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

Effectiveness of a small marine reserve in southern California

While relatively small, the San Diego-La Jolla Ecological Reserve is one of the oldest in California, and it contains giant-kelp-forest, boulder-reef, submarine-canyon and sandy-shelf habitats. We evaluated the effectiveness of this 'no-take' marine reserve and gauged its success according to the goals implicit in its design. To overcome the lack of data prior to its establishment, we employed habitat-specific analyses. Our study comprised 4 components: (1) an historical review of its establishment; (2) a survey of conspicuous species in kelp-forest, submarine-canyon, and boulder-reef habitats; (3) comparisons with historical data; (4) a public survey regarding awareness, knowledge, and support of the reserve. Despite 30 yr of protection, only a few sessile or residential species exhibit positive effects of protection, and most fished species have decreased in abundance inside the reserve. However, the reserve protects the largest remaining populations of green abalone Haliotis fulgens and vermillion rockfish Sebastes miniatus in the area, which therefore represent important sources of larvae. Implementation and enforcement of coastal reserves depends on public support, but the results of the public survey indicated a lack of knowledge of the reserve, highlighting the need for improved public education in this respect. The results of the study reflect the limited value of small reserves and document the inadequacy of inside/outside comparisons as tests of reserve effectiveness when baseline and historical data are lacking

Incorporating covariates into standard line transect analyses

Summary. An implicit assumption of standard line transect methodology is that detection probabilities depend solely on the perpendicular distance of detected objects to the transect line. Heterogeneity in detection probabilities is commonly minimized using stratification,but this may be precluded by small sample sizes. We develop a general methodology which allows the effects of multiple covariates to be directly incorporated into the estimation procedure using a conditional likelihood approach. Small sample size properties of estimators are examined via simulations. As an example the method is applied to eastern tropical Pacific dolphin sightings data

Purse-seine vessels as platforms for monitoring the population status of dolphin species in the eastern tropical Pacific Ocean:the use of fishing vessels as scientific platforms

In the eastern tropical Pacific Ocean, yellowfin tuna (Thunnus albacares) are often found in association with spotted (Stenella attenuata) and spinner (Stenella longirostris) dolphins. Purse-seine vessels use this co-occurrence to locate the tuna by searching for dolphins and associated birds. Data collected by onboard observers since the late 1970s were used to develop indices of relative abundance for dolphins, based on line-transect methodology, when the primary method of detection of dolphin herds was with binoculars. However, trend estimation was subsequently discontinued in 2000 due to concerns about changes in reporting rates of dolphin herd detections with increased use of helicopter and radar search. At present, as a result of a hiatus in fishery-independent surveys since 2006, fisheries observer data are the only source of information with which to monitor the status of eastern tropical Pacific Ocean dolphin populations. In this paper, trend estimation with the onboard observer data is revisited using a sightings-per-unit-effort approach. Despite different assumptions and model structure, the results indicate a lack of independence between the distribution of search effort and the search methods used, and the abundance of dolphin herds associated with tunas, on several spatial and temporal scales. This lack of independence poses a considerable challenge to the development of a reliable index of relative abundance for dolphins with these data. Given these results, alternatives for dolphin abundance estimation are discussed. One alternative is the use of purse-seine vessels for line-transect surveys during fishery closure periods. Another alternative is the use of purse-seine vessels during normal fishing operations as platforms for the collection of mark-recapture data (e.g., passive integrated transponder tags or genetics sampling). Life-history data collection, as a supplement to the collection of other data types, is also discussed. Further research and development is needed to assess whether these alternative methods will be useful

Purse-seine vessels as platforms for monitoring the population status of dolphin species in the eastern tropical Pacific Ocean : the use of fishing vessels as scientific platforms

In the eastern tropical Pacific Ocean, yellowfin tuna (Thunnus albacares) are often found in association with spotted (Stenella attenuata) and spinner (Stenella longirostris) dolphins. Purse-seine vessels use this co-occurrence to locate the tuna by searching for dolphins and associated birds. Data collected by onboard observers since the late 1970s were used to develop indices of relative abundance for dolphins, based on line-transect methodology, when the primary method of detection of dolphin herds was with binoculars. However, trend estimation was subsequently discontinued in 2000 due to concerns about changes in reporting rates of dolphin herd detections with increased use of helicopter and radar search. At present, as a result of a hiatus in fishery-independent surveys since 2006, fisheries observer data are the only source of information with which to monitor the status of eastern tropical Pacific Ocean dolphin populations. In this paper, trend estimation with the onboard observer data is revisited using a sightings-per-unit-effort approach. Despite different assumptions and model structure, the results indicate a lack of independence between the distribution of search effort and the search methods used, and the abundance of dolphin herds associated with tunas, on several spatial and temporal scales. This lack of independence poses a considerable challenge to the development of a reliable index of relative abundance for dolphins with these data. Given these results, alternatives for dolphin abundance estimation are discussed. One alternative is the use of purse-seine vessels for line-transect surveys during fishery closure periods. Another alternative is the use of purse-seine vessels during normal fishing operations as platforms for the collection of mark-recapture data (e.g., passive integrated transponder tags or genetics sampling). Life-history data collection, as a supplement to the collection of other data types, is also discussed. Further research and development is needed to assess whether these alternative methods will be useful.PostprintPeer reviewe