User: Mikolaj Krzyzanowski

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Variance matrix documentation

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

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

Attributions: Variance matrix

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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Mean matrix documentation

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

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

Attributions: Mean matrix

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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Calculate and Plot abundance over the years document...

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

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

Attributions: Calculate and Plot abundance over the years

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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

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

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

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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Calculate the quasi-extinction probability documenta...

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

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

Attributions: Calculate quasi-extinction threshold.

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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Simulate stochastic growth from a sequence of matric...

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

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

Attributions: Simulate stochastic growth from a sequence of matrices

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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

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

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

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

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

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

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

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