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Project Biovel

Workflow Input Ready (8)

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BioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform Short Bayesian Phylogenetic Inference Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [http://www.biovel.eu][1] [1]: http://www.biovel.eu ## 1 Description The Pack contain 3 workflows that perform and validate bayesian phylogenetic i...

Created: 2013-02-20 | Last updated: 2014-04-13

Credits: User Saverio Vicario User Giacinto Donvito User Bachirb

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Project Biovel

Blob Matrix Population Modelling documentation

Created: 2012-11-05 16:32:34 | Last updated: 2012-11-07 09:01:58

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document describes the Matrix Population Modelling workflow, and includes a tutorial on its use.

File type: Adobe PDF

Comments: 0 | Viewed: 102 times | Downloaded: 93 times

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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

Uploader
Project Biovel

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...

File type: Plain text

Comments: 0 | Viewed: 20 times | Downloaded: 8 times

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Uploader
Project Biovel

Blob Sample Input for Data Refinement Workflow

Created: 2012-11-02 16:10:54 | Last updated: 2012-11-07 08:48:11

Credits: User Cherian Mathew

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 This file is a sample input file for the Data Refinement Workflow. It is also the input file used in the tutorial section of the documentation.

File type: Plain text

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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

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

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

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

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