix (Confidence intervals of λ).Survival curveKeyfitz’s ΔCohen’s cumul...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix population models construction documentation

Created: 2014-07-25 11:02:01

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run a workflow) explains how to run a workflow that beolngs to the pack with the same name.The Creation of a stage matrix model Workflow provides an environment to construct a stage matrix model. This workflow create a stage matrix based on two years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population. The resulting is a stage matrix model.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Damping ratio documentation

Created: 2014-07-25 11:07:01

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Damping ratio

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Damping ratio Workflow provides an environment to calculate the damping ratio of several matrices and plot them.The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the populati...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Eigen analysis documentation

Created: 2014-07-25 11:18:44

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Eigen analysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Eigen analysis workflow provides an environment for the analysis of a stage-matrix and perform several analyses on it.The Eigen analysis results are a set of demographic statistics:Lambda or dominant eigenvalue (λ).The stable stage distribution (w).The sensitivity matrixThe Elasticity matrix.Reproductive value (v).The damping ratio (ρ)

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Generation Time (T) documentation

Created: 2014-07-25 11:22:18

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Generation time (T)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Generation Time (T) Workflow provides an environment to calculate the generation time. The generation time is the time T required for the population to increase by a factor of Ro (net reproductive rate). In other words, T calculates how much time takes to a plant/animal to replace itself by a factor of Ro.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Net reproductive rate (Ro) documentation

Created: 2014-07-25 11:25:19

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Net reproductive rate (Ro)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Net reproductive rate (Ro) Workflow provides an environment to calculate the net reproductive rate (Ro). Ro is the mean number of offspring by which a new-born individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Transient dynamics documentation

Created: 2014-07-25 12:16:46

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Transient Dynamics.

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Transient dynamics or Calculate population growth rates by projection Workflow provides an environment to calculates the population growth rate and stable stage distribution by repeated projections of the equation n(t+1)=An(t) and to produce plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.Transient dynamic ana...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Stage vectors, Survival and Growth rate curves (demo...

Created: 2014-07-25 12:41:06

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Stages vectors plots, Survival and Growth rate curves

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:Population projectionSurvival 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.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Simulate stochastic growth from a sequence of matric...

Created: 2014-07-30 13:47:47

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Mikolaj Krzyzanowski User Gerard Oostermeijer

Attributions: Workflow Simulate stochastic growth from a sequence of matrices

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices.Outputs:Equal selection dataStochastic projectionUnequal selection dataTo know more detail...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Life Table Response Experiments Fixed design Place e...

Created: 2014-08-14 08:03:58

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Life Table Response Experiment fixed design Place Effect

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Life Table Response Experiments place effect workflow provides an environment to analyse one or more matrices (e.g. matrices of different years from the same place) from two or more places. The objective of this workflow is to determine the effects of the research places or localities (2 or more) on λ. This workflow performs a fixed LTRE, one way design (Caswell ...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Life Table Response Experiments Fixed design years e...

Created: 2014-08-14 08:44:30 | Last updated: 2014-08-14 08:45:27

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Life Table Response Experiment Year Effect in One Location or Place

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The 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 retrospectiv...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Blob Calculate the quasi-extinction probability documenta...

Created: 2014-08-14 12:05:06

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Calculate quasi-extinction threshold.

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates by simulation the quasi-extinction probability time cumulative distribution function for a structured population in an independently and identically distributed (iid) stochastic environment. This workflow is based on the popbio package (stoch.quasi.ext - Calculate quasi-extinction threshold, Stubben, Milligan and Nantel, 2013) based on the MATLAB cod...

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Blob Mean matrix documentation

Created: 2014-08-14 17:52:17 | Last updated: 2014-08-28 13:50:22

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Mean matrix

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates the mean matrix from a list of matrices.

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Blob Life Table Response Experiments Fixed design year ef...

Created: 2014-08-21 08:05:38

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Life Table Response Experiment year effect for multiple places

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Life Table Response Experiments Year Effect for Multiple Places workflow provides an environment to analyse two or more matrices (e.g., two or more matrices of different years from one place) at two or more different locations. The objective of this workflow is to determine the effects of the research years (2 or more) on λ. This workflow performs a fixed LTRE, o...

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Blob Log-log plots of variance vs. sensitivity and CV vs....

Created: 2014-08-21 09:16:10

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This 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).

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Blob Demographic data Gentiana pneumonanthe 1987-1993

Created: 2014-08-22 12:01:38

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Calculate and Plot abundance over the years (http://www.myexperiment.org/packs/664.html)This table containing the demographic data on a series of individuals during 7 years, from 1987 to 1993 (6 periods: 1987-1988, 1988-1989 etc....

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Blob Decomposed matrix of Gentiana pneumonanthe

Created: 2014-08-28 11:28:44

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file (decomposed matrix) is used in the documentation as example to run the Elsticity and Sensitivity of the Vital rates Workflow.

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Blob Calculate and Plot abundance over the years document...

Created: 2014-08-28 13:17:28

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Calculate and Plot abundance over the years

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow calculate and plot the survival based on two or more years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population.

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Blob Variance matrix documentation

Created: 2014-08-28 13:53:09

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Variance matrix

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates the variance matrix from a list of matrices.

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Blob Southern Resident Killer Whale (SRKW) demographic data

Created: 2014-08-29 11:43:47

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Southern Resident Killer Whale (SRKW) demographic dataThe input data (a .csv-file) has to have the format of a table containing the Orcinus orca demographic data with the columns named: Year, Age, Count, Offspring and Cat1. Each year, the number of individuals per age and the number of offspring per age reproductive female category are counted (females ≥ 10 years old). IF A Female category does not have offspring equals to 0. For the called column, Cat1; Ages 1 to 9 belongs to Juv (Juvenil...

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Blob Northern Resident Killer Whale (NRKW) demographic data

Created: 2014-08-29 11:46:14 | Last updated: 2014-08-29 16:25:25

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Northern Resident Killer Whale (NRKW) demographic data.The input data (a .csv-file) has to have the format of a table containing the Orcinus orca demographic data with the columns named: Year, Age, Count, Offspring and Cat1. Each year, the number of individuals per age and the number of offspring per age reproductive female category are counted (females ≥ 10 years old). IF A Female category does not have offspring equals to 0. For the called column, Cat1; Ages 1 to 9 belongs to Juv (Juveni...

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Blob Vital Rates_combined

Created: 2014-08-29 11:51:09

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The stage-structured life cycle of resident killer whales with seven life stages:(1) calves; (Calf)(2) juveniles; (Juv)(3) young reproductive females; (F1)(4) old reproductive females; (F2)(5) post-reproductive females; (F3)(6) young mature males; and (M1)(7) old mature males (M2).Fi represent fertility; Gi represent stage transition probabilities, with female and male juvenile-to-adult transitions indicated as G2f and G2m, respectively; and, Pi represent the probability of surviving and rema...

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Blob Orcinus orca (Killer whale) demography and populatio...

Created: 2014-08-29 12:21:35 | Last updated: 2014-08-29 16:23:18

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Jon Giddy

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name Normal 0 false false false EN-US X-NONE X-NONE ...

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Blob Elasticity and Sensitivity of the Vital rates docume...

Created: 2014-08-29 14:49:44 | Last updated: 2014-08-29 14:50:15

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Elasticity and Sensitivity of the Vital rates

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow calculates the Elasticity and Sensitivity of population growth rate with respect to various vital rates. The goal in both cases is to determine which vital rate(s) has/have the most influence on population growth rate (λ).Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses.The sensitivity matrix: The sensitivity desc...

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Blob Comparative Demography and Viability of Northeastern...

Created: 2014-09-11 09:03:19

Credits: User Antonio Velez-Espino User Andres Araujo

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Comparative Demography and Viability of Northeastern Pacific Resident Killer Whale Populations at Risk.L.A. Vélez-Espino, J.K.B. Ford, H.A. Araujo, G. Ellis, C.K. Parken, and K.C. BalcombFisheries and Oceans CanadaScience Branch, Pacific RegionPacific Biological StationNanaimo, BCV9T 6N72014Canadian Technical Report ofFisheries and Aquatic Sciences 3084 Two distinct populations of resident killer whales (Orcinus orca) in the northeastern Pacific Ocean have been identified in Canad...

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Blob Sensitivity of resident killer whale population dyna...

Created: 2014-09-11 09:11:46 | Last updated: 2014-09-11 09:12:49

Credits: User Antonio Velez-Espino User Andres Araujo

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Sensitivity of resident killer whale population dynamics to Chinook salmon abundance.L. Antonio Vélez-Espino1,£, John K.B. Ford2, Charles K. Parken1, Graeme Ellis2, Eric Ward3, Larrie LaVoy4, Ken Balcomb5, M. Bradley Hanson3, Dawn P. Noren3, Tom Cooney4, Rishi Sharma6,7.(1) Salmon and Freshwater Ecosystems Division, Fisheries and Oceans Canada; (2) Marine Mammal Division, Fisheries and Oceans Canada; (3) Conservation Biology Division, Northwest Fisheries Science Center (NOAA); (4...

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Blob Resident killer whale-chinook salmon interactions an...

Created: 2014-09-26 12:09:28 | Last updated: 2014-09-26 12:11:12

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Andres Araujo User Jon Giddy User Francisco Quevedo

Attributions: Workflow Exploration of fishing scenarios Workflow Resident killer whale-chinook salmon interactions

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation contains the tutorial to run two related workflows. 1.    Resident killer whale-chinook salmon interactions workflow The Resident killer whale-chinook salmon interactions workflow provides an environment to create calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences in demographic rates be...

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Pack Matrix Population Model construction and analysis pack


Created: 2013-08-13 14:31:09 | Last updated: 2015-06-12 13:48:43

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Matrix Population Models Workflow provides an environment for create a stage-matrix with no density dependence and perform several analyses on it.Analyses:Eigen analysis.Age specific survival.Generation time (T).Net reproductive rate (Ro).Transient Dynamics.Bootstrap of observed census transitions (Confidence intervals of λ).Survival curveKeyfitz’s ΔCohen’s cumulative distanceTh...

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Pack Matrix Population Models analyses pack


Created: 2013-08-14 10:37:55 | Last updated: 2014-07-25 10:56:14

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Matrix Population Models Workflow provides an environment  to perform several analyses on a stage-matrix with no density dependence:Eigen analysis.Age specific survival.Generation time (T).Net reproductive rate (Ro).Transient Dynamics.Resample a projection matrix (Confidence intervals of λ).Survival curveKeyfitz’s ΔCohen’s cumulative distance This workflow has bee...

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Pack Life Table Response Experiments Fixed design Place e...


Created: 2014-01-29 10:42:06 | Last updated: 2014-08-14 08:04:25

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Life Table Response Experiments place effect workflow provides an environment to analyse one or more matrices (e.g. matrices of different years from the same place) from two or more places. The objective of this workflow is to determine the effects of the research places or localities (2 or more) on λ. This workflow performs a fixed LTRE, one way design (Caswell 2001). LTRE is a retrospectiv...

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Pack Life Table Response Experiments Fixed design year ef...


Created: 2014-02-21 13:12:33 | Last updated: 2014-08-21 08:06:21

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Life Table Response Experiments year effect for multiple places workflow provides an environment to analyse two or more matrices (e.g., two or more matrices of different years of one place) of two or more different locations. The objective of this workflow is to determine the effects of the research years (2 or more) on λ. This workflow performs a fixed LTRE, one way design (Caswell 2001).LTRE is...

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Pack Life Table Response Experiments Fixed design Year Ef...


Created: 2014-02-27 12:49:10 | Last updated: 2014-08-27 09:58:12

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Life Table Response Experiments Year Effect in One Location or 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),...

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Pack Stage vectors, Survival and Growth rate curves (demo...


Created: 2014-04-03 08:11:33 | Last updated: 2014-07-25 12:41:24

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:Population projectionSurvival 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.

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Pack Matrix Population Model construction pack


Created: 2014-06-19 11:23:27 | Last updated: 2014-07-25 12:48:25

This pack contains a workflow, a file and documentation (tutorial to run the workflow).Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow for local executionThe Creation of a stage matrix model Workflow allows us to construct a stage o several stage matrices. This workflow create a stage matrix based on two years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of...

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Pack Age specific survival analysis pack


Created: 2014-07-02 11:49:01 | Last updated: 2015-05-19 09:46:30

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The age-specific survival analysis pack has a workflow that analyse the basic information on 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.Analyses:Fundamental matrix (N)Variance (var)Coefficient of variation (CV)MeanetaVareta

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Pack Damping ratio pack


Created: 2014-07-02 13:32:31 | Last updated: 2014-07-25 11:07:16

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Damping ratio pack contains a workflow that provides an environment to calculate the damping ratio of several matrices and plot them.The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the population converges ...

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Pack Eigen analysis pack


Created: 2014-07-03 15:57:49 | Last updated: 2014-07-25 11:18:57

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Eigen analysis workflow provides an environment for the analysis of a stage-matrix and perform several analyses on it.The Eigen analysis results are a set of demographic statistics:Lambda or dominant eigenvalue (λ).The stable stage distribution (w).The sensitivity matrixThe Elasticity matrix.Reproductive value (v).The damping ratio (ρ).

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Pack Transient dynamics pack


Created: 2014-07-04 10:59:17 | Last updated: 2014-07-25 12:17:07

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Transient dynamics or Calculate population growth rates by projection Workflow provides an environment to calculates the population growth rate and stable stage distribution by repeated projections of the equation n(t+1)=An(t) and to produce plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.Transient dynamic analysisPopulation projectionLambda o...

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Pack Generation time (T) pack


Created: 2014-07-04 13:20:43 | Last updated: 2014-07-25 11:22:30

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Generation Time (T) Workflow provides an environment to calculate the generation time. Th generation time is the time T required for the population to increase by a factor of Ro (net reproductive rate). In other words, T calculates how much time takes to a plant/animal to replace itself by a factor of Ro.

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Pack Net reproductive rate (Ro) pack


Created: 2014-07-04 13:59:07 | Last updated: 2014-07-25 11:25:32

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The . Net reproductive rate (Ro) Workflow provides an environment to calculate the net reproductive rate (Ro). Ro is the mean number of offspring by which a new-born individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next.

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Pack Bootstrap of observed census transitions pack


Created: 2014-07-09 12:56:51 | Last updated: 2014-07-25 10:37:19

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Bootstrap of observed census transitions (confidence intervals of λ) workflow for local execution calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to estimate lambda, because lambda is es...

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Pack Parametric Bootstrap or Resample a projection matrix...


Created: 2014-07-09 14:03:43 | Last updated: 2014-07-25 09:41:32

This pack contains a workflow, a file and documentation (tutorial to run the workflow). The Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants surveyed. The projection matrix A is first split into separate transition and fertility matrices. Dead fates ar...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Pack Simulate stochastic growth from a sequence of matric...


Created: 2014-07-10 12:05:44 | Last updated: 2014-07-30 13:48:06

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices.Outputs:Equal selection dataStochastic projectionUnequal selection dataTo know more details about the analysis, Morris and D...

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Pack Keyfitz's delta pack


Created: 2014-07-23 11:19:37 | Last updated: 2014-07-24 08:25:22

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Keyfit delta Workflow provides an environment to calculate the Keyfit delta value. Keyfitz’s delta is a measure of the distance between any two probability vectors (Keyfitz 1968). In this case is a measure of the distance between n (Observed Stage Distribution) and w (Stable Stage Distribution). The maximum value is 1 and the minimum value is 0 (when the vectors are identical).

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Pack Cohen cumulative distance pack


Created: 2014-07-23 13:43:22 | Last updated: 2014-07-24 08:21:00

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Cohen’s cumulative distance Workflow provides an environment to calculate the Cohen’s cumulative distance. The Cohen’s cumulative distance measures the difference between observed and expected vectors along the matrix path that the population would take to reach the expected population vector. It is a function of both the observed stage distribution (n0) and the structure of the matrix...

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Pack Calculate quasi-extinction threshold pack


Created: 2014-07-30 14:00:20 | Last updated: 2014-08-14 12:05:20

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This workflow estimates by simulation the quasi-extinction probability time cumulative distribution function for a structured population in an independently and identically distributed (iid) stochastic environment. This workflow is based on the popbio package (stoch.quasi.ext - Calculate quasi-extinction threshold, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.5 (Morris and Doak ...

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Pack Mean matrix pack


Created: 2014-07-31 13:34:16 | Last updated: 2014-08-14 17:52:30

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This mean matrix workflow estimates the mean matrix from a list of matrices.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Pack Log-log plots of variance vs. sensitivity and CV vs....


Created: 2014-08-13 10:27:13 | Last updated: 2014-08-21 09:16:30

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This 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).

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
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Pack Variance matrix pack


Created: 2014-08-21 13:07:20 | Last updated: 2014-08-28 13:53:33

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This workflow estimates the variance matrix from a list of matrices.

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Pack Calculate and Plot abundance over the years pack


Created: 2014-08-22 07:50:23 | Last updated: 2014-08-28 13:17:48

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This workflow calculates and plots the abundance per stage per year from a list of matrices.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Elasticity and Sensitivity of the vital rates pack


Created: 2014-08-28 08:56:24 | Last updated: 2014-08-29 14:50:26

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This workflow calculate the Elasticity and Sensitivity of the vital rates. The goal in both cases is to determine which vital rates have the most influence on population growth or λ.

3 items in this pack

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Relative importance of Chinook salmon abundance on r...


Created: 2014-08-29 11:04:10 | Last updated: 2014-09-30 09:35:02

The pack contains three workflows, 13 files and 2 documentations (tutorials to run the workflows).Workflows:1) Demography of the killer whales.2) Resident killer whale-chinook salmon interactions.3) Exploration of fishing scenarios.These workflow uses input data of two different populations of Orcas in the northeastern Pacific Ocean of Canada and the U.S. But these workflows can also use input data from other populations of the Orcas in the world (see requirements for data entry in the docume...

19 items in this pack

Comments: 0 | Viewed: 89 times | Downloaded: 33 times

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Workflows (26)
Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Creation of a stage matrix model from demo... (2)

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This workflow create a stage matrix model based on two years census data of tagged or mapped individuals of an animal or plant population. Each annual census describes for each individual its life stage, reproductive output (estimated number offprings) and whether or not it is a new recruit. The workflow converts this data into a stage matrix model from 1 year to 2 that contains transitions probabilities from each stage to the next. This workflow has been created by the Biodiversity Virtual...

Created: 2012-11-01 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Blob Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Eigen analysis (3)

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The Eigen analysis results are a set of demographic statistics: 1) Lambda or dominant eigenvalue: The population will be stable, grow or decrease at a rate given by lambda: eg: ? = 1 (population is stable), ? > 1 (population is growing) and finally ? < 1 (populatiopn is decreasing) . 2) The stable stage distribution: It is the proportion of the number of individuals per stage and it is given by (w). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses....

Created: 2012-11-02 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Workflow Matrix Population Model analysis v12 Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Age specific analysis (3)

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The age specific analysis 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...

Created: 2012-11-02 | Last updated: 2014-07-24

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Workflow Matrix Population Model analysis v12 Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Transient Dynamics. (3)

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This workflow produces plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections. ============================================================ 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 based on Package ‘popbio’ in R. Stubben, C & B. Milligan. 2007. Estimating and Anal...

Created: 2012-11-02 | Last updated: 2014-07-31

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Workflow Matrix Population Model analysis v12 Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Generation time (T) (2)

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The time T required for the population to increase by a factor of Ro (net reproductive rate) e.g.: If Ro (net reproductive rate) = 5.56 and T (generation time) = 8.055 The average plant of the species Gentiana pneumonanthe in Terschelling in the year 1987 replaced itself with almost six new plants and took approximately 8.05 years to do so. ========================================================= This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.bio...

Created: 2012-11-02 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Workflow Matrix Population Model analysis v12 Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Net reproductive rate (Ro) (2)

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This workflow calculates the net reproductive rate (Ro) that is mean number of offspring by which a newborn individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next (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, gr...

Created: 2012-11-02 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Workflow Matrix Population Model analysis v12 Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Bootstrap of observed census transitions. (3)

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This workflow calculates bootstrap distributions of population growth rates (?), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to estimate lambda, because lambda is estimated from imperfect data, such estimation are uncertain. Therefore, when the results have policy implications it is important to quantify that uncertainty. Confidence interval is one of ...

Created: 2012-11-05 | Last updated: 2014-07-24

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Matrix Population Model construction and a... (3)

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The Matrix Population Models Workflow provides an environment to create stage-matrices with no density dependence and to perform several analyses on them: - Eigen analysis; - Age specific survival; - Generation time (T); - Net reproductive rate (Ro); - Transient Dynamics; - Bootstrap of observed census transitions (Confidence intervals of lambda); - Survival curve; - Keyfitz delta; - Cohen's cumulative distance. If multiple year transitions are selected, the results will be ordered by year. ...

Created: 2013-08-13 | Last updated: 2014-07-04

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Matrix Population Model construction and analysis Workflow Eigen analysis Workflow Age specific analysis Workflow Transient Dynamics. Workflow Generation time (T) Workflow Net reproductive rate (Ro) Workflow Bootstrap of observed census transitions. Blob Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Matrix Population Model analysis v12 (2)

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The Matrix Population Models Workflow provides an environment to perform several analyses on a stage-matrix with no density dependence: - Eigen analysis; - Age specific survival; - Generation time (T); - Net reproductive rate (Ro); - Transient Dynamics; - Bootstrap of observed census transitions (Confidence intervals of lambda); - Survival curve; - Keyfitz delta; - Cohen's cumulative distance. This workflow requires an instance of Rserve on localhost This workflow has been created by the Bi...

Created: 2013-08-13 | Last updated: 2014-07-09

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Eigen analysis Workflow Age specific analysis Workflow Transient Dynamics. Workflow Generation time (T) Workflow Net reproductive rate (Ro) Blob Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Parametric Bootstrap or Resample a project... (3)

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The Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants surveyed. The projection matrix A is first split into separate transition and fertility matrices. Dead fates are added to the transition matrix and the columns are then sampled from a Multinomial dis...

Created: 2014-06-18 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model analysis v12

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Damping ratio (2)

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The Damping ratio Workflow provides an environment to calculate the damping ratio of several matrices and plot them. The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the population converges. ============================================================= This workflow requires an instance of Rse...

Created: 2014-06-25 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Stages vectors plots, Survival and Growth ... (2)

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The 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 creat...

Created: 2014-07-02 | Last updated: 2014-08-29

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Keyfitz delta (1)

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The Keyfit delta Workflow provides an environment to calculate the Keyfit delta value. Keyfitz’s delta is a measure of the distance between any two probability vectors (Keyfitz 1968). In this case is a measure of the distance between n (Observed Stage Distribution) and w (Stable Stage Distribution). The maximum value is 1 and the minimum value is 0 (when the vectors are identical). ============================================================ This workflow has been created by the Biodiversit...

Created: 2014-07-23

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model analysis v12 Workflow Matrix Population Model construction and analysis v20

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Cohen’s cumulative distance (1)

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The Cohen’s cumulative distance Workflow provides an environment to calculate the Cohen’s cumulative distance. The Cohen’s cumulative distance measures the difference between observed and expected vectors along the matrix path that the population would take to reach the expected population vector. It is a function of both the observed stage distribution (n0) and the structure of the matrix (A) (Williams et al 2011). Cohen’s cumulative distance will not work for reducible matrices or imprimiti...

Created: 2014-07-23

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model analysis v12 Workflow Matrix Population Model construction and analysis v20

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Simulate stochastic growth from a sequence... (1)

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The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices. This workflow is based on the popbio package (script: stoch.projection - Simulate stochastic growth from a sequence of matrices, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.3 (Mo...

Created: 2014-07-30 | Last updated: 2014-08-14

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Life Table Response Experiment fixed desig... (1)

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The Life Table Response Experiments place effect workflow provides an environment to analyse one or more matrices (e.g. matrices of different years from the same place) from two or more places. The objective of this workflow is to determine the effects of the research places or localities (2 or more) on ?. 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 ? under two or more set...

Created: 2014-08-13

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Life Table Response Experiment Year Effect... (1)

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The 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 ?. 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 ? under two or more sets of environmental conditions...

Created: 2014-08-14

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Calculate quasi-extinction threshold. (1)

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This workflow estimates by simulation the quasi-extinction probability time cumulative distribution function for a structured population in an independently and identically distributed (iid) stochastic environment. This workflow is based on the popbio package (stoch.quasi.ext - Calculate quasi-extinction threshold, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.5 (Morris and Doak 2002). For more details of the analysis see: Calculating the probability of hitting a q...

Created: 2014-08-14

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Mean matrix (1)

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This mean matrix workflow estimates the mean matrix from a list of matrices. 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 Caswel...

Created: 2014-08-14

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Life Table Response Experiment year effect... (1)

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The Life Table Response Experiments Year Effect for Multiple Places workflow provides an environment to analyse two or more matrices (e.g., two or more matrices of different years from one place) at two or more different locations. The objective of this workflow is to determine the effects of the research years (2 or more) on ?. 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 ?...

Created: 2014-08-21

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Log-log plots of variance vs. sensitivity ... (1)

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This 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 implica...

Created: 2014-08-21

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Calculate and Plot abundance over the years (1)

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This 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. 20...

Created: 2014-08-28

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Variance matrix (1)

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This workflow estimates the variance matrix from a list of matrices. 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. 20...

Created: 2014-08-28

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Elasticity and Sensitivity of the Vital rates (1)

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This workflow calculates the Elasticity and Sensitivity of population growth rate with respect to various vital rates. The goal in both cases is to determine which vital rates has/ve the most influence on population growth rate (?). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses. a) The sensitivity matrix: The sensitivity describes the effect on ? of changes in vital rates of the matrix. The derivative tells what would happened to ? if aij was to c...

Created: 2014-08-29

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Killer whale demography (1)

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This workflow analyzes the demography and population growth of resident killer whale populations. Originally created for comparative studies of Northeastern Pacific populations at risk, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW), the workflow can be used for other killer whale populations or cetaceans counting with census data and life cycles that can be represented using the matrix models described in this document. This workflow perform the follow...

Created: 2014-09-24

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Andres Araujo User Jon Giddy User Francisco Quevedo

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Resident killer whale-chinook salmon inter... (1)

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The resident killer whale-chinook salmon interactions workflow provides an environment to calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences in demographic rates between killer whale (Orcinus orca) population that explain population growth; (ii) to determine the relative influence of vital rates and Chinook (Oncorhynchus tshawytsc...

Created: 2014-09-26

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Andres Araujo User Jon Giddy User Francisco Quevedo

Attributions: Workflow Killer whale demography

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