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Maria Paula Balcazar-Vargas

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Matrix Population Models analysis documentation

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: 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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Maria Paula Balcazar-Vargas

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Matrix Population Models construction and analyses d...

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: 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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analysis
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biovel
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bootstrap of observed census transitions
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cohen’s cumulative distance
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confidence interval of lambda
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damping ratio
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demography
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eigen analysis
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elasticity analysis
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fundamental matrix (n)
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generation time (t)
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gentiana pneumonanthe
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growth rates (lambda)
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keyfitz’s delta
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lambda or dominant eigenvalue
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matrix
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matrix population models
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meaneta
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net reproductive rate (ro)
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package ‘popbio’ in r
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package ‘popdemo’ in r
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population
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reproductive value (v)
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sensitivity analysis
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stable stage distribution (w)
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stage matrix
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vareta

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Maria Paula Balcazar-Vargas

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Bootstrap of observed census transitions documentation

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy 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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biovel
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bootstrap of observed census transitions
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confidence interval of lambda
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demography
|
gentiana pneumonanthe
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histogram
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lambda or dominant eigenvalue
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matrix
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matrix population models
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model
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package ‘popbio’ in r
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population
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population projection
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projection
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stage matrix

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Maria Paula Balcazar-Vargas

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Parametric Bootstrap or Resample a projection matrix...

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: 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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Maria Paula Balcazar-Vargas

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Age-specific survival documentation

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: 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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Maria Paula Balcazar-Vargas

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Keyfitz’s delta documentation

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: 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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Maria Paula Balcazar-Vargas

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Cohen’s cumulative distance documentation

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: 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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Alan Williams

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XPath tutorial presentation

Created: 2014-07-16 12:16:48

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial introducing how to use Taverna's XPath capabilities

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tutorial exercise

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Alan Williams

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Taverna Workbench introduction presentation

Created: 2014-07-16 12:15:19

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial designed to introduce the basic features of Taverna Workbench

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Alan Williams

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Help presentation

Created: 2014-07-16 12:13:54

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a presentation of information on where to find help on myGrid tools

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Alan Williams

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Introduction to using components presentation

Created: 2014-07-16 12:12:13

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a quick tutorial on how to use components within a workflow

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tutorial exercise

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Alan Williams

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Advanced Taverna Features Presentation

Created: 2014-07-16 12:09:47 | Last updated: 2014-07-16 12:10:55

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial on some of Taverna's advanced features.

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Alex Nenadic

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myGrid Tools for Scientists Presentation

Created: 2014-07-16 12:03:42 | Last updated: 2014-07-18 14:43:15

Credits: Alex Nenadic

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to myGrid tools for scientists

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Amrish Mahes

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example output of the concept profile generation pip...

Created: 2014-06-26 14:52:48

Credits: Amrish Mahes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an example output the workflow "Concept Profile Generation Pipeline" produces when the input for the thesaurus is the thesaurus example in the workflow itself and the abstract input is from the SQL file named "example standard input for Concept Profile Generation Pipeline". This SQL file needs to be run in a SQL program with a pre-created database/schema called mydb. It produces 5 tables. These consists out of the co-occurrence, occurrence, unce...

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Amrish Mahes

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example standard input for Concept Profile Generatio...

Created: 2014-06-26 14:36:00

Credits: Amrish Mahes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a SQL file containing example standard input values for testing the concept profile generation pipeline. Run this SQL file in your SQL program with a pre-created database/schema named mydb. It will insert 1 table called abstracts with 10 abstracts and their pubmed id. The workflow will use this table as input for finding concept occurrences.

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Rekha Maryanne Louis

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Usability test file

Created: 2014-06-10 14:27:16

Credits: Rekha Maryanne Louis

License: No license

This is a test .doc file for usability study of myExperiment from May to August 2014