Data from: Accounting for uncertainty in dormant life stages in stochastic demographic models

Paniw M, Quintana-Ascencio PF, Ojeda F, Salguero-Gómez R

Date Published: October 11, 2016

DOI: http://dx.doi.org/10.5061/dryad.rq7t3

 

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Title dataDroso - census data
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Description Demographic transitions of Drosophyllum lusitanicum populations recorded in annual censuses (from 2011 to 2015) in five populations. These data are used to quantify vital rates of above-ground individuals.
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Title dataDrosoSB - seed bank
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Description Seed fates (in a binary format) inferred from two experiments. These data are used to quantify the transitions related to the seed bank and associated parameter uncertainties.
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Title BayModel - Bayesian vital rate GLMMs
Downloaded 10 times
Description Executes and saves the results of a Bayesian model quantifying all vital rates; illustrates basic diagnostics that can be run on the results of an MCMC run (i.e., the posterior parameter distribution) to check for model convergence and autocorrelation of the posterior samples.
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Title mcmcOUT - parameter samples
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Description In case the reader wishes to forego the step of fitting the Bayesian models, we provided a mcmcOUT.csv file with 1000 posterior parameter values for each of the parameters estimated with Bayesian models using uninformative priors
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Title makeIPM
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Description Demonstrates how to construct IPMs including continuous and discrete (seed bank) transitions for (A) mean parameter values and (B) from the parameter distributions of the Bayesian models; saves IPMs for all parameters related to seed-bank ingression, stasis, and ingression. The code is based on the supporting material in Ellner and Rees (2006), Am. Nat., 167, 410-428
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Title perturbVR - vital rate perturbations
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Description Demonstrates how to construct IPMs from perturbed vital rates. Each IPM is obtained by (a) perturbing a vital rate by its mean or standard deviation (see makeVRmu.R on constructing mean vital-rate kernels) and (b) constructing a new IPM kernel incorporating the perturbed vital rate
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Title makeIPMmu
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Description function to constructs IPMs for average environments
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Title makeVRmu
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Description functions to constructs vital-rate kernels for average environments.
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Title sLambdaSimul - stochastic lambda simulations
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Description Runs simulations, based on different fire return intervals, of the stochastic population growth rate using IPMs constructed (A) from mean parameter values, (B) from perturbed vital rates, and (C) for each posterior sample of the parameters describing seed-bank ingression (goSB), stasis (staySB) and egression (outSB); calculates the stochastic population growth rate, its elasticities, and the probability of quasi-extinction at time t. The structure of the code is based on Tuljapurkar et al. (2003), Am. Nat., 162, 489-502 and Trotter et al. (2013), Methods Ecol. Evol., 4, 290-298.
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Title sLambdaRmpi - stochastic simulations on parallel processors
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Description Implements the simulations of the stochastic population growth rate using parallel processing, where simulations are split into different processors of a supercomputer to greatly speed up computational time.
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When using this data, please cite the original publication:

Paniw M, Quintana-Ascencio PF, Ojeda F, Salguero-Gómez R (2017) Accounting for uncertainty in dormant life stages in stochastic demographic models. Oikos 126(6): 900-909. http://dx.doi.org/10.1111/oik.03696

Additionally, please cite the Dryad data package:

Paniw M, Quintana-Ascencio PF, Ojeda F, Salguero-Gómez R (2016) Data from: Accounting for uncertainty in dormant life stages in stochastic demographic models. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.rq7t3
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