myExperiment

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Maria Paula Balcazar-Vargas

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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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Maria Paula Balcazar-Vargas

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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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biovel
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cumulative distribution function (cdf)
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demography
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gentiana pneumonanthe
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matrix
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matrix population models
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morris and doak 2002.
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package ‘popbio’ in r
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population viability analysis (pva)
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probability of quasi-extinction threshold by time t
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simulating extinction probabilities
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stage matrix
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stochastic environment

Creator

Maria Paula Balcazar-Vargas

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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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Maria Paula Balcazar-Vargas

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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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Maria Paula Balcazar-Vargas

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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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Tags:

biovel
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demography
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gentiana pneumonanthe
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independently and identically distributed (iid)
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matrix population models
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model
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morris and doak 2002.
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package ‘popbio’ in r
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population
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population viability analysis (pva)
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stage matrix
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stochastic environment
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stochastic growth
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stochastic projection

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Sven

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ARC to WARC migration with quality assurance scripts

Created: 2014-07-10 08:39:49

These are the tool service scripts used in Taverna workflow available on myExperiment (http://www.myexperiment.org/workflows/4333). The Taverna workflow is configured by adapting the values of the constant values (light-blue boxes) which define the paths to configuration files, deployment files, and scripts in the processing environment. However, as Taverna is just used as an orchestration tool to build a sequence of bash script invocations, it is also possible to just use the individual scri...

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Creator

Maria Paula Balcazar-Vargas

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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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Maria Paula Balcazar-Vargas

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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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Creator

Alex Nenadic

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Taverna - VPH-Share workshop 17-18 July 2014

Created: 2014-07-09 11:36:13 | Last updated: 2014-08-13 14:37:51

Taverna - VPH-Share workshop 17-18 July 2014Location: The Pam Liversidge Building, Sir Frederick Mappin Building – Sheffield S1 3JD, UKRegistration link: http://bit.ly/vph-share-trainingFormat: The workshop is a two-day hands-on training event about workflows in the biomedical arena, with a focus on VPH-Share and Taverna.Target community & qualifications: The target community is developers and research scientists working in all areas of biomedical/healthcare research within the...

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Alan Williams

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openphacts

Created: 2014-07-06 15:46:09 | Last updated: 2014-07-06 15:47:27

Set of components corresponding to the OpenPHACTS API

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component family

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