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Publications
Publications (582)
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
We live in the era of big data. However, small data sets are still common for ethical, financial, and practical reasons. Small sample sizes can cause researchers to particularly seek the most powerful methods to analyse their data; but they may be wary that some methodologies rely on assumptions that may not be appropriate when samples are small. T...
Recently, it was recommended to omit tied observations before applying the two-sample Wilcoxon-Mann-Whitney test McGee M. et al. (2018). Using a simulation study, we argue for exact tests using all the data (including tied values) as a preferable approach. Exact tests, with tied observations included guarantee the type I error rate with a better ex...
Ecologists and evolutionary biologists are regularly tasked with the comparison of binary data across groups. There is, however, some discussion in the biostatistics literature about the best methodology for the analysis of data comprising binary explanatory and response variables forming a 2 × 2 contingency table.
We assess several methodologies f...
This chapter introduces the importance of good graphing. It starts by acknowledging that data is the heart of all science. Since gathering data could be a messy process, data visualization allows the organization of data into a clear summary that showcases the findings in an accessible and engaging way. However, the best type of figure to use in gr...
This chapter discusses the features and functions that concern plotting figures in R code. R has a vast range of customizable graphical parameters that enable people to control the way their figures are displayed. Thus, controlling the way the figures are displayed means that the figures can improve their respective functionality and aesthetic appe...
This chapter considers pie charts and tables as a choice of qualitative data presentation. It explains how to produce clear and effective pie charts using nominal data or ordinal data and Word. Pie charts are most likely to be useful with qualitative data in percentage form and data that add up to 100 per cent. Thus, segments of pie charts are most...
This chapter discusses using boxplots and histograms when comparing multiple samples. It explains how multiple samples can be graphed for comparison through boxplots, histograms, and bar charts. Bar charts are generally less informative than boxplots, giving the reader less detail about each sample. The chapter mentions how boxplots are better than...
This chapter looks at ways for producing clear and effective histograms and boxplots when presenting single-sample data. It explains the advantages and disadvantages of each figure type relative to the other. The customization of histograms primarily revolves around the features of bin size, cell colour, and axis features. Boxplot customization inv...
This chapter outlines walk-throughs of R code using specific data examples. The aim of this is to provide generic and editable code for a range of plotting and design features. The chapter showcases the R code using examples of a bar chart and a scatterplot as a base to reference its respective customization. Design components (frames, images, back...
This chapter explains how to use bar charts to express qualitative data or categorical data. Even if bar charts can simultaneously display nominal data and ordinal data, different data types can influence the design of the bar charts themselves. Bar charts are an effective way to display data due to their linear arrangement of bars, their visibilit...
This chapter explains how a scatterplot is a good choice for presenting quantitative data. It explains that scatterplots are the most effective way of plotting data points of two variables and determining the relationship between those variables. Time series is a common type of scatterplot when plotting the change in one continuous variable over ti...
Presenting Scientific Data with R provides a guide to data presentation using R. It offers valuable and applicable advice on how to choose the most appropriate type of graph for different types of data, and guides readers from the basics of plotting clear figures to producing polished and effective visuals, illustrating the core concepts and featur...
Some data are collected on circular (rather than linear) scales. Often researchers are interested in comparing two samples of such circular data to test the hypothesis that they came from the same underlying population. Recently, we compared 18 statistical approaches to testing such a hypothesis, and recommended two as particularly effective. A ver...
Our understanding of aposematism (the conspicuous signalling of a defence for the deterrence of predators) has advanced notably since its first observation in the late nineteenth century. Indeed, it extends the scope of a well-established game-theoretical model of this very same process both from the analytical standpoint (by considering regimes of...
In a variety of aposematic species, the conspicuousness of an individual's warning signal and the quantity of its chemical defence are positively correlated. This apparent honest signalling is predicted by resource competition models which assume that the production and maintenance of aposematic defences compete for access to antioxidant molecules...
Background
: Birch species such as Betula pendula have conspicuous white bark and the evolutionary drivers for this colouration remain unresolved.
Aims
We evaluated our hypothesis that the white bark is a visual warning signal to deter mammals from bark-stripping. Many species of deer (Cervidae) and multiple other mammals consume bark. White birch...
Facultative endosymbionts can induce benefits and costs to their aphid hosts. In the pea aphid, Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae), infection with the γ‐proteobacterium Hamiltonella defensa Moran et al. can confer resistance against parasitoids, but may also reduce the frequency of aggressive and escape behaviours exhibited in resp...
Deimatic behaviours, also referred to as startle behaviours, are used against predators and rivals. Although many are spectacular, their proximate and ultimate causes remain unclear. In this review we aim to synthesise what is known about deimatic behaviour and identify knowledge gaps. We propose a working hypothesis for deimatic behaviour, and dis...
Background
A broad range of scientific studies involve taking measurements on a circular, rather than linear, scale (often variables related to times or orientations). For linear measures there is a well-established statistical toolkit based on linear modelling to explore the associations between this focal variable and potentially several explanat...
In a variety of aposematic species, the conspicuousness of an individual’s warning signal and the quantity of its chemical defence are positively correlated. This apparent honest signalling is predicted by resource competition models which assume that the production and maintenance of aposematic defences compete for access to antioxidant molecules...
Spontaneous Magnetic Alignment (SMA), or the phenomenon by which animals orientate their bodies non-randomly with respect to a magnetic field, has been demonstrated in many taxa. While a 2013 study could only detect SMA in domestic dogs under calm magnetic field conditions, a more recent study has reported an extremely strong effect of magnetic ali...
Many biological variables are recorded on a circular scale and therefore need different statistical treatment. A common question that is asked of such circular data involves comparison between two groups: Are the populations from which the two samples are drawn differently distributed around the circle? We compared 18 tests for such situations (by...
A common situation in experimental science involves comparing a number of treatment groups each with a single reference (control group). For example, we might compare diameters of fungal colonies subject to a range of inhibitory agents with those from a control group to which no agent was applied. In this situation, the most commonly applied test i...
A broad range of scientific studies involve taking measurements on a circular rather than linear scale (often times or orientations). For linear measures there is a well-established statistical toolkit based on linear modelling to explore the associations between this focal variable and potentially several explanatory factors and covariates. Howeve...
Dropping behavior is an effective antipredator defense utilized by many insects including aphids, which drop from plants to lower plant parts or underlying substrates to avoid attack from predatory invertebrates. While research commonly focusses on triggers of dropping, less attention is given to what happens to prey individuals following escape dr...
The many different islands of the Pacific provide a natural experiment that is ideal for studying predictors affecting plant cover and habitat-type. Previous research into pre-European deforestation and forest replacement across the Pacific islands detected multiple significant environmental and cultural variables. Here we re-analyse data for 67 is...
For herbivorous insects, dropping from the host plant is a commonly-observed antipredator defence. The use of dropping compared to other behaviours and its timing in relation to contact with a predator was explored in both pea aphids ( Acyrthosiphon pisum ) and potato aphids ( Macrosiphum euphorbiae ). Pea aphids dropped more frequently in response...
Many biological variables, often involving timings of events or directions, are recorded on a circular rather than linear scale, and need different statistical treatment for that reason. A common question that is asked of such circular data involves comparison between two groups or treatments: Are the populations from which the two samples drawn di...
Visual crypsis of prey is determined by the interaction between an individual’s physical appearance to their predators and visual aspects of their environment. Physical size will impact visual appearance and thus potentially influence crypsis. However, research on this topic is limited, leaving the effect of size in cryptic prey largely unexplored....
Turn alternation is a locomotory behaviour wherein an animal makes consecutive turns in opposite directions (left-then-right or right-then-left). It has been suggested that its adaptive function is to maintain locomotion in a relatively constant general direction while negotiating obstacles. Previous work has focussed on the use of turn alternation...
It is not uncommon for researchers to want to interrogate paired binomial data. For example, researchers may want to compare an organism’s response (positive or negative) to two different stimuli. If they apply both stimuli to a sample of individuals, it would be natural to present the data in a 2 × 2 table. There would be two cells with concordant...
The most common statistical procedure with a sample of circular data is to test the null hypothesis that points are spread uniformly around the circle without a preferred direction. An array of tests for this has been developed. However, these tests were designed for continuously distributed data, whereas often (e.g. due to limited precision of mea...
Many studies in biology involve data measured on a circular scale. Such data require different statistical treatment from those measured on linear scales. The most common statistical exploration of circular data involves testing the null hypothesis that the data show no aggregation and are instead uniformly distributed over the whole circle. The mo...
Propensity scores are often used to adjust for between-group variation in covariates, when individuals cannot be randomized to groups. There is great flexibility in how these scores can be appropriately used. This flexibility might encourage p-value hacking – where several alternative uses of propensity scores are explored and the one yielding the...
Camouflage – adaptations that prevent detection and/or recognition – is a key example of evolution by natural selection, making it a primary focus in evolutionary ecology and animal behaviour. Most work has focused on camouflage as an anti‐predator adaptation. However, predators also display specific colours, patterns and behaviours that reduce vis...
Parent birds employ various strategies to protect their offspring against nest predators. Two well‐researched anti‐nest‐predation strategies involve visual concealment of the nest by way of parental camouflage and egg camouflage. By contrast, camouflage of nest structures is relatively under‐researched, particularly in the case of cup‐nests in tree...
How foraging predators explore their environment is a fundamental aspect of predator-prey interactions. Girling et al. (2007) tested Coccinella septempunctata in a Y-maze, finding that approximately 45% of individuals displayed significant turning biases. We extend the work of Girling et al. in three ways: (1) turning bias was tested on vertical as...
Recent years have seen great interest in the suggestion that between-group aggression and within-group altruism have coevolved. However, these efforts have neglected the possibility that warfare – via its impact on demography – might influence human social behaviours more widely, not just those directly connected to success in war. Moreover, the po...
O'Hara and Kotze ( Methods Ecol Evol 1: 118–122, 2010) present simulation results that appear to show very poor behaviour (as judged by bias and overall accuracy) of linear models applied to count data, especially in relation to GLM analysis.
We considered O'Hara and Kotze's (2010) comparisons, and determined that the finding occurred primarily bec...
Distraction displays are conspicuous behaviours functioning to distract a predator's attention away from the displayer's nest or young, thereby reducing the chance of offspring being discovered and predated. Distraction is one of the riskier parental care tactics, as its success derives from the displaying parent becoming the focus of a predator's...
The key selective pressure shaping the morphology of samaras is seen as enhancing primary wind‐borne dispersal from the parent plant to the ground. However, the consequences of the samara wing of primarily wind‐dispersed tree species for post‐dispersal processes has not been well studied. We explored whether the presence of this wing in Acer pseudo...
40 years ago, the “life‐dinner principle” was proposed as an example of an asymmetry that may lead prey species to experience stronger selection than their predators, thus accounting for the high frequency with which prey escape alive from interaction with a predator. This principle remains an influential concept in the scientific literature, despi...
Background: Circular data are gathered in diverse fields of science where measured traits are cyclical in nature: such as compass directions or times of day. The most common statistical question asked of a sample of circular data is whether the data seems to be drawn from a uniform distribution or one that is concentrated around one or more preferr...
Winged seeds, or samaras, are believed to promote the long‐distance dispersal and invasive potential of wind‐dispersed trees, but the full dispersive potential of these seeds has not been well characterised. Previous research on the ecology of winged seeds has largely focussed on the initial abscission and primary dispersal of the samara, despite i...
Background:
For data collected on a circular rather than linear scale, a very common procedure is to test whether the underlying distribution appears to deviate from circular uniformity. Rao's spacing test is often used to evaluate the support the data offers for the null hypothesis of uniformity. Here we demonstrate that the traditional version o...
The field of predator eavesdropping concentrates on the detection by a predator or parasite of signals that prey direct at conspecifics, and the subsequent evolution by prey to avoid or lessen such detection. Here, we first point out that signaling prey species are often found in mixed-species moving groups or stationary aggregations, and ask the q...
Nguyen et al. (2016) offered advice to researchers in the commonly-encountered situation where they are interested in testing for a difference in central tendency between two populations. Their data and the available literature support very simple advice that strikes the best balance between ease of implementation, power and reliability. Specifical...
While several manipulated host behaviours are accepted as extended phenotypes of parasites, there remains debate over whether other altered behaviours in hosts following parasitic invasion represent cases of parasite manipulation, host defence or the pathology of infection. One particularly controversial subject is ‘suicidal behaviour’ in infected...
Animals can use other prey species to learn about the presence of predators and reduce their risk of predation. Species living in the same area can eavesdrop on other species’ alarm signals or cues. Animals may also temporarily join other species to mob predators, or may associate more stably with other species in mixed-species groups, in which com...
Pearson’s product moment correlation coefficient (more commonly Pearson’s r) tends to underestimate correlations that exist in the underlying population. This phenomenon is generally unappreciated in studies of ecology, although a range of corrections are suggested in the statistical literature. The use of Pearson’s r as the classical measure for c...
Dropping is a common antipredator defence that enables rapid escape from a perceived threat. However, despite its immediate effectiveness in predator–prey encounters (and against other dangers such as a parasitoid or an aggressive conspecific), it remains an under‐appreciated defence strategy in the scientific literature. Dropping has been recorded...
Interest in the evolutionary origins and drivers of warfare in ancient and contemporary small-scale human societies has greatly increased in the last decade, and has been particularly spurred by exciting archaeological discoveries that suggest our ancestors led more violent lives than previously documented. However, the striking observation that wa...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these s...
Circular data are common in biological studies. The most fundamental question that can be asked of a sample of circular data is whether it suggests that the underlying population is uniformly distributed around the circle, or whether it is concentrated around at least one preferred direction (e.g. a migratory goal or activity phase). We compared th...
Animal camouflage represents one of the most important ways of preventing (or facilitating) predation. It attracted the attention of the earliest evolutionary biologists, and today remains a focus of investigation in areas ranging from evolutionary ecology, animal decision-making, optimal strategies, visual psychology, computer science, to material...
Introduction
Non-interventional and other observational studies have become important in medical research. In such observational, non-randomized studies, groups usually differ in some baseline covariates. Propensity scores are increasingly being used in the statistical analysis of these studies. Stratification, also called subclassification, based...
Deflection occurs in predator-prey interactions where prey possess traits that influence the position of the predator's initial contact with the prey's body in a way that enhances the prey's probability of survival when attacked. As an anti-predatory defence occurring late in the sequence of an attack, deflection is an understudied but fascinating...
Signals and cues are fundamental to social interactions. A well-established concept in the study of animal communication is an amplifier, defined as a trait that does not add extra information to that already present in the original cue or signal, but rather enhances the fidelity with which variation in the original cue or signal is correctly perce...
Insects are often chemically defended against predators. There is considerable evidence for a group-beneficial element to their defenses, and an associated potential for individuals to curtail their own investment in costly defense while benefitting from the investments of others, termed “automimicry.” Although females in chemically defended taxa o...
Non-normality and heteroscedasticity are common in applications. For the comparison of two samples in the non-parametric Behrens–Fisher problem, different tests have been proposed, but no single test can be recommended for all situations. Here, we propose combining two tests, the Welch t test based on ranks and the Brunner–Munzel test, within a max...
Thanatosis—also known as death-feigning and, we argue more appropriately, tonic immobility (TI)—is an under-reported but fascinating anti-predator strategy adopted by diverse prey late on in the predation sequence, and frequently following physical contact by the predator. TI is thought to inhibit further attack by predators and reduce the perceive...