Pack: Calculate quasiextinction threshold pack
Title: Calculate quasiextinction threshold pack
Description
This pack contains a workflow, a file and documentation (tutorial to run the workflow).
This workflow estimates by simulation the quasiextinction 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 quasiextinction 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 quesiextinction threshold by time t, method: simulating extinction probabilities (; Morris and Doak 2002, pag: 241244 and Caswell 2001, pag: 443444).
This models do not permit extinction, however we can study quasiextinction (Caswell 2001). A population is quasiextinct if it shrinks to a specific fraction of its current size (Ginsbur et al 1982 in Caswell 2001). The quasiextinction threshold can be chosen in the belief that it would pose a significant threat of the real exaction (Caswell 2001).
METHOD: SIMULATING EXTINCTION PROBABILITIES Keep track of whether the total population density (or the density summed across a subset of the classes with which we are particularly concerned, such as the reproductive classes) has fallen below the quasiextinction threshold each year. The fraction of realizations that first hit the threshold during or before year t gives the cumulative probability of extinction (Morris and Doak 2002). This tutorial performs such a calculation using the Gentiana matrices (See setion 5.2 Input data).
Items (8)

Workflow: Calculate quasiextinction threshold. (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140814 11:53:50)

File: Calculate the quasiextinction probability documentation (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140814 12:05:20)

File: Matrix Terschelling 8788 (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140730 14:20:23)

File: Matrix Terschelling 8889 (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140730 14:20:12)

File: Matrix Terschelling 8990 (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140730 14:20:04)

File: Matrix Terschelling 9091 (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140730 14:19:46)

File: Matrix Terschelling 9192 (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140730 14:19:37)

File: Matrix Terschelling 9293 (Maria Paula BalcazarVargas)
Added by Maria Paula BalcazarVargas ... more than 1 year ago (20140730 14:19:28)
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Tags from Items (20)
 analysis
 
 biovel
 
 cumulative distribution function (cdf)
 
 demography
 
 environment
 
 gentiana pneumonanthe
 
 gerard oostermeijer
 
 life table response experiments
 
 life table response experiments (ltre)
 
 matrix
 
 matrix population models
 
 morris and doak 2002.
 
 package ‘popbio’ in r
 
 population viability analysis (pva)
 
 probability of quasiextinction threshold by time t
 
 retrospective analysis.
 
 simulating extinction probabilities
 
 stage matrix
 
 stochastic environment
 
 threshold
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