Standardizing catch and effort data: a review of recent approaches

We discuss a method for analyzing data that are positively skewed and contain a substantial proportion of zeros. Such data commonly arise in ecological applications, when the focus is on the abundance of a species. The form of the distribution is then due to the patchy nature of the environment and/or the inherent heterogeneity of the species. The method can be used whenever we wish to model the data as a response variable in terms of one or more explanatory variables. The analysis consists of three stages. The first involves creating two sets of data from the original: one shows whether or not the species is present; the other indicates the logarithm of the abundance when it is present. These are referred to as the ‘presence data’ and the ‘log-abundance’ data, respectively. The second stage involves modelling the presence data using logistic regression, and separately modelling the log-abundance data using ordinary regression. Finally, the third stage involves combining the two models in order to estimate the expected abundance for a specific set of values of the explanatory variables. A common approach to analyzing this sort of data is to use a ln (y+c) transformation, where c is some constant (usually one). The method we use here avoids the need for an arbitrary choice of the value of c, and allows the modelling to be carried out in a natural and straightforward manner, using well-known regression techniques. The approach we put forward is not original, having been used in both conservation biology and fisheries. Our objectives in this paper are to (a) promote the application of this approach in a wide range of settings and (b) suggest that parametric bootstrapping be used to provide confidence limits for the estimate of expected abundance.

/pdf/modelling-skewed-data-with-many-zeros-a-simple-approach-3r2afkthvm.pdf

Modelling skewed data with many zeros: A simple approach combining ordinary and logistic regression

Catchability is an important parameter in many stock assessment models because it relates an index of abundance to stock size. We review the theory and evidence for time-varying catchability, its effects on stock assessment estimates, and methods to include time-varying catchability in stock assessments. Numerous studies provide strong evidence that time-varying catchability is common in most fisheries and many fishery-independent surveys and can be caused by anthropogenic, environmental, biological, and management processes. Trends in catchability over time can cause biased estimates of stock size and fishing mortality rates in stock assessment models that do not compensate for them. Methods that use descriptive and functional relationships have been developed to incorporate time-varying catchability in stock assessment models. We recommend that the default assumption for stock assessments should be that catchability varies over time and that multiple methods of including time-varying catchability should...

/pdf/incorporating-time-varying-catchability-into-population-4xznosbrgj.pdf

Incorporating Time-Varying Catchability into Population Dynamic Stock Assessment Models

Application of the Tweedie distribution to zero-catch data in CPUE analysis

James T. Thorson1*, Andrew O. Shelton2, Eric J. Ward2, and Hans J. Skaug3 Fisheries Resource Assessment and Monitoring Division (FRAM), Northwest Fisheries Science Center, National Marine Fisheries Service (NMFS), NOAA, 2725 Montlake Boulevard E, Seattle, WA 98112, USA Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service (NMFS), NOAA, 2725 Montlake Boulevard E, Seattle, WA 98112, USA Department of Mathematics, University of Bergen, PO Box 7800 5020 Bergen, Norway *Corresponding author: tel: +1 206 302 1772; fax: +1 206 860 6792; e-mail: James.Thorson@noaa.gov

/pdf/geostatistical-delta-generalized-linear-mixed-models-improve-5a6fk6hq75.pdf

Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes

Fish spotters are pilots in small aircraft employed by commercial fishermen to locate, identify, estimate the size of, and direct boats toward pelagic fish schools. Data describing species, locatio...

N. Chyan-huei Lo

Papers

Indices of Relative Abundance from Fish Spotter Data based on Delta-Lognornial Models