P.A. Whigham

University of Otago · Department of Information Science

Movement analysis is distinguished by an emphasis on understanding via observation and association. However, an important component of movement from the human and computer modeling perspective is the processes that bring about movement behavior in the first place. This article contextualizes the graphical causal modeling framework (for association,...

A common method for quantifying the interdisciplinarity of a publication is to measure the diversity of the publication’s cited references based on their disciplines. Here we examine the criteria that must be satisfied to develop a meaningful interdisciplinary measure based on citations and discuss the stages where uncertainty or bias may be introd...

Reproducibility is important for having confidence in evolutionary machine learning algorithms. Although the focus of reproducibility is usually to recreate an aggregate prediction error score using fixed random seeds, this is not sufficient. Firstly, multiple runs of an algorithm, without a fixed random seed, should ideally return statistically eq...

Modelling a complex system of autonomous individuals moving through space and time essentially entails understanding the (heterogeneous) spatiotemporal context, interactions with other individuals, their internal states and making any underlying causal interrelationships explicit, a task for which agents (including vector-agents) are specifically w...

The important process of choosing between algorithms and their many module choices is difficult, even for experts. Automated machine learning allows users at all skill levels to perform this process. It is currently performed using aggregated total error, which does not indicate whether a stochastic algorithm or module is stable enough to consisten...

Genetic programming (GP) is a common method for performing symbolic regression that relies on the use of ephemeral random constants in order to adequately scale predictions. Suitable values for these constants must be drawn from appropriate, but typically unknown, distributions for the problem being modeled. While rarely used with GP, $Z$ -score...

Grammars provide a convenient and powerful mechanism to define the space of possible solutions for a range of problems. However, when used in grammatical evolution (GE), great care must be taken in the design of a grammar to ensure that the polymorphic nature of the genotype-to-phenotype mapping does not impede search. Additionally, recent work has...

While interdisciplinary research (IDR) has attracted much attention, this has not yet resulted in a coherent body of knowledge of interdisciplinarity. One of the impediments is a lack of consensus on its conceptualization and measurement. Some of the proposed measures have shown to misalign empirically, meaning that conclusions about IDR can differ...

Modelling a complex system of autonomous individuals moving through space and time essentially entails understanding the (heterogeneous) spatiotemporal context, interactions with other individuals, their internal states and making any underlying causal interrelationships explicit, a task for which agents (including vector-agents) are specifically w...

Software effort estimation models are typically developed based on an underlying assumption that all data points are equally relevant to the prediction of effort for future projects. The dynamic nature of several aspects of the software engineering process could mean that this assumption does not hold in at least some cases. This study employs thre...

Current spatiotemporal data has facilitated movement studies to shift objectives from descriptive models to explanations of the underlying causes of movement. From both a practical and theoretical standpoint, progress in developing approaches for these explanations should be founded on a conceptual model. This paper presents such a model in which t...

The Hill–Robertson effect describes how, in a finite panmictic diploid population, selection at one diallelic locus reduces the fixation probability of a selectively favoured allele at a second, linked diallelic locus. Here we investigate the influence of population structure on the Hill–Robertson effect in a population of size N . We model populat...

Software effort estimation (SEE) is a core activity in all software processes and development lifecycles. A range of increasingly complex methods has been considered in the past 30 years for the prediction of effort, often with mixed and contradictory results. The comparative assessment of effort prediction methods has therefore become a common app...

Software effort estimation (SEE) models are typically developed based on an underlying assumption that all data points are equally relevant to the prediction of effort for future projects. The dynamic nature of several aspects of the software engineering process could mean that this assumption does not hold in at least some cases. This study employ...

It seems logical to assert that the dynamic nature of software engineering practice would mean that software effort estimation (SEE) modelling should take into account project start and completion dates. That is, we should build models for future projects based only on data from completed projects; and we should prefer data from recent similar proj...

Software effort estimation models are typically developed based on an underlying assumption that all data points are equally relevant to the prediction of effort for future projects. The dynamic nature of several aspects of the software engineering process could mean that this assumption does not hold in at least some cases. This study employs thre...

An error function can be used to select between candidate models but it does not provide a thorough understanding of the behaviour of a model. A greater understanding of an algorithm can be obtained by performing a bias-variance decomposition. Splitting the error into bias and variance is effective for understanding a deterministic algorithm such a...

Translocated populations often share demographic, environmental and genetic risks associated with relict populations. Models that predict translocation impacts on source and founder populations are therefore necessary to ensure that harvesting for release does not jeopardize either population. However, current models generally focus on maximizing t...

The ability of organizations to produce, collect, manage, analyze, and transform data has increased rapidly over the past decade (Delen & Zolbanin, 2018). This has resulted in significant new challenges regarding how data can be leveraged for improving business decisions and how this new scenario changes business processes and operations (Vidgen, S...

This paper presents a novel approach to constructing ensembles for prediction using a bootstrap aggregation (bagging) model. The proposed method uses analogies from ecological modelling to view bootstrap samples as a local adaptation resource in a spatially structured population. Through local competition and breeding, adaptation towards specific b...

The taxonomic status of some of New Zealand's endemic and threatened leiopelmatid frogs has been debated for decades. Clarifying this uncertainty is vital to their conservation, especially given the risk of extinction of cryptic taxa. We reexamined leiopelmatid diversity through multivariate analyses of the skeletal and external morphology of extin...

Analogies with molecular biology are frequently used to guide the development of artificial evolutionary search. A number of assumptions are made in using such reasoning, chief among these is that evolution in natural systems is an optimal, or at least best available, search mechanism, and that a decoupling of search space from behaviour encourages...

This response examines the context and implications of the comments to "On the Mapping of Genotype to Phenotype in Evolutionary Algorithms" that appears in this journal. The notion of metaphor is first considered and then the general themes of the commentaries addressed. The response subsequently focuses on representation and operators, noting that...

Lakes influence the distribution and structure of freshwater fish fauna in catchments. Whilst the impact of lakes on downstream fish communities is well known, changes in upstream fish communities have received little attention. Particularly in species exhibiting migratory and non-migratory life-history strategies. We examined the relationship betw...

Network rewiring as a method for producing a range of structures was first introduced in 1998 by Watts & Strogatz (Nature393, 440-442. (doi:10.1038/30918)). This approach allowed a transition from regular through small-world to a random network. The subsequent interest in scale-free networks motivated a number of methods for developing rewiring app...

Background Geographic perspectives of disease and the human condition often involve point-based observations and questions of clustering or dispersion within a spatial context. These problems involve a finite set of point observations and are constrained by a larger, but finite, set of locations where the observations could occur. Developing a rigo...

Habitat modification is one of the largest threats to global terrestrial biodiversity, yet management tools such as translocations often fail because of insufficient knowledge about species' habitat suitability and requirements in release areas. Resource selection is a useful technique that can address this issue. In 2014, we investigated resource...

The distribution of migratory and non-migratory fish species in the New Zealand landscape is related to the differences in their larval life-history, specifically, pelagic and benthic larvae, respectively. Migratory species require access to pelagic habitats to complete their life cycle, but gain a significant fecundity benefit. Here, we examine th...

Periodic monitoring over 52 years have revealed temporal changes in the vegetation and floristic patterns associated with what has been acclaimed to be the world's oldest known experimental snow fence, which is located on an exposed high-alpine cushionfield on the Old Man Range in south-central New Zealand. The induced pattern of intermittent snow-...

A small 18 × 1–5 m, distinctive, teardrop-shaped alpine tarn about 55-cm deep with a variable schist plate rock-silty bed, a wetland rim and surrounding snowbank community is described from a shallow depression in the headwaters of a small primary stream at 1400 m on the crest of the Rock and Pillar Range (1450 m), south-central South Island, New Z...

Understanding the influence of spatial scale on ecological processes that occur with exotic plant invasion can help us identify underlying mechanisms of successful invasion. Here we studied spatial associations between Thymus vulgaris invasion and plant community species richness, composition and abundance at multiple spatial scales. These scales i...

Alterations to ecosystem nitrogen (N) cycling by introduced plant species may increase the invasibility of habitat providing a positive feedback for the introduced species to become invasive. Spatial patterns of foliar and soil δ15N ratios reflect variation in rates and process of N-cycling across invaded landscapes and provide insight into N-sourc...

Grammatical Evolution (GE) has a long history in evolutionary computation. Central to the behaviour of GE is the use of a linear representation and grammar to map individuals from search spaces into problem spaces. This genotype to phenotype mapping is often argued as a distinguishing property of GE relative to other techniques, such as context-fre...

Software effort estimation (SEE) is a core activity in all software processes and development lifecycles. A range of increasingly complex methods has been considered in the past 30 years for the prediction of effort, often with mixed and contradictory results. The comparative assessment of effort prediction methods has therefore become a common app...

Cold adapted plants, such as cushion plants, may be particularly sensitive to climate warming because of their compact growth form and high branch density. In the oceanic southern hemisphere, cushion communities tend to have large range distributions at low latitudes (sea level to low alpine), thus providing an opportunity to test the effects of te...

This paper examines the use of a linear model in combination with a multi-objective optimisation. A simple linear model is constructed and trained using data that has been automatically transformed based on skewness. These transformations, and their inverse, can then be used on the test data without having to make any assumptions of the underlying...

Agricultural modification commonly leads to reductions in vegetation matrix quality and a resultant decrease in functional connectivity. In this study, a network analysis approach was used to assess the impact of agriculturally-induced reductions in vegetation matrix quality on the metapopulation dynamics of the critically endangered New Zealand gr...

The aim of this research was to increase understanding of how exotic plant invasion can alter abiotic and biotic soil properties across multiple sites encompassing the geographic distribution of the study species, between aspects at each site, and across the edge of invasion. Our research questions were: do soil physicochemical properties and soil...

This preface gives an overview of the seven papers featured in the SIRC NZ 2013 Special Feature of the Journal of Spatial Science, to be published in September 2014.

This commentary demonstrates that for genetic programming with recombination and drift repeated motif patterns emerge within individuals more often than chance. This demonstrates that such patterns emerge without the need for selection. In addition, this effect is amplified when the effective population size is reduced.

A computational model of a limit order book is used to study the effect of different limit order distribution offsets. Reference prices such as same side/contra side best market prices and last traded price are considered in combination with different price offset distributions. We show that when characterizing limit order prices, varying the offse...

Modelling metapopulation dynamics is a potentially very powerful tool for conservation biologists. In recent years, scientists have broadened the range of variables incorporated into metapopulation modelling from using almost exclusively habitat patch size and isolation, to the inclusion of attributes of the matrix and habitat patch quality. We inv...

Use of trading strategies to mislead other market participants, commonly termed trade-based market manipulation, has been identified as a major problem faced by present day stock markets. Although some mathematical models of trade-based market manipulation have been previously developed, this work presents a framework for manipulation in the contex...

The concept of bloat -- the increase of program size without a corresponding increase in fitness -- presents a significant drawback to the application of genetic programming. One approach to controlling bloat, dubbed spatial structure with elitism (SS+E), uses a combination of spatial population structure and local elitist replacement to implicitly...

The maintenance of sexual populations has been an ongoing issue for evolutionary biologists, largely due to the two-fold cost of sexual versus asexual reproduction. Many explanations have been proposed to explain the benefits of sex, including the role of recombination in maintaining diversity and the elimination of detrimental mutations, the advan...

Increasing our understanding of spatial patterns of plant secondary chemistry variation may help us understand the mechanisms that underlie plant invasions involving species which exhibit chemical phenotypic variation. We analysed qualitative and quantitative variation in the essential oil terpenes produced by Thymus vulgaris L. (thyme) plants insi...

Local sharing is a method designed for efficient multimodal optimisation that combines fitness sharing with spatially structured populations and elitist replacement. In local sharing, the bias towards sharing and the influence of spatial structure is controlled by the deme (neighbourhood) size. This introduces an undesirable trade-off; to maximise...

Long‐term effects of two nearby disturbances, mechanical blading 34 years ago and an approximately century‐old sheep graveyard, in high‐alpine cushionfield share certain vegetation features despite their contrasting soil nutrient status. Secondary succession following blading has continued beyond that recorded over the first 24 years with continued...

A computational model of a double auction market is introduced and extended to allow a controlled cyclic behaviour in the price signal to be developed. Traders are evolved to maximise profit in this market using Grammatical Evolution, and their properties studied for a range of periods and amplitude of the trend in the price signal. The trader gram...

Grammar formalisms are one of the key representation structures in Computer Science. So it is not surprising that they have also become important as a method for formalizing constraints in Genetic Programming (GP). Practical grammar-based GP systems first appeared in the mid 1990s, and have subsequently become an important strand in GP research and...

A grammatical evolutionary model (GE) is used to evolve trading strategies for a limit-order book model. A modified version of a limit-order book generator, based on the original work of Maslov, is used to produce limit-order book tick data. The evolved trading strategies demonstrate profit-making ability even though the Maslov model is fundamental...

During the evolution of solutions using genetic programming (GP) there is generally an increase in average tree size without a corresponding increase in fitness-a phenomenon commonly referred to as bloat. Although previously studied from theoretical and practical viewpoints there has been little progress in deriving controls for bloat which do not...

This paper examines the behaviour of bloat for GP tree structures us-ing three different topologies: a panmictic, ring and star structure. Initially ge-netic drift is examined and the results showing the influence of a lower absorbing boundary are examined for each space. A simple selection model is then applied and analysed for bloat. A conjecture...

People living in poor areas suffer higher mortality than those in wealthy areas. Environmental factors partly explain this association, including exposure to pollutants and accessibility of healthcare. We sought to determine whether proximity to alcohol outlets varied by area deprivation in New Zealand. Roadway travel distance from each census unit...

The field of evolutionary art is generally concerned with evolving patterns that have little constraint. This paper describes an evolutionary art system that is constrained to form flag designs, following a set of common design patterns. The resulting genotype representation, genetic operators and forms of user interaction are chosen to allow an ex...

Geospatial methods have been used extensively to examine associations between alcohol outlet density and various harms; however, the literature offers too little methodological detail to assess possible geocoding biases in these studies. We used New Zealand liquor licensing and crime data to assess geocoding error. For the year with the best data,...

Local sharing is a method designed for efficient multimodal optimisation that combines fitness sharing, spatially-structured populations and elitist replacement. In local sharing the bias toward sharing or spatial effect is controlled by the deme (neighbourhood) size. This introduces an undesirable trade-off; to maximise the sharing effect, deme si...

Genetic drift in finite populations ultimately leads to the loss of genetic variation. This paper examines the rate of neutral gene loss for a range of population structures defined by a graph. We show that, where individuals reside at fixed points on an undirected graph with equal degree nodes, the mean time to loss differs from the panmictic valu...

Spatially-explicit, individual based models are used to explore the consequences of introducing two simple genetic tradeoff mechanisms to the gradient response of monoecious diploid individuals. A simple linear gradient is used to produce a structured environment. One tradeoff relates the plasticity of an individual to its overall fitness, where in...

Evolutionary dynamics for the Moran process have been previously examined within the context of fixation behaviour for introduced mutants, where it was demonstrated that certain spatial structures act as amplifiers of selection. This article will revisit the assumptions for this spatial Moran process and show that proportional global fitness, intro...

The evolution of a population is determined by many factors, including the geographic separation of individuals in the population (spatial structure), parent selection via assortative mating (biasing who breeds with whom), environmental gradients, founder effects, disturbance, selection, stochastic effects characterised as genetic drift and so on....

Spatially-structured populations are one approach to increasing genetic diversity in an evolutionary algorithm (EA). However, they are susceptible to convergence to a single peak in a multimodal fitness landscape. Niching methods, such as fitness sharing, allow an EA to maintain multiple solutions in a single population, however they have rarely be...

Based on data of 662 households from 75 districts in the city of São Paulo, this paper investigates the relations between electric-ity consumption and household income, with use of geographic weighted regressions (GWR). Findings reveal that electricity con-sumption is useful for characterizing household income, a fre-quently used proxy for purchasi...

The aim of this research was to determine the behavior and habitat selection of red deer (Cervus elaphus ) hinds during the calving period, on an extensively managed rangeland in the high-country of New Zealand's South Island. The research was developed using ArcView and eCognition software, GPS collars on five red deer hinds, an aerial photograph...

1. An ecological model was developed using genetic programming (GP) to predict the time-series dynamics of the diatom, Stephanodiscus hantzschii for the lower Nakdong River, South Korea. Eight years of weekly data showed the river to be hypertrophic (chl. a, 45.1 ± 4.19 μg L−1, mean ± SE, n = 427), and S. hantzschii annually formed blooms during th...

This paper introduces vector agents (VA), an approach to impose a systematic framework on the geometric element of Torrens and Benenson’s Geographic Automata System (GAS). Both schemes use vector geometry as an antidote to the geographically unrealistic regular tessellation cellular automata (CA). The work reported here explores the properties of i...

Collecting natural data at regular, fine scales is an onerous and often costly procedure. However, there is a basic need for fine scale data when applying inductive methods such as neural networks or genetic algorithms for the development of ecological models. This paper will address the issues involved in interpolating data for use in machine lear...

This paper summarises the current literature on immune system function and behaviour, including pattern recognition receptors, danger theory, central and peripheral tolerance, and memory cells. An artificial immune system framework is then presented based on the analogies of these natural system components and a rule and feature-based problem repre...

Evolutionary dynamics on graphs for the Moran process have been previously examined within the context of fixation behaviour for introduced mutants, where it was demonstrated that certain spatial structures act as amplifiers of selection. This paper will revisit the assumptions for this spatial Moran process and show that the assumption of proporti...

Spatially-structured populations are one approach to in- creasing genetic diversity in an evolutionary algorithm (EA). However, they are susceptible to convergence to a single peak in a multimodal fit- ness landscape. Niching methods, such as fitness sharing, allow an EA to maintain multiple solutions in a single population, however they have rarel...

Spatially-structured evolutionary algorithms are frequently implemented using a homogeneous environment throughout space. Such a configuration does not promote local adaptation of individuals in space. This paper introduces an evolutionary algorithm using space and localised environments to promote speciation. Surprisingly, a randomly generated “ru...