Made available in DSpace on 2016-06-02T20:06:04Z (GMT). No. of bitstreams: 1 2751.pdf: 886213 bytes, checksum: 2f07f7329a7f25f1759ddb5d7a6edd66 (MD5) Previous issue date: 2010-01-15 / Financiadora de Estudos e Projetos / In this study, we used the capture-recapture procedure to estimate the size of a closed population. We analysed three di_erent statistics models. For each one of these models we determined - through several methods of eliminating nuisance parameters - the likelihood function and the pro_le, conditional, uniform integrated, Je_reys integrated and generalized integrated likelihood functions of the population size, except for the last model where we determined a function that is analogous to the conditional likelihood function, called integrated restricted likelihood function. In each instance we determined the respectives maximum likelihood estimates, the empirical con_dence intervals and the empirical mean squared errors of the estimates for the population size and we studied, using simulated data, the performances of the models. / Nesta dissertação utilizamos o processo de captura-recaptura para estimar o tamanho de uma população fechada. Analisamos três modelos estatísticos diferentes e, para cada um deles, através de diversas metodologias de eliminação de parâmetros perturbadores, determinamos as funções de verossimilhança e de verossimilhança perfilada, condicional, integrada uniforme, integrada de Jeffreys e integrada generalizada do tamanho populacional, com exceção do último modelo onde determinamos uma função análoga à função de verossimilhança condicional, denominada função de verossimilhança restrita integrada. Em cada capítulo determinamos as respectivas estimativas de máxima verossimilhança e construímos intervalos de confiança empíricos para o tamanho populacional, bem como determinamos os erros quadráticos médios empíricos das estimativas e estudamos, através de dados simulados, as performances dos modelos.

Made available in DSpace on 2016-06-02T20:06:05Z (GMT). No. of bitstreams: 1 4034.pdf: 873658 bytes, checksum: 8c8e2d629291b4edab052dd0ee734f94 (MD5) Previous issue date: 2005-02-25 / Financiadora de Estudos e Projetos / In this work, a bayesian methodology is shown to estimate the size of a diabethic-su¤ering population through lists containing information data of patients. The applied methodology is analogous of capture-recaptures in animal population. We assume correct the registers of relative information to the patients as well as we take in account correct and incorrect registers of the information. In case the supposed registers are correct, the methodology is developed for two or more lists and the Bayes estimate is determined for the size of a population. In a second model, the occurrency of correct and incorrect registers are considered, presenting a two-stage estimation method for the model parameters using two lists. For both models there are results with simulated and real examples. / Nesta dissertação apresentamos uma metodologia bayesiana para estimar o tamanho de uma população de diabéticos através de listas contendo informações sobre dados dos indivíduos. A metodologia aplicada é análoga a de captura-recaptura em população animal. Supomos corretos os registros de informações relativas aos pacientes assim como levamos em consideração registros corretos e incorretos das informações. No caso da suposição dos registros serem corretos, a metodologia é desenvolvida para duas ou mais listas e determinamos estimativas de Bayes para o tamanho populacional. Em um segundo modelo, consideramos a ocorrência de registros corretos e incorretos dos dados relativos aos pacientes, e apresentamos um método de estimação em dois estágios para os parâmetros do modelo utilizando duas listas. Para ambos os modelos, apresentamos resultados com exemplos simulados e reais.

Made available in DSpace on 2016-06-02T20:06:10Z (GMT). No. of bitstreams: 1 6083.pdf: 1151427 bytes, checksum: 24c39bb02ef8c214a3e10c3cc5bae9ef (MD5) Previous issue date: 2014-03-14 / Financiadora de Estudos e Projetos / In this work, we consider the estimation of the number of errors in a software from a closed population. The process of estimating the population size is based on the capture-recapture method which consists of examining the software, in parallel, by a number of reviewers. The probabilistic model adopted accommodates situations in which reviewers are independent and homogeneous (equally efficient), and each error is an element that is part of a disjoint partition in relation to its detection probability. We propose an iterative process to obtain maximum likelihood estimates in which the EM algorithm is used to the nuisance parameters estimation. The estimates of population parameters were also obtained under the Bayesian approach, in which Monte Carlo on Markov Chains (MCMC) simulations through Gibbs sampling algorithm with insertion of latent variables were used on the conditional posterior distributions. The two approaches were applied to simulated data and in two real data sets from the literature. / Neste trabalho, consideramos a estimação do número de erros em um software provenientes de uma população fechada. O processo de estimação do tamanho populacional é baseado no método de captura-recaptura, que consiste em examinar o software, em paralelo, por certo número de revisores. O modelo probabilístico adotado acomoda situações em que os revisores são independentes e homogêneos (igualmente eficientes) e que cada erro é um elemento que faz parte de uma partição disjunta quanto à sua probabilidade de detecção. Propomos um processo iterativo para obtenção das estimativas de máxima verossimilhança em que utilizamos o algoritmo EM na estimação dos parâmetros perturbadores. As estimativas dos parâmetros populacionais também foram obtidas sob o enfoque Bayesiano, onde utilizamos simulações de Monte Carlo em Cadeias de Markov (MCMC) através do algoritmo Gibbs sampling com a inserção de variáveis latentes nas distribuições condicionais a posteriori. As duas abordagens foram aplicadas em dados simulados e em dois conjuntos de dados reais da literatura.

In a single capture-recapture problem, two new Wilson methods for interval estimation of population size are derived. Classical Chapman interval, Wilson and Wilson-cc intervals are examined and compared in terms of their expected interval width and exact coverage properties in two models. The new approach performs better than the Chapman in each model. Bayesian analysis also gives a different way to estimate population size.

To underpin and improve advice given to government and other interested parties on the state of Britain’s common songbird populations, new models for analysing ecological data are developed in this thesis. These models use data from the British Trust for Ornithology’s Constant Effort Sites (CES) scheme, an annual bird-ringing programme in which catch effort is standardised. Data from the CES scheme are routinely used to index abundance and productivity, and to a lesser extent estimate adult survival rates. However, two features of the CES data that complicate analysis were previously inadequately addressed, namely the presence in the catch of “transient” birds not associated with the local population, and the sporadic failure in the constancy of effort assumption arising from the absence of within-year catch data. The current methodology is extended, with efficient Bayesian models developed for each of these demographic parameters that account for both of these data nuances, and from which reliable and usefully precise estimates are obtained. Of increasing interest is the relationship between abundance and the underlying vital rates, an understanding of which facilitates effective conservation. CES data are particularly amenable to an integrated approach to population modelling, providing a combination of demographic information from a single source. Such an integrated approach is developed here, employing Bayesian methodology and a simple population model to unite abundance, productivity and survival within a consistent framework. Independent data from ring-recoveries provide additional information on adult and juvenile survival rates. Specific advantages of this new integrated approach are identified, among which is the ability to determine juvenile survival accurately, disentangle the probabilities of survival and permanent emigration, and to obtain estimates of total seasonal productivity. The methodologies developed in this thesis are applied to CES data from Sedge Warbler, Acrocephalus schoenobaenus, and Reed Warbler, A. scirpaceus.

The Raso lark is a Critically Endangered bird endemic to the islet of Raso, Cape Verde. This thesis investigates two phenomena that particularly put the species at risk: its extreme fluctuations in population size, and its potentially very low genetic diversity arising from small population size and severe past population contraction. More specifically, two chapters estimate year-to-year survival and explore the factors - environmental and individual - that influence it, while two other chapters examine the lark’s genetic characteristics compared to its two continental closest relatives, including phylogenetic relationships and levels of genetic diversity. The conclusion of the thesis then uses these results to make recommendations for the conservation of the Raso lark. Each of the data chapters is summarized below: Chapter 3 estimates adult survival in the Raso lark and tests whether it could be linked to two population phenomena observed in the field: a highly variable population size and a male-biased sex ratio in certain years. Using a dataset spanning 10 years, I estimated survival for both sexes to fluctuate between 0.76 and 0.94 over this period. This is much higher than the survival rate of its closest relative, the skylark. I also found strong evidence for survival fluctuating over time and differing between males and females (with males having higher survival until 2011, at which point the trend inverted), which could play a role in the aforementioned population size fluctuations and male-biased sex ratio, respectively. Chapter 4 aims at understanding which factors shape survival in the Raso lark. Two types of variables were considered: year-dependent (rainfall, population size, population mean clutch size) and individual-dependent (age, body size characters, size ratio with mate, Ase18 genotype). Amongst the year-dependent variables, only sameyear rainfall impacted survival, with a 13% decrease in survival in the wettest year compared to the driest year, making it the most likely explanation for the inter-annual fluctuations in survival found in Chapter 3. Results also hint at some of the individual factors - morphological measurements and Ase18 genotype - influencing survival. The picture that emerges is that of a species whose life history strategy is to invest heavily in maintenance and survival, but less into fecundity, which stands in sharp contrast with the mainland-dwelling skylark. This is consistent with the theory that island birds generally have slower life history strategies than their continental counterparts. Chapter 5 determines the precise relationship between members of the Alauda clade, resolving a node on the phylogenetic tree of all larks that the study by Alström et al. (2013) was unable to resolve. My RADseq results indicate that the Raso lark and the skylark are sister species, and that the Oriental lark is likely to be a subpopulation, or maybe a subspecies, of the skylark. Chapter 6 compares the population genetics of the Raso lark with those of the skylark. In particular, it estimates the genetic diversity of the Raso lark and investigates the drivers behind it. I found unexpectedly high nucleotide diversity in the Raso lark, and explain this by showing that the population contraction that the species underwent was recent enough for most of the diversity to still be present. Moreover, 16% of the Raso lark genome has levels of heterozygosity on average 6.6 times higher than elsewhere on the genome, likely due to suppressed recombination and the existence of a neo-sex chromosome in larks. Despite this, I found high levels of relatedness and of linkage disequilibrium in the Raso lark, two clear genetic signs that it underwent a severe population contraction several centuries ago.

Made available in DSpace on 2016-06-02T20:04:51Z (GMT). No. of bitstreams: 1 4032.pdf: 1016886 bytes, checksum: 6e1eb83f197a88332f8951b054c1f01a (MD5) Previous issue date: 2011-11-18 / Financiadora de Estudos e Projetos / The capture-recapture process, largely used in the estimation of the number of elements of animal population, is also applied to other branches of knowledge like Epidemiology, Linguistics, Software reliability, Ecology, among others. One of the _rst applications of this method was done by Laplace in 1783, with aim at estimate the number of inhabitants of France. Later, Carl G. J. Petersen in 1889 and Lincoln in 1930 applied the same estimator in the context of animal populations. This estimator has being known in literature as _Lincoln-Petersen_ estimator. In the mid-twentieth century several researchers dedicated themselves to the formulation of statistical models appropriated for the estimation of population size, which caused a substantial increase in the amount of theoretical and applied works on the subject. The capture-recapture models are constructed under certain assumptions relating to the population, the sampling procedure and the experimental conditions. The main assumption that distinguishes models concerns the change in the number of individuals in the population during the period of the experiment. Models that allow for births, deaths or migration are called open population models, while models that does not allow for these events to occur are called closed population models. In this work, the goal is to characterize likelihood functions obtained by applying methods of elimination of nuissance parameters in the case of closed population models. Based on these likelihood functions, we discuss methods for point and interval estimation of the population size. The estimation methods are illustrated on a real data-set and their frequentist properties are analised via Monte Carlo simulation. / O processo de captura-recaptura, amplamente utilizado na estimação do número de elementos de uma população de animais, é também aplicado a outras áreas do conhecimento como Epidemiologia, Linguística, Con_abilidade de Software, Ecologia, entre outras. Uma das primeiras aplicações deste método foi feita por Laplace em 1783, com o objetivo de estimar o número de habitantes da França. Posteriormente, Carl G. J. Petersen em 1889 e Lincoln em 1930 utilizaram o mesmo estimador no contexto de popula ções de animais. Este estimador _cou conhecido na literatura como o estimador de _Lincoln-Petersen_. Em meados do século XX muitos pesquisadores se dedicaram à formula ção de modelos estatísticos adequados à estimação do tamanho populacional, o que causou um aumento substancial da quantidade de trabalhos teóricos e aplicados sobre o tema. Os modelos de captura-recaptura são construídos sob certas hipóteses relativas à população, ao processo de amostragem e às condições experimentais. A principal hipótese que diferencia os modelos diz respeito à mudança do número de indivíduos da popula- ção durante o período do experimento. Os modelos que permitem que haja nascimentos, mortes ou migração são chamados de modelos para população aberta, enquanto que os modelos em que tais eventos não são permitidos são chamados de modelos para popula- ção fechada. Neste trabalho, o objetivo é caracterizar o comportamento de funções de verossimilhança obtidas por meio da utilização de métodos de eliminação de parâmetros perturbadores, no caso de modelos para população fechada. Baseado nestas funções de verossimilhança, discutimos métodos de estimação pontual e intervalar para o tamanho populacional. Os métodos de estimação são ilustrados através de um conjunto de dados reais e suas propriedades frequentistas são analisadas via simulação de Monte Carlo.

<p dir="ltr">To examine how forest management affects terrestrial salamanders, this dissertation: (1) examines the effects of timber harvesting strategies on salamanders; (2) examines the effects of prescribed fire for oak regeneration on salamander populations; and (3) explores the influence of artificial cover object (ACO) wood type, size and shape, and placement on salamander monitoring results. These projects were conducted at the Hardwood Ecosystem Experiment (HEE) and Martell Experimental Forest in Indiana. Long-term salamander monitoring data from the HEE were used to examine the effects of clearcuts, shelterwoods, and patch cuts on salamander captures collected up to eleven years post-harvest and were analyzed with a before-after-control-impact (BACI) design. Clearcuts and patch cuts had negative effects on salamanders 4-6 years post-harvest, which coincided with a drought; however, preparatory and establishment shelterwood harvests showed no effects on salamander captures, suggesting that retaining canopy cover may protect salamanders from compound disturbances such as drought. Also at the HEE, capture-recapture techniques were used to examine salamander population estimates before and after fire. Only two of three fires affected salamander populations. In the short term, prescribed fire effects on salamanders may be weak and intermittent and microclimate may have a greater effect on populations, although the longer-term effects of fire remain unknown. At Martell Experimental Forest, salamander numbers were compared beneath ACOs of different wood types, sizes and shapes, and grid arrays of different spacings. Pine ACOs were preferred over ash, while several small ACOs yielded equal salamander numbers to one large ACO of equal total area. High ACO density may increase capture probability but reduce the area sampled by each ACO, while lower density ACO grids may cover a larger area with the same sampling effort and produce more comparable results, but with less precision; choice of ACO experimental design will therefore require careful consideration of management goals. This dissertation also suggests strategies to support salamander populations as guidelines for managers to consider in management planning.</p>

Increasing time trends in the recorded incidence of childhood cancer have been reported in many different settings. The extent to which these trends reflect real changes in incidence, rather than improvements in methods for diagnosis and registration, is controversial. Using data from the National Registry of Childhood Tumours (NRCT), this thesis investigates time trends in cancer diagnosed under age 15 in residents of Britain during 1966-2005 (54650 cases), and considers potential sources of artefact in detail. Several different methods are used to estimate completeness of NRCT registration. The history of methods for diagnosis and registration of childhood cancers in Britain is described, and predictions are made for effects on recorded incidence. For each of the 12 main diagnostic groups, Poisson regression is used to fit continuous time trends and ‘step’ models to the annual age-sex-standardised rates by year of birth and year of diagnosis. Age-specific rates by period, and quinquennial standardised rates for diagnostic subgroups, are shown graphically. For three broad groups (leukaemia, CNS tumours and other cancer), geographical variation is compared by period of diagnosis. The results of these analyses are discussed in relation to the predicted artefacts. The evidence for a positive association between affluence and recorded incidence of childhood leukaemia is briefly reviewed. A special form of diagnostic artefact, the ‘fatal infection’ hypothesis, is proposed as an explanation of both this association and the leukaemia time trend. This hypothesis is examined in a novel test based on clinical data. The recorded incidence of childhood cancer in Britain increased in each of 12 diagnostic groups during 1966-2005 (from 0.5% per year for bone cancer to 2.5% for hepatic cancer, with 0.7% for leukaemia). Evidence presented here suggests that these increases are probably artefacts of diagnosis and registration. The potential implications for epidemiological studies of childhood cancer should be considered.