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Taverna_logo Age specific analysis
Population Modelling

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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
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Uploaded 14 Aug 2014 18:13:08 UTC

Taverna_logo Bootstrap of observed census transitions.
Population Modelling

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This workflow 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
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Uploaded 21 Aug 2014 15:11:10 UTC

Taverna_logo Calculate and Plot abundance over the years
Population Modelling

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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
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Uploaded 28 Aug 2014 16:58:06 UTC

Taverna_logo Calculate quasi-extinction threshold.
Population Modelling

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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
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Uploaded 21 Aug 2014 17:56:34 UTC

Taverna_logo Cohen’s cumulative distance
Population Modelling

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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.
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Uploaded 21 Aug 2014 18:13:35 UTC

Taverna_logo Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population
Population Modelling

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This workflow create a stage matrix model based on two years census data of tagged or mapped individuals of an animal or plant population. Each annual census describes for each individual its life stage, reproductive output (estimated number offprings) and whether or not it is a new recruit. The
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Uploaded 21 Aug 2014 15:15:49 UTC

Taverna_logo Damping ratio
Population Modelling

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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
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Uploaded 21 Aug 2014 15:29:57 UTC

Taverna_logo Eigen analysis
Population Modelling

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The Eigen analysis results are a set of demographic statistics:

1) Lambda or dominant eigenvalue: The population will be stable, grow or decrease at a rate given by lambda: eg: λ = 1 (population is stable), λ > 1 (population is growing) and finally λ < 1 (populatiopn is decreasing) .

2) The stable
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Uploaded 21 Aug 2014 15:37:15 UTC

Taverna_logo Elasticity and Sensitivity of the Vital rates
Population Modelling

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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 rates has/ve the most influence on population growth rate (λ).

Elasticity and Sensitivity: Sensitivity and elasticity analyses are
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Uploaded 29 Aug 2014 14:56:26 UTC

Taverna_logo Exploration of fishing scenarios
Population Modelling

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This workflow must run after the workflow: Resident killer whale-chinook salmon interactions. The interaction workflows generates a PostWorkspace file, this is a zip file and it is an R Workspace that transfers values from the Resident killer whale-chinook salmon interactions (main) workflow to the
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Uploaded 26 Sep 2014 08:29:47 UTC

Taverna_logo Generation time (T)
Population Modelling

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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
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Uploaded 21 Aug 2014 15:41:00 UTC

Taverna_logo Integral Projection Model for Demographic Modelling v34
Population Modelling

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This workflow constructs and analyses an IPM with only continuous stages and without ramet production based on the IPMpack (R).

Information about the Input file:

The data must be organized in a table (in .csv format), where each row represents one observation of an organism in the population at one
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Uploaded 14 Aug 2014 19:02:48 UTC

Taverna_logo Keyfitz delta
Population Modelling

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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).
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Uploaded 21 Aug 2014 18:15:48 UTC

Taverna_logo Killer whale demography
Population Modelling

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This workflow analyzes the demography and population growth of resident killer whale populations. Originally created for comparative studies of Northeastern Pacific populations at risk, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW), the workflow can be used for
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Uploaded 24 Sep 2014 14:14:47 UTC

Taverna_logo Life Table Response Experiment fixed design Place Effect
Population Modelling

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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)
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Uploaded 21 Aug 2014 15:44:18 UTC

Taverna_logo Life Table Response Experiment year effect for multiple places
Population Modelling

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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
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Uploaded 21 Aug 2014 15:46:46 UTC

Taverna_logo Life Table Response Experiment Year Effect in One Location or Place
Population Modelling

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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
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Uploaded 21 Aug 2014 15:48:42 UTC

Taverna_logo Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements
Population Modelling

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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.
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Uploaded 21 Aug 2014 18:10:49 UTC

Taverna_logo Matrix Population Model analysis v12
Population Modelling

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The Matrix Population Models Workflow provides an environment to perform several analyses on a stage-matrix with no density dependence:
- Eigen analysis;
- Age specific survival;
- Generation time (T);
- Net reproductive rate (Ro);
- Transient Dynamics;
- Bootstrap of observed census transitions
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Uploaded 14 Aug 2014 18:48:32 UTC

Taverna_logo Matrix Population Model construction and analysis v20
Population Modelling

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The Matrix Population Models Workflow provides an environment to create stage-matrices with no density dependence and to perform several analyses on them:
- Eigen analysis;
- Age specific survival;
- Generation time (T);
- Net reproductive rate (Ro);
- Transient Dynamics;
- Bootstrap of observed
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Uploaded 14 Aug 2014 18:23:11 UTC

Taverna_logo Mean matrix
Population Modelling

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This 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
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Uploaded 21 Aug 2014 18:09:14 UTC

Taverna_logo Net reproductive rate (Ro)
Population Modelling

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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)

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Uploaded 21 Aug 2014 15:50:35 UTC

Taverna_logo Parametric Bootstrap or Resample a projection matrix Workflow
Population Modelling

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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
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Uploaded 21 Aug 2014 15:52:22 UTC

Taverna_logo Resident killer whale-chinook salmon interactions
Population Modelling

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The resident killer whale-chinook salmon interactions workflow provides an environment to calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences
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Uploaded 26 Sep 2014 08:15:52 UTC

Taverna_logo Simulate stochastic growth from a sequence of matrices
Population Modelling

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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
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Uploaded 21 Aug 2014 17:53:59 UTC

Taverna_logo Stages vectors plots, Survival and Growth rate curves
Population Modelling

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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;
-
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Uploaded 21 Aug 2014 15:58:26 UTC

Taverna_logo Transient Dynamics.
Population Modelling

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This workflow produces plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.

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This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/)
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Uploaded 21 Aug 2014 15:55:12 UTC

Taverna_logo Variance matrix
Population Modelling

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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
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Uploaded 28 Aug 2014 16:53:22 UTC
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BioVeL has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 283359.

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