Using an individual-based model to select among alternative foraging strategies of woodpigeons: data support a memory-based model with a flocking mechanism

Population modelling is increasingly recognised as a useful tool for pesticide risk assessment. For vertebrates that may ingest pesticides with their food, such as woodpigeon (Columba palumbus), population models that simulate foraging behaviour explicitly can help predicting both exposure and population-level impact. Optimal foraging theory is often assumed to explain the individual-level decisions driving distributions of individuals in the field, but it may not adequately predict spatial and temporal characteristics of woodpigeon foraging because of the woodpigeons’ excellent memory, ability to fly long distances, and distinctive flocking behaviour. Here we present an individual-based model (IBM) of the woodpigeon. We used the model to predict distributions of foraging woodpigeons that use one of six alternative foraging strategies: optimal foraging, memory-based foraging and random foraging, each with or without flocking mechanisms. We used pattern-oriented modelling to determine which of the foraging strategies is best able to reproduce observed data patterns. Data used for model evaluation were gathered during a long-term woodpigeon study conducted between 1961 and 2004 and a radiotracking study conducted in 2003 and 2004, both in the UK, and are summarised here as three complex patterns: the distributions of foraging birds between vegetation types during the year, the number of fields visited daily by individuals, and the proportion of fields revisited by them on subsequent days. The model with a memory-based foraging strategy and a flocking mechanism was the only one to reproduce these three data patterns, and the optimal foraging model produced poor matches to all of them. The random foraging strategy reproduced two of the three patterns but was not able to guarantee population persistence. We conclude that with the memory-based foraging strategy including a flocking mechanism our model is realistic enough to estimate the potential exposure of woodpigeons to pesticides. We discuss how exposure can be linked to our model, and how the model could be used for risk assessment of pesticides, for example predicting exposure and effects in heterogeneous landscapes planted seasonally with a variety of crops, while accounting for differences in land use between landscapes.

Incorporating toxicokinetics into an individual-based model for more realistic pesticide exposure estimates: A case study of the wood mouse

The potential risk of agricultural pesticides to mammals typically depends on internal concentrations within individuals, and these are determined by the amount ingested and by absorption, distribution, metabolism, and excretion (ADME). Pesticide residues ingested depend, amongst other things, on individual spatial choices which determine how much and when feeding sites and areas of pesticide application overlap, and can be calculated using individual-based models (IBMs). Internal concentrations can be calculated using toxicokinetic (TK) models, which are quantitative representations of ADME processes. Here we provide a population model for the wood mouse (Apodemus sylvaticus) in which TK submodels were incorporated into an IBM representation of individuals making choices about where to feed. This allows us to estimate the contribution of individual spatial choice and TK processes to risk. We compared the risk predicted by four IBMs: (i) “AllExposed-NonTK”: assuming no spatial choice so all mice have 100% exposure, no TK, (ii) “AllExposed-TK”: identical to (i) except that the TK processes are included where individuals vary because they have different temporal patterns of ingestion in the IBM, (iii) “Spatial-NonTK”: individual spatial choice, no TK, and (iv) “Spatial-TK”: individual spatial choice and with TK. The TK parameters for hypothetical pesticides used in this study were selected such that a conventional risk assessment would fail. Exposures were standardised using risk quotients (RQ; exposure divided by LD50 or LC50). We found that for the exposed sub-population including either spatial choice or TK reduced the RQ by 37–85%, and for the total population the reduction was 37–94%. However spatial choice and TK together had little further effect in reducing RQ. The reasons for this are that when the proportion of time spent in treated crop (PT) approaches 1, TK processes dominate and spatial choice has very little effect, and conversely if PT is small spatial choice dominates and TK makes little contribution to exposure reduction. The latter situation means that a short time spent in the pesticide-treated field mimics exposure from a small gavage dose, but TK only makes a substantial difference when the dose was consumed over a longer period. We concluded that a combined TK-IBM is most likely to bring added value to the risk assessment process when the temporal pattern of feeding, time spent in exposed area and TK parameters are at an intermediate level; for instance wood mice in foliar spray scenarios spending more time in crop fields because of better plant cover.

Earthworm distribution and abundance predicted by a process-based model

Earthworms are significant ecosystem engineers and are an important component of the diet of many vertebrates and invertebrates, so the ability to predict their distribution and abundance would have wide application in ecology, conservation and land management. Earthworm viability is known to be affected by the availability and quality of food resources, soil water conditions and temperature, but has not yet been modelled mechanistically to link effects on individuals to field population responses. Here we present a novel model capable of predicting the effects of land management and environmental conditions on the distribution and abundance of Aporrectodea caliginosa, the dominant earthworm species in agroecosystems. Our process-based approach uses individual based modelling (IBM), in which each individual has its own energy budget. Individual earthworm energy budgets follow established principles of physiological ecology and are parameterised for A. caliginosa from experimental measurements under optimal conditions. Under suboptimal conditions (e.g. food limitation, low soil temperatures and water contents) reproduction is prioritised over growth. Good model agreement to independent laboratory data on individual cocoon production and growth of body mass, under variable feeding and temperature conditions support our representation of A. caliginosa physiology through energy budgets. Our mechanistic model is able to accurately predict A. caliginosa distribution and abundance in spatially heterogeneous soil profiles representative of field study conditions. Essential here is the explicit modelling of earthworm behaviour in the soil profile. Local earthworm movement responds to a trade-off between food availability and soil water conditions, and this determines the spatiotemporal distribution of the population in the soil profile. Importantly, multiple environmental variables can be manipulated simultaneously in the model to explore earthworm population exposure and effects to combinations of stressors. Potential applications include prediction of the population-level effects of pesticides and changes in soil management e.g. conservation tillage and climate change.

Calibration and evaluation of individual-based models using Approximate Bayesian Computation

This paper investigates the feasibility of using approximate Bayesian computation (ABC) to calibrate and evaluate complex individual-based models (IBMs). As ABC evolves, various versions are emerging, but here we only explore the most accessible version, rejection-ABC. Rejection-ABC involves running models a large number of times, with parameters drawn randomly from their prior distributions, and then retaining the simulations closest to the observations. Although well-established in some fields, whether ABC will work with ecological IBMs is still uncertain. Rejection-ABC was applied to an existing 14-parameter earthworm energy budget IBM for which the available data consist of body mass growth and cocoon production in four experiments. ABC was able to narrow the posterior distributions of seven parameters, estimating credible intervals for each. ABC’s accepted values produced slightly better fits than literature values do. The accuracy of the analysis was assessed using cross-validation and coverage, currently the best available tests. Of the seven unnarrowed parameters, ABC revealed that three were correlated with other parameters, while the remaining four were found to be not estimable given the data available. It is often desirable to compare models to see whether all component modules are necessary. Here we used ABC model selection to compare the full model with a simplified version which removed the earthworm’s movement and much of the energy budget. We are able to show that inclusion of the energy budget is necessary for a good fit to the data. We show how our methodology can inform future modelling cycles, and briefly discuss how more advanced versions of ABC may be applicable to IBMs. We conclude that ABC has the potential to represent uncertainty in model structure, parameters and predictions, and to embed the often complex process of optimizing an IBM’s structure and parameters within an established statistical framework, thereby making the process more transparent and objective.

Predicting how many animals will be where: how to build, calibrate and evaluate individual-based models

Individual-based models (IBMs) can simulate the actions of individual animals as they interact with one another and the landscape in which they live. When used in spatially-explicit landscapes IBMs can show how populations change over time in response to management actions. For instance, IBMs are being used to design strategies of conservation and of the exploitation of fisheries, and for assessing the effects on populations of major construction projects and of novel agricultural chemicals. In such real world contexts, it becomes especially important to build IBMs in a principled fashion, and to approach calibration and evaluation systematically. We argue that insights from physiological and behavioural ecology offer a recipe for building realistic models, and that Approximate Bayesian Computation (ABC) is a promising technique for the calibration and evaluation of IBMs. IBMs are constructed primarily from knowledge about individuals. In ecological applications the relevant knowledge is found in physiological and behavioural ecology, and we approach these from an evolutionary perspective by taking into account how physiological and behavioural processes contribute to life histories, and how those life histories evolve. Evolutionary life history theory shows that, other things being equal, organisms should grow to sexual maturity as fast as possible, and then reproduce as fast as possible, while minimising per capita death rate. Physiological and behavioural ecology are largely built on these principles together with the laws of conservation of matter and energy. To complete construction of an IBM information is also needed on the effects of competitors, conspecifics and food scarcity; the maximum rates of ingestion, growth and reproduction, and life-history parameters. Using this knowledge about physiological and behavioural processes provides a principled way to build IBMs, but model parameters vary between species and are often difficult to measure. A common solution is to manually compare model outputs with observations from real landscapes and so to obtain parameters which produce acceptable fits of model to data. However, this procedure can be convoluted and lead to over-calibrated and thus inflexible models. Many formal statistical techniques are unsuitable for use with IBMs, but we argue that ABC offers a potential way forward. It can be used to calibrate and compare complex stochastic models and to assess the uncertainty in their predictions. We describe methods used to implement ABC in an accessible way and illustrate them with examples and discussion of recent studies. Although much progress has been made, theoretical issues remain, and some of these are outlined and discussed.

Template-based quadrilateral meshing

Generating quadrilateral meshes is a highly non-trivial task, as design decisions are frequently driven by specific application demands. Automatic techniques can optimize objective quality metrics, such as mesh regularity, orthogonality, alignment and adaptivity; however, they cannot make subjective design decisions. There are a few quad meshing approaches that offer some mechanisms to include the user in the mesh generation process; however, these techniques either require a large amount of user interaction or do not provide necessary or easy to use inputs. Here, we propose a template-based approach for generating quad-only meshes from triangle surfaces. Our approach offers a flexible mechanism to allow external input, through the definition of alignment features that are respected during the mesh generation process. While allowing user inputs to support subjective design decisions, our approach also takes into account objective quality metrics to produce semi-regular, quad-only meshes that align well to desired surface features. Published by Elsevier Ltd.

PedVis: A Structured, Space-Efficient Technique for Pedigree Visualization

Public genealogical databases are becoming increasingly populated with historical data and records of the current population`s ancestors. As this increasing amount of available information is used to link individuals to their ancestors, the resulting trees become deeper and more dense, which justifies the need for using organized, space-efficient layouts to display the data. Existing layouts are often only able to show a small subset of the data at a time. As a result, it is easy to become lost when navigating through the data or to lose sight of the overall tree structure. On the contrary, leaving space for unknown ancestors allows one to better understand the tree`s structure, but leaving this space becomes expensive and allows fewer generations to be displayed at a time. In this work, we propose that the H-tree based layout be used in genealogical software to display ancestral trees. We will show that this layout presents an increase in the number of displayable generations, provides a nicely arranged, symmetrical, intuitive and organized fractal structure, increases the user`s ability to understand and navigate through the data, and accounts for the visualization requirements necessary for displaying such trees. Finally, user-study results indicate potential for user acceptance of the new layout.

Two-Phase Mapping for Projecting Massive Data Sets

Most multidimensional projection techniques rely on distance (dissimilarity) information between data instances to embed high-dimensional data into a visual space. When data are endowed with Cartesian coordinates, an extra computational effort is necessary to compute the needed distances, making multidimensional projection prohibitive in applications dealing with interactivity and massive data. The novel multidimensional projection technique proposed in this work, called Part-Linear Multidimensional Projection (PLMP), has been tailored to handle multivariate data represented in Cartesian high-dimensional spaces, requiring only distance information between pairs of representative samples. This characteristic renders PLMP faster than previous methods when processing large data sets while still being competitive in terms of precision. Moreover, knowing the range of variation for data instances in the high-dimensional space, we can make PLMP a truly streaming data projection technique, a trait absent in previous methods.

Interactive Vector Field Feature Identification

We introduce a flexible technique for interactive exploration of vector field data through classification derived from user-specified feature templates. Our method is founded on the observation that, while similar features within the vector field may be spatially disparate, they share similar neighborhood characteristics. Users generate feature-based visualizations by interactively highlighting well-accepted and domain specific representative feature points. Feature exploration begins with the computation of attributes that describe the neighborhood of each sample within the input vector field. Compilation of these attributes forms a representation of the vector field samples in the attribute space. We project the attribute points onto the canonical 2D plane to enable interactive exploration of the vector field using a painting interface. The projection encodes the similarities between vector field points within the distances computed between their associated attribute points. The proposed method is performed at interactive rates for enhanced user experience and is completely flexible as showcased by the simultaneous identification of diverse feature types.

Solar position diagram

Program SOLVEJ är ett användarvänligt program som visar solens vandring över himlavalvet vid upp till fem valfria datum och vid valfri ort. Programmet är utvecklat av två skäl. För det första, att demonstreras för en intresserad allmänhet som del av vandringsutställning om solenergi, vilken är initierad och utarbetad av SERC. För det andra, att användas av solenerglintressenter för att snabbt få en uppfattning om solinstrålningen på en ort vid olika tidpunkter på året.Indata till programmet ges från tangentbordet. Som svar på frågor skrivs för vilken ort diagrammet skall gälla, max fem datum, ortens latitud och longitud, som anges positiv i västlig riktning, samt tidszonen. Varje uppgift avslutas med tryck på tangenten ENTER. Programmet kommer nu att rita ett koordinatsystem på skärmen. Första axeln visar vädersträcken, norr, öster, söder, väster och norr, varje delstreck utgör 10 grader. För södra halvklotet byter norr och söder plats. Andra axeln visar höjden över horisonten i grader, 0 till 90 grader och 10 grader för varje delstreck. Efter några sekunder ritas diagrammet upp med solhöjden som funktion av väderstrecket och varje hel timme markerad. Se fig. 1-4. Slutligen frågas efter om diagrammet skall ritas ut på printer. SOLVEJ avbrytes med att trycka CTRL+BREAK.SOLVEJ är skrivet i Quick-BASIC (se App. 1) och leveras både som källkod och körklar version. Lämplig dator är IBM-kompatibel AT med EGA- eller VGA-skärmkort (ej Herkules Lämplig printer är IBM Proprinter eller liknande matrisskrivare, kopplad till LPT1 på kommunikationskortet.Till grund för beräkningarna har använts artikeln On Calculating the Position of the Sun, publicerad i nr. 1 1988 av The International Journal of Ambient Energy. Fem empiriska ekvationer beträffande beräkningar av solens position har studerats för att undersöka deras tillförlitlighet. Felaktigheter på fem grader eller mer kan uppträda om man använder sig av de enkla ekvationer som kan hittas solenergi-böcker och som inte kräver tillgång till dator. FORTRAN-rutinen SUNAE2 (se App. 2) beräknar solpositionen med noggrannast kända metod. Program SOLVEJ är en utveckling av SUNAE2.

WEB & arte: desafios comunicacionais na educação

Dissertação apresentada ao Programa de Mestrado em Comunicação da Universidade Municipal de São Caetano do Sul - USCS

Mineração de dados utilizando aprendizado não-supervisionado: um estudo de caso para bancos de dados da saúde

A mineração de dados constitui o processo de descoberta de conhecimento interessante, com a utilização de métodos e técnicas que permitem analisar grandes conjuntos de dados para a extração de informação previamente desconhecida, válida e que gera ações úteis, de grande ajuda para a tomada de decisões estratégicas. Dentre as tarefas de mineração de dados, existem aquelas que realizam aprendizado não-supervisionado, o qual é aplicado em bases de dados não-classificados, em que o algoritmo extrai as características dos dados fornecidos e os agrupa em classes. Geralmente, o aprendizado não-supervisionado é aplicado em tarefas de agrupamento, que consistem em agrupar os dados de bancos de dados volumosos, com diferentes tipos de dados em classes ou grupos de objetos que são similares dentro de um mesmo grupo e dissimilares em diferentes grupos desses bancos de dados, de acordo com alguma medida de similaridade. Os agrupamentos são usados como ponto de partida para futuras investigações. Este trabalho explora, mediante a realização de um estudo de caso, o uso de agrupamento como tarefa de mineração de dados que realiza aprendizado nãosupervisionado, para avaliar a adequação desta tecnologia em uma base de dados real da área de saúde. Agrupamento é um tema ativo em pesquisas da área pelo seu potencial de aplicação em problemas práticos. O cenário da aplicação é o Sistema de Informações Hospitalares do SUS, sob a gestão da Secretaria Estadual de Saúde do Rio Grande do Sul. Mensalmente, o pagamento de um certo número de internações é bloqueado, uma vez que a cobrança de internações hospitalares é submetida a normas do SUS e a critérios técnicos de bloqueio estabelecidos pela Auditoria Médica da SES para verificar a ocorrência de algum tipo de impropriedade na cobrança dos procedimentos realizados nessas internações hospitalares. A análise de agrupamento foi utilizada para identificar perfis de comportamentos ou tendências nas internações hospitalares e avaliar desvios ou outliers em relação a essas tendências e, com isso, descobrir padrões interessantes que auxiliassem na otimização do trabalho dos auditores médicos da SES. Buscou-se ainda compreender as diferentes configurações de parâmetros oferecidos pela ferramenta escolhida para a mineração de dados, o IBM Intelligent Miner, e o mapeamento de uma metodologia de mineração de dados, o CRISP-DM, para o contexto específico deste estudo de caso. Os resultados deste estudo demonstram possibilidades de criação e melhora dos critérios técnicos de bloqueio das internações hospitalares que permitem a otimização do trabalho de auditores médicos da SES. Houve ainda ganhos na compreensão da tecnologia de mineração de dados com a utilização de agrupamento no que se refere ao uso de uma ferramenta e de uma metodologia de mineração de dados, em que erros e acertos evidenciam os cuidados que devem ser tomados em aplicações dessa tecnologia, além de contribuírem para o seu aperfeiçoamento.

Um Estudo de um sistema de informações hipermídia : caso particular da Assembléia Legislativa do Rio Grande do Sul

O presente trabalho se insere dentro de uma aplicação real na Assembléia Legislativa do Rio Grande do Sul (ALERGS), desenvolvida no Departamento de Sistemas de Informações, aproveitando-se do Sistema PRIMA/Vídeo – um sistema de veiculação interna de sinais de vídeo – já existente desde novembro de 1996. O PRIMA/Vídeo surgiu da necessidade de implantação de um sistema que permitisse o acompanhamento das múltiplas reuniões realizadas simultaneamente no âmbito do Palácio Farroupilha. Um projeto foi elaborado pela IBM do Brasil e implantado um sistema composto por dezesseis câmeras de sinais de vídeo ligadas a uma rede de 120 estações, que recebem analogicamente e em tempo real os sinais de vídeo. Este sistema permite o acompanhamento on-line de qualquer reunião nas dependências da ALERGS, além de receber imagens dos canais das emissoras a cabo. Entretanto, surgiu a necessidade de gravação destes vários eventos ocorridos para posterior exibição, criando, assim, um estudo para um sistema de informações composto de dados multimídia (sinais de vídeo do PRIMA/Vídeo). O Sistema de Informações Hipermídia da Assembléia Legislativa (SIHAL) visa o armazenamento e a disponibilização de sinais de vídeo (imagem e som) aos usuários internos da ALERGS. Através deste novo Sistema, os usuários poderão assistir a reuniões realizadas anteriormente e terão opções com capacidade de: • armazenar e organizar fisicamente os vídeos analógicos das Sessões Plenárias; • organizar o agendamento das Sessões Plenárias solicitadas no canal analógico de vídeo do PRIMA/Vídeo; • armazenar digitalmente os principais trechos de vídeo dos eventos da Assembléia; • fornecer o download dos trechos digitalizados aos usuários pela interface do Sistema; • fornecer a fita de vídeo aos usuários do Sistema; • criar uma base de dados de vídeo referente às imagens digitalizadas das Sessões Plenárias; • fornecer acesso à base de dados de vídeo. A principal contribuição desta dissertação é o estudo sobre soluções mistas, integrando dados multimídia analógicos e digitais com o intuito de propor um Sistema de Informações Hipermídia, o qual foi denominado de SIHAL. Um protótipo do SIHAL será implementado como demonstração da viabilidade das idéias citadas no sistema proposto.

Desenvolvimento de sistemas de informação com base em objetos de negócios : um protocolo de análise com vistas à reutilização de software

O objetivo da pesquisa atém-se primeiramente em elaborar um protocolo que permita analisar, por meio de um conjunto de indicadores, o processo de reutilização de software no desenvolvimento de sistemas de informação modelando objetos de negócios. O protocolo concebido compõe-se de um modelo analítico e de grades de análise, a serem empregadas na classificação e tabulação dos dados obtidos empiricamente. Com vistas à validação inicial do protocolo de análise, realiza-se um estudo de caso. A investigação ocorre num dos primeiros e, no momento, maior projeto de fornecimento de elementos de software reutilizáveis destinados a negócios, o IBM SANFRANCISCO, bem como no primeiro projeto desenvolvido no Brasil com base no por ele disponibilizado, o sistema Apontamento Universal de Horas (TIME SHEET System). Quanto à aplicabilidade do protocolo na prática, este se mostra abrangente e adequado à compreensão do processo. Quanto aos resultados do estudo de caso, a análise dos dados revela uma situação em que as expectativas (dos pesquisadores) de reutilização de elementos de software orientadas a negócio eram superiores ao observado. Houve, entretanto, reutilização de elementos de baixo nível, que forneceram a infra-estrutura necessária para o desenvolvimento do projeto. Os resultados contextualizados diante das expectativas de reutilização (dos desenvolvedores) são positivos, na medida em que houve benefícios metodológicos e tecnológicos decorrentes da parceria realizada. Por outro lado, constatam-se alguns aspectos restritivos para o desenvolvedor de aplicativos, em virtude de escolhas arbitrárias realizadas pelo provedor de elementos reutilizáveis.