Alain Zuur

Highland Statistics

Major power outages have risen over the last two decades, largely due to more extreme weather conditions. However, there is a lack of knowledge on the distribution of power outages and its relationship to social vulnerability and co-occurring hazards. We examined the associations between localized outages and social vulnerability factors (demograph...

Abundance estimation of wildlife populations is frequently derived from systematic survey data. Accuracy and precision of estimates, however, depend on the number of replicate surveys, and on adjustments made for animals unavailable to (availability bias), or available but undetected (perception bias) by observers. This study offers a comprehensive...

Aim To evaluate how the spatial distribution of a heavily exploited marine gastropod (i.e. Queen conch) varies in response to a number of known biotic and abiotic variables within and between study areas that vary in environmental conditions. Location Three study areas in the north-eastern Caribbean, Anguilla, Saba Bank and St. Eustatius. Methods...

In the last 50 years, traditionally nomadic indigenous communities in Amazonia have increasingly adopted more sedentary lifestyles as a result of external influences. Permanent settlements lead to the concentration of disturbances (e.g., forest extraction and hunting) and threaten vulnerable species as well as those that provide important ecosystem...

Members of the widespread arid Australian mulga (Acacia aneura) complex are fire-sensitive shrubs or small trees that can resprout epicormically following low-severity burning, but are readily killed by high-severity fire. The seeds of many species of mulga are stimulated to germinate by heat during burning, although post-fire regeneration rates ar...

Scientific investigation is of value only insofar as relevant results are obtained and communicated, a task that requires organizing, evaluating, analysing and unambiguously communicating the significance of data. In this context, working with ecological data, reflecting the complexities and interactions of the natural world, can be a challenge. Re...

Conflicts between humans and crocodilians are a widespread conservation challenge and the number of crocodile attacks is increasing worldwide. We identified the factors that most effectively decide whether a victim is injured or killed in a crocodile attack by fitting generalized linear models to a 42-year dataset of 87 attacks (27 fatal and 60 non...

In subarctic waters winter may be the period during which seabirds face the greatest environmental and physiological pressures, yet seabird distribution during this time is poorly understood. Using at-sea surveys conducted in Prince William Sound, Alaska on research ships of opportunity from November 2007 to March 2009, we investigated how seabird...

Variability in the fluctuations of two Scottish lobster populations, the Hebrides and Southeast, was investigated from available long dataseries of fishery and environmental variables. In a multivariate context, relationships between selected environmental variables and the fishery data were studied at different spatial and temporal (annual, spring...

Using a unique 50-year high-resolution time series of daily kom-fyke catches, long-term patterns of scyphomedusae in the western Dutch Wadden Sea were analysed and related to changes in environmental conditions [eutrophication in the 1980s–1990s and recent climate change (increased water temperature)] in the area. Over the years, species compositio...

Corresponding editor: Roger Harris Using a unique 50-year high-resolution time series of daily kom-fyke catches, long-term patterns of scyphomedusae in the western Dutch Wadden Sea were analysed and related to changes in environmental conditions [eutrophication in the 1980s– 1990s and recent climate change (increased water temperature)] in the area...

Download via Deltares: http://kennisonline.deltares.nl/product/30737 Het kabinet heeft in 2006 in een planologische kernbeslissing een besluit genomen over het Project Mainportontwikkeling Rotterdam (PMR). Onderdeel hiervan is de aanleg van de Tweede Maasvlakte, een nieuw haven- en industriegebied. De aanleg en aanwezigheid hiervan hebben mogelijk...

Environmental conditions during the larval phase (food concentration and temperature) impact recruitment success of marine bivalves by affecting growth and survival. We analysed the seasonal match between environmental conditions and larval presence of six coastal bivalve species over eight consecutive years (2006–2013) in the western Wadden Sea, t...

Mast seeding, the intermittent production of large synchronised seed crops among plant populations, is a phenomenon that occurs at exceptionally long intervals in spinifex grasses (Triodia spp.) from arid regions of Australia. This is despite the reliance of these fire- sensitive plants on seeds for post-fire regeneration, and that spinifex grass...

This article shows how to apply generalized additive models and generalized additive mixed models to single-case design data. These models excel at detecting the functional form between two variables (often called trend), that is, whether trend exists, and if it does, what its shape is (e.g., linear and nonlinear). In many respects, however, these...

Fieldwork was carried out between 2009 and 2012. We used a combination of methods to study the occurrence and ecology of the scoters, including; • year-round aerial surveys to record numbers and distribution; • reconstruction of diet based on shell remains in the stomachs of dead birds; • scuba-diving sampling of benthos at places with foraging sco...

This book begins with an introduction to generalised additive models (GAM) using stable isotope ratios from squid. In Chapter 2 we explain additive mixed effects using polar bear movement data. In Chapter 3 we apply additive mixed effects models on coral reef data. Ruddy turnstone data are used in Chapter 4 to explain Poisson generalised additive m...

Benthic monitoring programs can be used to investigate the relationship between shore birds and their intertidal food supply, and are particularly helpful in areas of rapid habitat fragmentation and deterioration resulting from human disturbance. Samborombon Bay in Buenos Aires Province, Argentina is an area of importance for migratory shorebirds t...

Mnemiopsis leidyi is an invasive comb jelly which has successfully established itself in European seas. The species is known to produce spectacular blooms yet it is holoplanktonic and not much is known about its population dynamics in between. One way to gain insight on how M. leidyi might survive between blooms and how it can bloom so fast is to s...

The book presents complete R code and explanation for estimating GLM and GLMM models from both the frequentist and Bayesian perspective. JAGS is used for Bayesian modeling.

Explaining the coexistence of large numbers of rainforest tree species is a major challenge in tropical ecology. A possible coexistence mechanism is the partitioning of the forest light environment; species that grow well under a given light regime may not thrive in another. To test this hypothesis, Philipson et al. (2012) investigated how tree spe...

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The purpose of the current study was to investigate the factors which influence the prevalence of stereotypical behaviour in captive cheetahs. An information theory approach highlighted that the most optimal model was the controllable husbandry factors model with the size of enclosures, group membership, feeding regime and the ability to view other...

Estuaries cover <1% of marine habitats, but the carbon dioxide (CO(2)) effluxes from these net heterotrophic systems contribute significantly to the global carbon cycle. Anthropogenic eutrophication of estuarine waterways increases the supply of labile substrates to the underlying sediments. How such changes affect the form and functioning of the r...

Model output from the NH4-N concentration data analysis. The optimal model (OM) was a LME model that incorporated core identity as a random effect (L. ratio = 14.230, df1, pcorr<0.001) and allowed the residual spread to increase exponentially over time (L. ratio = 44.507, df1, p<0.001): where ai is a random intercept and the index i refers to the c...

Model output from the TOx-N concentration data analysis. The optimal model (OM) was a LME model that incorporated core identity as a random effect (L. ratio = 5.390, df1, pcorr = 0.010) and allowed the residual spread to increase exponentially over time (L. ratio = 15.366, df1, p<0.001): where ai is a random intercept and the index i refers to the...

Model output from the oxygen concentration data analysis. The optimal model (OM) was a LME model that incorporated core identity as a random effect (L. ratio = 19.467, df1, p<0.001): where ai is a random intercept and the index i refers to the core identity (i = 1,…, 12), and j to the observations within each core (j = 1,…,7). Random effect (a), co...

Model output from the DIC concentration data analysis. The optimal model (OM) was a LME model that incorporated core identity as a random effect (L. ratio = 48.237, df1, pcorr<0.001) and allowed the residual spread to increase exponentially over time and to vary by treatment (L. ratio = 179.335, df3, p<0.001): where ai is a random intercept and the...

Deep-sea sediments cover ~70% of Earth's surface and represent the largest interface between the biological and geological cycles of carbon. Diatoms and zooplankton faecal pellets naturally transport organic material from the upper ocean down to the deep seabed, but how these qualitatively different substrates affect the fate of carbon in this perm...

Offshore wind turbines are an alien element at sea, a “landscape” that is normally wide and open. Large, turning turbines might affect the local seabirds, that are dependent on the sea. One of the possible effects of offshore wind farms might be that the seabirds will be displaced from the sites, which would mean habitat destruction or at least hab...

Detecting and predicting how populations respond to environmental variability are eminent challenges in conservation research and management. This is particularly true for wildlife populations at high latitudes, many of which demonstrate changes in population dynamics associated with global warming. The Falkland Islands (Southwest Atlantic) hold on...

The veined squid, Loligo forbesii, is found throughout the northeast Atlantic, including the waters off the Iberian Peninsula, and is a socio-economically important cephalopod species, sustaining several small-scale commercial and local artisanal fisheries. This study uses Iberian and Azorean trawl survey and fishery landings data from 1990 to 1992...

We analyzed long-term winter survey data (1956–2007) for three endangered waterbirds endemic to the Hawaiian Islands, the Hawaiian moorhen (Gallinula chloropus sandvicensis), Hawaiian coot (Fulica alai), and Hawaiian stilt (Himantopus mexicanus knudseni). Time series were analyzed by species–island combinations using generalized additive models, wi...

Parametric size-selection curves are often combined over hauls to estimate a mean selection curve using a mixed model in which between-haul variation in selection is treated as a random effect. This paper shows how the mixed model can be extended to estimate a mean selection curve when smooth nonparametric size-selection curves are used. The method...

This paper presents optimum sampling levels in discard sampling programs considering cost and precision objectives simultaneously and explores their dependence on both variables. The analysis is based on the Irish discard program: an onboard-observer voluntary sampling scheme aimed at estimating discard rates in trawl fisheries. Multistage analysis...

This chapter discusses the multimetric TRophic IndeX (TRIX). It describes the effects of pollution over time, in order to inform management strategies such as cleanup operations and to set new regulations. The chapter presents two different statistical approaches. First it uses additive models incorporating temporal autocorrelation along with a spa...

Measurements of the density of deep pelagic bioluminescent zooplankton (BL) were made with the Intensified Silicon Intensifier Target (ISIT) profiler in the Ligurian, Tyrrhenian, Adriatic, Ionian Seas and the Strait of Sicily from ∼300m to near seafloor. Mean BL densities ranged from 2.61m−3 at 500–1000m depth in the Adriatic Sea to 0.01m−3 at 4000...

The Balgzand intertidal is an important nursery area for early life stages of various epibenthic crustacean and fish species. Especially in summer, extremely high numbers of individuals occur. This study analyses whether these high densities in summer lead to food limitation using 0-group plaice Pleuronectes platessa L. as a model species. Between...

1. Marine copepods of the genus Calanus can reproduce prior to the spring bloom in the absence of sufficient food. Their starvation physiology, and hence the factors limiting their pre-bloom population growth (egg production), remain poorly understood. 2. Stoichiometric theory can provide insights into the factors controlling an organism’s growth a...

The time of year and day, the state of the tide and prevailing environmental conditions significantly influence seal haulout behaviour. Understanding these effects is fundamentally important in deriving accurate estimates of harbour seal abundance from haulout data. We present a modelling approach to assess the influence of these variables on seals...

Forensic pathologists and entomologists estimate the minimum post-mortem interval since a long time by describing the stage of succession and development of the necrophagous fauna (Amendt et al. 2004). From very simple calculations at the beginning, (Bergeret, see also Smith 1986) the discipline has evolved into a more mathematical one (e.g. Marche...

Analyses of long-term field observations (1974–2007) on chlorophyll-a concentrations in the western Wadden Sea showed no long-term trends in the timing of the wax and wane of phytoplankton spring blooms. There is weak evidence, however, that the height of the autumn bloom has decreased since the early 1990s. This fading of the autumn bloom may have...

1. While teaching statistics to ecologists, the lead authors of this paper have noticed common statistical problems. If a random sample of their work (including scientific papers) produced before doing these courses were selected, half would probably contain violations of the underlying assumptions of the statistical techniques employed. 2. Some vi...

The factors affecting patterns of benthic [seabed] biology and chemistry around 50 Scottish fish farms were investigated using linear mixed-effects models that account for inherent correlations between observations from the same farm. The abundance of benthic macrofauna and sediment concentrations of organic carbon were both influenced by a signifi...

Results are presented of an extensive ichthyoplankton survey that covered the continental slope, the offshore banks and oceanic regions west of Ireland. Oceanographic measurements revealed domes of cold, less saline water over the Porcupine, Rockall and Faroese Banks, constituting Taylor columns. The most species-rich stations were those found on a...

In this chapter, we discuss models for zero-truncated and zero-inflated count data. Zero truncated means the response variable cannot have a value of 0. A typical example from the medical literature is the duration patients are in hospital. For ecological data, think of response variables like the time a whale is at the surface before re-submerging...

This chapter analyses amphibian fatalities along a road in Portugal. The data are counts of kills making a Gaussian distribution unlikely; restricting our choice of techniques. We began with generalised linear models (GLM) and generalised additive models (GAM) with a Poisson distribution, but these models were overdispersed. To solve this, you can...

Cephalopods are highly sensitive to environmental conditions and changes at a range of spatial and temporal scales. Relationships documented between cephalopod stock dynamics and environmental conditions are of two main types: those concerning the geographic distribution of abundance, for which the mechanism is often unknown, and those relating to...

A severe scarcity of life history and population data for deep-water fishes is a major impediment to successful fisheries management. Long-term data for non-target species and those living deeper than the fishing grounds are particularly rare. We analysed a unique dataset of scientific trawls made from 1977 to 1989 and from 1997 to 2002, at depths...

In this chapter, we apply mixed modelling to honeybee data. The data are considered nested because multiple observations were taken from the same hive. A total of 24 hives were sampled.

In the previous chapter, we discussed violation of independence for measurements taken repeatedly over time and how temporal correlation structures can be added to linear regression and additive models. We used a regular spaced data set. In this chapter, we consider data measured at multiple spatial locations, and we show how similar correlation st...

In this chapter, we continue with Gaussian linear and additive mixed modelling methods and discuss their application on nested data. Nested data is also referred to as hierarchical data or multilevel data in other scientific fields (Snijders and Boskers, 1999; Raudenbush and Bryk, 2002).

This chapter revises the basic concepts of linear regression, shows how to apply linear regression in R, discusses model validation, and outlines the limitations of linear regression when applied to ecological data. Later chapters present methods to overcome some of these limitations; but as always before doing any complicated statistical analyses,...

Predicting the spatial distribution of wildlife populations is an important component of the development of management strategies for their conservation. Landscape structure and composition are important determinants of where species occur and the viability of their populations. In particular, the amount of suitable habitat and its level of fragmen...

Information on the haul-out behaviour of pinnipeds is essential for increasing the accuracy of population estimates necessary for the effective conservation of protected species, as well as improving survey design. The haul-out behaviour of 10 harbour seals Phoca vitulina L. in southwest Ireland was examined using a novel telemetry system based on...