Package CatDyn 1.0-3 is now available on CRAN.
The package allows the estimation of the absolute abundance of a wild population during a capture season using a nonlinear and recursive discrete-time structural model.
The response variable is the catch, assumed a random variable produced by either a multiplicative stochastic process (lognormal distribution) or an additive stochastic process (normal distribution).
The predictor variables are capture effort, assumed observed exactly, and stock abundance, a latent predictor.
The data are high frequency (e.g. daily) observations of catch and capture effort during the season.
The structural model comes in five varieties. The simplest model assumes that all individuals that can be captured during the season were available at the start of the season, thus during the season the abundance always decreases (a pure depletion model), due to natural mortality and capture mortality. The other versions include one, two, three or four positive perturbations, such as immigration of recruits, that occur at certain time steps during the season. The models also includes nonlinear (power) relations between response and predictors. The models can be fit with natural mortality fixed at a given value or letting this parameter be estimated as well. Taking into account structural and stochastic options, CatDyn can fit up to 20 model versions to the same data.
CatDyn uses the recently released optimx package for maximum flexibility in selecting and using numerical methods implemented in R. CatDyn also has analytical gradients but in the current version these gradients are not yet passed to the optimizer; instead they are computed after convergence using numerical gradients, in order to compare analytical versus numerical gradients at the maximum likelihood estimates using various methods.
CatDyn estimates all parameters in the log scale and uses function deltamethod() from package msm to return back-transformed estimates vectors and covariance matrices.
CatDyn has been used already to estimate abundance of several fish and invertebrate stocks harvested by industrial and artisanal fishing fleets over the world.
A manuscript is under preparation with the first application (a squid stock from the Falkland Islands) and will be submitted to a marine science journal.
Dr. Rubén H. Roa-Ureta,
AZTI Tecnalia, Txatxarramendi Ugartea z/g, Sukarrieta, Bizkaia, SPAIN
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