Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS

Summary: 1. Ecologists often use nonlinear fitting techniques to estimate the parameters of complex ecological models, with attendant frustration. This paper compares three open-source model fitting tools and discusses general strategies for defining and fitting models. 2. R is convenient and (relatively) easy to learn, AD Model Builder is fast and robust but comes with a steep learning curve, while BUGS provides the greatest flexibility at the price of speed. 3. Our model-fitting suggestions range from general cultural advice (where possible, use the tools and models that are most common in your subfield) to specific suggestions about how to change the mathematical description of models to make them more amenable to parameter estimation. 4. A companion web site (https://groups.nceas.ucsb.edu/nonlinear-modeling/projects) presents detailed examples of application of the three tools to a variety of typical ecological estimation problems; each example links both to a detailed project report and to full source code and data

A simple model to quantitatively account for periodic outbreaks of the measles in the Dutch Bible Belt

In the Netherlands there has been nationwide vaccination against the measles since 1976. However, in small clustered communities of orthodox Protestants there is widespread refusal of the vaccine. After 1976, three large outbreaks with about 3000 reported cases of the measles have occurred among these orthodox Protestants. The outbreaks appear to occur about every twelve years. We show how a simple Kermack-McKendrick-like model can quantitatively account for the periodic outbreaks. Approximate analytic formulae to connect the period, size, and outbreak duration are derived. With an enhanced model we take the latency period in account. We also expand the model to follow how different age groups are affected. Like other researchers using other methods, we conclude that large scale underreporting of the disease must occur

Global extent and drivers of mammal population declines in protected areas under illegal hunting pressure

Illegal hunting is a persistent problem in many protected areas, but an overview of the extent of this problem and its impact on wildlife is lacking. We reviewed 40 years (1980–2020) of global research to examine the spatial distribution of research and socio-ecological factors influencing population decline within protected areas under illegal hunting pressure. From 81 papers reporting 988 species/site combinations, 294 mammal species were reported to have been illegally hunted from 155 protected areas across 48 countries. Research in illegal hunting has increased substantially during the review period and showed biases towards strictly protected areas and the African continent. Population declines were most frequent in countries with a low human development index, particularly in strict protected areas and for species with a body mass over 100 kg. Our results provide evidence that illegal hunting is most likely to cause declines of large-bodied species in protected areas of resource-poor countries regardless of protected area conservation status. Given the growing pressures of illegal hunting, increased investments in people’s development and additional conservation efforts such as improving anti-poaching strategies and conservation resources in terms of improving funding and personnel directed at this problem are a growing priority

Population dynamics of measles epidemics in developed countries

SIGLEAvailable from British Library Document Supply Centre-DSC:D063412 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Effects of colonization asymmetries on metapopulation persistence.

Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical models (the island, the stepping stone and the distance-dependent model), we explore how metapopulation persistence is affected by (i) asymmetry in dispersal strength, in which the colonization rate between two patches differs in direction, and (ii) asymmetry in connectivity, in which the overall colonization pattern displays asymmetry (circulating or dendritic networks). Viability can be drastically reduced when directional bias in dispersal strength is higher than 25%. Re-colonization patterns that allow for strong local connectivity provide the highest persistence compared to systems that allow circulation. Finally, asymmetry has relatively weak effects when metapopulations maintain strong general connectivity

Time is of the essence: exploring a measles outbreak response vaccination in Niamey, Niger.

The current World Health Organization recommendations for response during measles epidemics focus on case management rather than outbreak response vaccination (ORV) campaigns, which may occur too late to impact morbidity and mortality and have a high cost per case prevented. Here, we explore the potential impact of an ORV campaign conducted during the 2003-2004 measles epidemic in Niamey, Niger. We measured the impact of this intervention and also the potential impact of alternative strategies. Using a unique geographical, epidemiologic and demographic dataset collected during the epidemic, we developed an individual-based simulation model. We estimate that a median of 7.6% [4.9-8.9] of cases were potentially averted as a result of the outbreak response, which vaccinated approximately 57% (84563 of an estimated 148600) of children in the target age range (6-59 months), 23 weeks after the epidemic started. We found that intervening early (up to 60 days after the start of the epidemic) and expanding the age range to all children aged 6 months to 15 years may lead to a much larger (up to 90%) reduction in the number of cases in a West African urban setting like Niamey. Our results suggest that intervening earlier even with lower target coverage (approx. 60%), but a wider age range, may be more effective than intervening later with high coverage (more than 90%) in similar settings. This has important implications for the implementation of reactive vaccination interventions as they can be highly effective if the response is fast with respect to the spread of the epidemic