PROFILE: I am a Biologist with a PhD in Ecology and Biodiversity (2013) with a great passion for animals and plants, and 24 years (1996 -2020) of vast experience in botany, taxonomy, ethnobotany, demography, conservation and advising students. I have a strong modelling and organisational skills gained in research.

Other contact details:

Not specified

Interests:

Matrix population models and Integral projection models

Field/Industry: Academy

Occupation/Role(s): Post-doc

Organisation(s):

University of Amsterdam

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Killer whale demography documentation

Created: 2014-09-26 12:19:25

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Killer whale demography

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation contains the tutorial to run the Killer whale demography workflows. This tutorial explains the type of input data needed to run the workflow. The corresponding analysis use data from two distinct O. orca populations in Canada, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW). The Killer whale demography workflow performs the following analyses: • Vital rates estimation and probability dis...

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animals
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biovel
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birth-flow matrix model
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census
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damping time
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demography
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eigen analysis
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elasticity analysis (deterministic and stochastic)
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fisheries and oceans of canada. bc. canada (nanaimo).
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vital rates estimation and probability distributions

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Resident killer whale-chinook salmon interactions an...

Created: 2014-09-26 12:09:28 | Last updated: 2014-09-26 12:11:12

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Exploration of fishing scenarios Resident killer whale-chinook salmon interactions

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation contains the tutorial to run two related workflows. 1. Resident killer whale-chinook salmon interactions workflow The Resident killer whale-chinook salmon interactions workflow provides an environment to create 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 in demographic rates be...

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Orcinus orca (Killer whale) demography and populatio...

Created: 2014-08-29 12:21:35 | Last updated: 2014-08-29 16:23:18

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Jon Giddy

Attributions:

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 Normal 0 false false false EN-US X-NONE X-NONE ...

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Elasticity and Sensitivity of the Vital rates docume...

Created: 2014-08-29 14:49:44 | Last updated: 2014-08-29 14:50:15

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Elasticity and Sensitivity of the Vital rates

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.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 rate(s) has/have the most influence on population growth rate (λ).Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses.The sensitivity matrix: The sensitivity desc...

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Pooled_matrix_file_Gentiana_LTRE

Created: 2014-03-27 10:37:46 | Last updated: 2014-08-29 13:23:06

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pooled_matrix_file or weighted main Matrix - what popbio (R package) calls pooled matrix (to see more details: Horvitz, Schemske and Caswell 1997; Horvitz, and Schemske 1995). This is a matrix in a .txt format, all decimal numbers in each matrix must be indicated by dots e.g.: 0.578.To understand how to calculate a pooled matrix or a weighted main Matrix, please see: Choice of a reference matrix (pag: 253, in Horvitz, Schemske and Caswell 1997). This list of matrices will be used to perf...

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Demographic data Gentiana pneumonanthe 1987-1988 fro...

Created: 2012-11-05 09:47:37 | Last updated: 2013-08-13 12:06:34

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

Attributions: Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population 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...

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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

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates the variance matrix from a list of matrices.

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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

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates the mean matrix from a list of matrices.

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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

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow calculate and plot the survival based on two or more years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population.

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Decomposed matrix of Gentiana pneumonanthe

Created: 2014-08-28 11:28:44

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file (decomposed matrix) is used in the documentation as example to run the Elsticity and Sensitivity of the Vital rates Workflow.

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Demographic data Gentiana pneumonanthe 1987-1993

Created: 2014-08-22 12:01:38

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of 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 Calculate and Plot abundance over the years (http://www.myexperiment.org/packs/664.html)This table containing the demographic data on a series of individuals during 7 years, from 1987 to 1993 (6 periods: 1987-1988, 1988-1989 etc....

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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

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.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).

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analysis
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biovel
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demography
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gentiana pneumonanthe
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log-log plot cv vs. elasticity in matrix elements
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log-log plot of variance vs. sensitivity
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matrix
|
matrix population models
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package ‘popbio’ in r
|
stage matrix

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Life Table Response Experiments Fixed design year ef...

Created: 2014-08-21 08:05:38

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

Attributions: Life Table Response Experiment year effect for multiple places

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 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 research years (2 or more) on λ. This workflow performs a fixed LTRE, o...

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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

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.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 MATLAB cod...

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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
|
stochastic environment

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Life Table Response Experiments Fixed design years e...

Created: 2014-08-14 08:44:30 | Last updated: 2014-08-14 08:45:27

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

Attributions: Life Table Response Experiment Year Effect in One Location or Place

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 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 a fixed LTRE, one way design (Caswell 2001).LTRE is a retrospectiv...

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Life Table Response Experiments Fixed design Place e...

Created: 2014-08-14 08:03:58

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

Attributions: Life Table Response Experiment fixed design Place Effect

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 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) on λ. This workflow performs a fixed LTRE, one way design (Caswell ...

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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

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.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 detail...

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biovel
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demography
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gentiana pneumonanthe
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histogram
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independently and identically distributed (iid)
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matrix
|
matrix population models
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package ‘popbio’ in r
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population projection
|
projection
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stage matrix
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stochastic environment
|
stochastic projection

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Stage vectors, Survival and Growth rate curves (demo...

Created: 2014-07-25 12:41:06

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

Attributions: Stages vectors plots, Survival and Growth rate curves

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 Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:Population projectionSurvival 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.

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Transient dynamics documentation

Created: 2014-07-25 12:16:46

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

Attributions: Transient Dynamics.

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 Transient dynamics or Calculate population growth rates by projection Workflow provides an environment to calculates the population growth rate and stable stage distribution by repeated projections of the equation n(t+1)=An(t) and to produce plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.Transient dynamic ana...

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Net reproductive rate (Ro) documentation

Created: 2014-07-25 11:25:19

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Net reproductive rate (Ro)

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 Net reproductive rate (Ro) Workflow provides an environment to calculate the net reproductive rate (Ro). Ro is the mean number of offspring by which a new-born 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.

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Generation Time (T) documentation

Created: 2014-07-25 11:22:18

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Generation time (T)

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 Generation Time (T) Workflow provides an environment to calculate the generation time. The generation time is the time T required for the population to increase by a factor of Ro (net reproductive rate). In other words, T calculates how much time takes to a plant/animal to replace itself by a factor of Ro.

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Eigen analysis documentation

Created: 2014-07-25 11:18:44

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Eigen 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 same name.The Eigen analysis workflow provides an environment for the analysis of a stage-matrix and perform several analyses on it.The Eigen analysis results are a set of demographic statistics:Lambda or dominant eigenvalue (λ).The stable stage distribution (w).The sensitivity matrixThe Elasticity matrix.Reproductive value (v).The damping ratio (ρ)

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Damping ratio documentation

Created: 2014-07-25 11:07:01

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Damping ratio

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 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 populati...

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Matrix population models construction documentation

Created: 2014-07-25 11:02:01

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run a workflow) explains how to run a workflow that beolngs to the pack with the same name.The Creation of a stage matrix model Workflow provides an environment to construct a stage matrix model. This workflow create a stage matrix based on two years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population. The resulting is a stage matrix model.

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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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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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Tags:

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

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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
|
bootstrap of observed census transitions
|
confidence interval of lambda
|
demography
|
gentiana pneumonanthe
|
histogram
|
lambda or dominant eigenvalue
|
matrix
|
matrix population models
|
model
|
package ‘popbio’ in r
|
population
|
population projection
|
projection
|
stage matrix

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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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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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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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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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Demographic data Gentiana pneumonanthe 1987-1991 fr...

Created: 2012-11-02 12:37:19 | Last updated: 2014-07-04 12:31:17

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

Attributions: Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Matrix Population Model construction and analysis v20

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This is a .txt file of four years 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 analysis v...

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Integral Projection Model documentation

Created: 2013-08-13 13:22:56 | Last updated: 2014-07-04 12:20:25

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Integral Projection Model for Demographic Modelling v34 Demographic data Cryptantha flava

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 Integral Projection Model Workflow provides an environment for create an integral projection model and to calculate its population growth, structure, sensitivities and elasticities analyses, age-specific metrics, etc.Create an IPM with no density dependence and perform several analyses on it.Analyses:Lambda (λ).Sensitivity analysis.Elasticity analysis.Parameters ...

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Matrix Terschelling pooled data or weighted main matrix

Created: 2014-03-28 14:38:43

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix 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: Life Table Response Experiments (LTRE)_Year Effect One Location V1 (http://www.myexperiment.org/packs/590.html)If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 19...

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Matrix Terschelling 92-93

Created: 2014-03-28 14:31:44

Credits: Maria Paula Balcazar-Vargas

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Matrix Terschelling 91-92

Created: 2014-03-28 14:30:15

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

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Matrix Terschelling 90-91

Created: 2014-03-28 14:24:33

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

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Matrix Terschelling 87-88

Created: 2014-03-28 14:22:32

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

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Stage Matrix of Gentiana pneumonanthe 1987-88

Created: 2013-08-13 12:17:28

Credits: Maria Paula Balcazar-Vargas Gerard Oostermeijer

Attributions: Matrix Population Model analysis v12

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of a stage matrix 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 Matrix Population Model analysis v10 (http://www.myexperiment.org/workflows/3686.html) If you use the file please quote as:Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 1996. Temporal and Spatial Varia...

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Matrix Population Modelling documentation

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

Credits: Jon Giddy Maria Paula Balcazar-Vargas 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.

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Demographic data Gentiana pneumonanthe 1987-1988 fro...

Created: 2012-11-02 10:59:24 | Last updated: 2012-11-07 08:56:00

Credits: Jon Giddy Maria Paula Balcazar-Vargas Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Small example file to allow users to run population modelling workflow

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Maria Paula Balcazar-Vargas

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Exploration of fishing scenarios (1)

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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 Exploration of fishing scenario (post-processing) workflow. This workflow merges statistical inference derived from linkages between RKW vital rates (survival probability and fecundity rates) a...

Created: 2014-09-26

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Resident killer whale-chinook salmon interactions

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Maria Paula Balcazar-Vargas

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Resident killer whale-chinook salmon inter... (1)

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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 in demographic rates between killer whale (Orcinus orca) population that explain population growth; (ii) to determine the relative influence of vital rates and Chinook (Oncorhynchus tshawytsc...

Created: 2014-09-26

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Killer whale demography

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Maria Paula Balcazar-Vargas

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Killer whale demography (1)

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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 other killer whale populations or cetaceans counting with census data and life cycles that can be represented using the matrix models described in this document. This workflow perform the follow...

Created: 2014-09-24

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

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Maria Paula Balcazar-Vargas

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Elasticity and Sensitivity of the Vital rates (1)

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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 (?). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses. a) The sensitivity matrix: The sensitivity describes the effect on ? of changes in vital rates of the matrix. The derivative tells what would happened to ? if aij was to c...

Created: 2014-08-29

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

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Maria Paula Balcazar-Vargas

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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

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Maria Paula Balcazar-Vargas

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Cohen’s cumulative distance (1)

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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. It is a function of both the observed stage distribution (n0) and the structure of the matrix (A) (Williams et al 2011). Cohen’s cumulative distance will not work for reducible matrices or imprimiti...

Created: 2014-07-23

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model analysis v12 Matrix Population Model construction and analysis v20

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Maria Paula Balcazar-Vargas

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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

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Maria Paula Balcazar-Vargas

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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

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Maria Paula Balcazar-Vargas

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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

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Maria Paula Balcazar-Vargas

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Life Table Response Experiment year effect... (1)

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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 research years (2 or more) on ?. This workflow performs a fixed LTRE, one way design (Caswell 2001). LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on ?...

Created: 2014-08-21

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

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Maria Paula Balcazar-Vargas

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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

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Maria Paula Balcazar-Vargas

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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

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Maria Paula Balcazar-Vargas

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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

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Maria Paula Balcazar-Vargas

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Life Table Response Experiment Year Effect... (1)

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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 ?. This workflow performs a fixed LTRE, one way design (Caswell 2001). LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on ? under two or more sets of environmental conditions...

Created: 2014-08-14

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

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Maria Paula Balcazar-Vargas

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Life Table Response Experiment fixed desig... (1)

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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) on ?. This workflow performs a fixed LTRE, one way design (Caswell 2001). LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on ? under two or more set...

Created: 2014-08-13

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

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Maria Paula Balcazar-Vargas

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Keyfitz delta (1)

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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). The maximum value is 1 and the minimum value is 0 (when the vectors are identical). ============================================================ This workflow has been created by the Biodiversit...

Created: 2014-07-23

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model analysis v12 Matrix Population Model construction and analysis v20

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Taverna 2

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Maria Paula Balcazar-Vargas

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Parametric Bootstrap or Resample a project... (3)

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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 surveyed. The projection matrix A is first split into separate transition and fertility matrices. Dead fates are added to the transition matrix and the columns are then sampled from a Multinomial dis...

Created: 2014-06-18 | Last updated: 2014-07-25

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model analysis v12

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Taverna 2

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Maria Paula Balcazar-Vargas

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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: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model construction and analysis v20 Stage Matrix of Gentiana pneumonanthe 1987-88

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Maria Paula Balcazar-Vargas

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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

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Biodiversity eLaboratory

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Matrix Population Model construction and a... (2)

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This workflow is deprecated. To obtain a more recent version of this workflow, please refer to: http://www.myexperiment.org/packs/483.html For historic access to this workflow, please view an earlier version.

Created: 2012-11-02 | Last updated: 2014-09-17

Credits: Jon Giddy Maria Paula Balcazar-Vargas Gerard Oostermeijer

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Biodiversity eLaboratory

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Matrix Population Model construction and a... (3)

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Created: 2012-11-02 | Last updated: 2014-09-17

Credits: Jon Giddy Gerard Oostermeijer Maria Paula Balcazar-Vargas

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Maria Paula Balcazar-Vargas

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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: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model construction and analysis v20 Matrix Population Model analysis v12 Stage Matrix of Gentiana pneumonanthe 1987-88

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Taverna 2

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Maria Paula Balcazar-Vargas

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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: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model construction and analysis v20 Matrix Population Model analysis v12 Stage Matrix of Gentiana pneumonanthe 1987-88

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Maria Paula Balcazar-Vargas

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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: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model construction and analysis v20 Matrix Population Model analysis v12 Stage Matrix of Gentiana pneumonanthe 1987-88

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Taverna 2

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Maria Paula Balcazar-Vargas

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Eigen analysis (3)

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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: ? = 1 (population is stable), ? > 1 (population is growing) and finally ? < 1 (populatiopn is decreasing) . 2) The stable stage distribution: It is the proportion of the number of individuals per stage and it is given by (w). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses....

Created: 2012-11-02 | Last updated: 2014-07-25

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model construction and analysis v20 Matrix Population Model analysis v12 Stage Matrix of Gentiana pneumonanthe 1987-88

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Taverna 2

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Maria Paula Balcazar-Vargas

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Creation of a stage matrix model from demo... (2)

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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 workflow converts this data into a stage matrix model from 1 year to 2 that contains transitions probabilities from each stage to the next. This workflow has been created by the Biodiversity Virtual...

Created: 2012-11-01 | Last updated: 2014-07-25

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model construction and analysis v20 Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

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Taverna 2

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Maria Paula Balcazar-Vargas

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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: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model construction and analysis v20 Matrix Population Model analysis v12 Stage Matrix of Gentiana pneumonanthe 1987-88

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Taverna 2

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Maria Paula Balcazar-Vargas

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Matrix Population Model construction and a... (3)

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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 census transitions (Confidence intervals of lambda); - Survival curve; - Keyfitz delta; - Cohen's cumulative distance. If multiple year transitions are selected, the results will be ordered by year. ...

Created: 2013-08-13 | Last updated: 2014-07-04

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Matrix Population Model construction and analysis Eigen analysis Age specific analysis Transient Dynamics. Generation time (T) Net reproductive rate (Ro) Bootstrap of observed census transitions. Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

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Taverna 2

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Maria Paula Balcazar-Vargas

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Integral Projection Model for Demographic ... (1)

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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 census time t with the following column names: size: size of individuals in census time t sizeNext: size of individuals in census time t +1 surv: survival of individuals from census time t to t...

Created: 2013-08-13

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

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Taverna 2

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Maria Paula Balcazar-Vargas

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Matrix Population Model analysis v12 (2)

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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 (Confidence intervals of lambda); - Survival curve; - Keyfitz delta; - Cohen's cumulative distance. This workflow requires an instance of Rserve on localhost This workflow has been created by the Bi...

Created: 2013-08-13 | Last updated: 2014-07-09

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Eigen analysis Age specific analysis Transient Dynamics. Generation time (T) Net reproductive rate (Ro) Demographic data Gentiana pneumonanthe 1987-1988 from Terschelling File.

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