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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
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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 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
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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 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
Project Biovel
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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
Project Biovel
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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
Project Biovel
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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
Project Biovel
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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
Project Biovel
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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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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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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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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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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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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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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.

File type: Excel workbook

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