TMB: Automatic Differentiation and Laplace Approximation

TMB is an open source R package that enables quick implementation of complex nonlinear random effect (latent variable) models in a manner similar to the established AD Model Builder package (ADMB, admb-project.org). In addition, it offers easy access to parallel computations. The user defines the joint likelihood for the data and the random effects as a C++ template function, while all the other operations are done in R; e.g., reading in the data. The package evaluates and maximizes the Laplace approximation of the marginal likelihood where the random effects are automatically integrated out. This approximation, and its derivatives, are obtained using automatic differentiation (up to order three) of the joint likelihood. The computations are designed to be fast for problems with many random effects (~10^6) and parameters (~10^3). Computation times using ADMB and TMB are compared on a suite of examples ranging from simple models to large spatial models where the random effects are a Gaussian random field. Speedups ranging from 1.5 to about 100 are obtained with increasing gains for large problems. The package and examples are available at http://tmb-project.org

Accounting for correlated observations in an age-based state-space stock assessment model

Abstract Fish stock assessment models often rely on size- or age-specific observations that are assumed to be statistically independent of each other. In reality, these observations are not raw observations, but rather they are estimates from a catch-standardization model or similar summary statistics based on observations from many fishing hauls and subsamples of the size and age composition of the data. Although aggregation mitigates the strong intra-haul correlation between sizes/ages that is usually found in haul-by-haul data, violations of the independence assumption can have a large impact on the results and specifically on reported confidence bounds. A state-space assessment model that allows for correlations between age groups within years in the observation model for catches and surveys is presented and applied to data on several North Sea fish stocks using various correlation structures. In all cases the independence assumption is rejected. Less fluctuating estimates of the fishing mortality is obtained due to a reduced process error. The improved model does not suffer from correlated residuals unlike the independent model, and the variance of forecasts is decreased.</jats:p

The mental health of preschoolers in a Norwegian population-based study when their parents have symptoms of borderline, antisocial, and narcissistic personality disorders: at the mercy of unpredictability

BACKGROUND: Clinical studies have shown that children of parents with mental health problems are most likely to develop psychiatric problems themselves when their parents have a Personality Disorder characterized by hostility. The Personality Disorders that appear most associated with hostility, with the potential to affect children, are Borderline Personality Disorder, Antisocial Personality Disorder and Narcissistic Personality Disorder. The question addressed in this study is whether the risk to children’s mental health extends to the normal population of parents who have subclinical symptomlevels of these disorders. METHODS: This inquiry used data from a Trondheim, Norway community sample of 922 preschoolers and one parent for each child. The mean age of the children was 53 months (SD 2.1). Parents reported symptoms of Borderline, Antisocial and Narcissistic Personality Disorders on the DSM-IV ICD-10 Personality Questionnaire, and the children’s symptoms of DSM-IV behavioral and emotional diagnoses were measured with the Preschool Age Psychiatric Assessment, a comprehensive interview. Multigroup Structural Equation Modeling was used to assess the effect of parents’ symptoms on their preschoolers’ behavioral and emotional problems. RESULTS: The analyses yielded strongly significant values for the effect of parents’ Personality Disorder symptoms on child problems, explaining 13.2% of the variance of the children’s behavioral symptoms and 2.9% of the variance of internalizing symptoms. Biological parents’ cohabitation status, i.e., whether they were living together, emerged as a strong moderator on the associations between parental variables and child emotional symptoms; when parents were not cohabiting, the variance of the children’s emotional problems explained by the parents’ Personality Disorder symptoms increased from 2.9% to 19.1%. CONCLUSIONS: For the first time, it is documented that parents’ self-reported symptoms of Borderline, Antisocial, and Narcissistic Personality Disorders at a predominantly subclinical level had a strong effect on their children’s psychiatric symptoms, especially when the biological parents were not living together. Child service providers need to be aware of these specific symptoms of parental Personality Disorders, which may represent a possible risk to children

Welfare of ducks, geese and quail on farm

This Scientific Opinion concerns the welfare of Domestic ducks (Anas platyrhynchos domesticus),Muscovy ducks (Cairina moschata domesticus) and their hybrids (Mule ducks), Domestic geese (Anseranser f. domesticus) and Japanese quail (Coturnix japonica) in relation to the rearing of breeders, birdsfor meat, Muscovy and Mule ducks and Domestic geese for foie gras and layer Japanese quail for eggproduction. The most common husbandry systems (HSs) in the European Union are described for eachanimal species and category. The following welfare consequences are described and assessed for eachspecies: restriction of movement, injuries (bone lesions including fractures and dislocations, soft tissuelesions and integument damage and locomotory disorders including lameness), group stress, inabilityto perform comfort behaviour, inability to perform exploratory or foraging behaviour and inability toexpress maternal behaviour (related to prelaying and nesting behaviours). Animal-based measuresrelevant for the assessment of these welfare consequences were identified and described. The relevanthazards leading to the welfare consequences in the different HSs were identified. Specific factors suchas space allowance (including minimum enclosure area and height) per bird, group size,floor quality,characteristics of nesting facilities and enrichment provided (including access to water to fulfilbiological needs) were assessed in relation to the welfare consequences and, recommendations onhow to prevent the welfare consequences were provided in a quantitative or qualitative way