Estimating and Analyzing Demographic Models Using the<b>popbio</b>Package in<i>R</i>

Stubben, Chris; Milligan, Brook G.

doi:10.18637/jss.v022.i11

Cited by 596 publications

(501 citation statements)

References 18 publications

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“…To test the demographic sensitivity and elasticity of the current wild populations we used the 'popbio' package in Program R (Stubben and Milligan 2007). We applied the sensitivity and elasticity functions in the 'popbio' package to the deterministic projection matrix for the Base Model.…”

Section: Testing Demographic Sensitivitymentioning

confidence: 99%

Extinction Risk and Conservation Options for Maui Parrotbill, an Endangered Hawaiian Honeycreeper

Mounce

Warren

McGowan

et al. 2018

Journal of Fish and Wildlife Management

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Extinction rates for island birds around the world have been historically high. For forest passerines, the Hawaiian archipelago has suffered some of the highest extinction rates and reintroduction is a conservation tool that can be used to prevent the extinction of some of the remaining endangered species. Population viability analyses can be used to assess risks to vulnerable populations and evaluate the relative benefits of conservation strategies. Here we present a population viability analysis to assess the long-term viability for Maui parrotbill (Kiwikiu) Pseudonestor xanthophrys, a federally endangered passerine on the Hawaiian island of Maui. Contrary to indications from population monitoring, our results indicate Maui parrotbills may be unlikely to persist beyond 25 y. Our modeling suggests female mortality as a primary factor driving this decline. To evaluate and compare management options involving captive-rearing and translocation strategies we made a female-only stage-structured, meta-population simulation model. Maui parrotbills have low reproductive potential in captivity; therefore, the number of individuals (~20% of the global population) needed to source a reintroduction solely from captive reared birds is unrealistic. A reintroduction strategy that incorporates a minimal contribution from captivity and instead translocates mostly wild individuals was found to be the most feasible management option. Habitat is being restored on leeward east Maui, which may provide more favorable climate and habitat conditions and promote increased reproductive output. Our model provides managers with benchmarks for fecundity and survival needed to ensure reintroduction success, and highlights the importance of establishing a new population in potentially favorable habitat to ensure long-term persistence.

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Section: Testing Demographic Sensitivitymentioning

confidence: 99%

Extinction Risk and Conservation Options for Maui Parrotbill, an Endangered Hawaiian Honeycreeper

Mounce

Warren

McGowan

et al. 2018

Journal of Fish and Wildlife Management

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“…vital rate) on the population growth rate (Caswell, 2001). Matrix population models were analyzed using the package popbio (Stubben and Milligan, 2007) for program R (R Development Core Team, 2011). All results obtained from survival, fecundity and population modeling are given as mean ± standard error, unless otherwise indicated.…”

Section: Population Modelingmentioning

confidence: 99%

Habitat- and density-dependent demography of a colonial raptor in Mediterranean agro-ecosystems

Maggio

Campobello

Tavecchia

et al. 2016

Biological Conservation

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“…We used a mark-recapture population estimate of 94 individuals from the Aspen study (P.M. Lukacs, Colorado Parks and Wildlife, Personal Communication) to set the initial stage densities for the three older stage classes and calculated the number of cubs so that each simulation began at a stable stage distribution (SSD). We used the R package popbio version 2.4 (Stubben and Milligan, 2007) to calculate a SSD for each scenario determined from the eigen-vector associated with the dominate eigen-value of a projection matrix populated with good year vital rate means. Natural food failures in Aspen are often attributed to late spring freezes, so we used 30 years of minimum daily temperatures during the month of June and assumed temperatures below −2.2 • C caused a failure of the main natural food sources (Neilson and Wullstein, 1980;Pierre, 1989).…”

Section: Simulation: 50-year Projectionsmentioning

confidence: 99%

Modeling black bear population dynamics in a human-dominated stochastic environment

Lewis

Breck

Wilson

et al. 2014

Ecological Modelling

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a b s t r a c tMany large carnivore populations exist in human-influenced stochastic environments where availability of natural food sources vary annually and anthropogenic food sources can supplement energetic demands, but at a potential demographic cost due to human-wildlife conflict and subsequent conflict management. Understanding how these competing factors influence a population is complex and difficult to study, but here we demonstrate the utility of using a stochastic projection matrix model and perturbation analysis to gain insight into this problem. We modeled a black bear population subjected to stochastic failures of fruiting and masting species, but with access to garbage in urban environments. We parameratized our model with data from a 6-year study on black bears in Aspen, Colorado and data synthesized from other research studies. Using computer simulation, we investigated the effect that different levels of conflict-bear removal can have on a bear population by comparing a "reference" scenario where bears did not benefit from human food sources or experience conflict-bear removals with two urban scenarios where bears had varying access to human foods, but conflict bears were removed. We used perturbation analyses to evaluate consequences for changing population vital rates and to estimate the impact each vital rate change had on population growth. Simulations were used to identify how much variation in each vital rate influenced variation in the population growth rate. We identified the survival rate of breeding adult females during good natural food years as having the highest elasticity value. We found that the benefit of increased cub production from available human food sources during natural food failure years was quickly negated if management of conflict bears through removal reduced adult female survival. Increasing the frequency of years when natural food production fails resulted in disproportionate impacts from available urban food and conflict-bear removals, where population growth rates in a High Removal scenario declined 1.5 times faster than in the reference scenario. Our findings suggest that for regions where changing climates will increase the frequency of natural food failures, managers may need to utilize non-lethal practices in managing conflict bears and municipalities will need to secure human food sources to reduce the need for conflict-bear removals and potential population declines.

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Estimating and Analyzing Demographic Models Using thepopbioPackage inR

Cited by 596 publications

References 18 publications

Extinction Risk and Conservation Options for Maui Parrotbill, an Endangered Hawaiian Honeycreeper

Extinction Risk and Conservation Options for Maui Parrotbill, an Endangered Hawaiian Honeycreeper

Habitat- and density-dependent demography of a colonial raptor in Mediterranean agro-ecosystems

Modeling black bear population dynamics in a human-dominated stochastic environment

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