In this thesis a number of statistical methods have been developed and applied to habitat suitability modelling for rare and threatened species. Data available on these species are typically limited. Therefore, developing these models from these data can be problematic and may produce prediction biases. To address these problems there are three aims of this thesis. The _rst aim is to develop and implement frequentist and Bayesian statistical modelling approaches for these types of data. The second aim is develop and implement expert elicitation methods. The third aim is to apply these novel approaches to Australian rare and threatened species case studies with the intention of habitat suitability modelling. The _rst aim is ful_lled by investigating two innovative approaches for habitat suitability modelling and sensitivity analysis of the second approach to priors. The _rst approach is a new multilevel framework developed to model the species distribution at multiple scales and identify excess zeros (absences outside the species range). Applying a statistical modelling approach to the identi_cation of excess zeros has not previously been conducted. The second approach is an extension and application of Bayesian classi_cation trees to modelling the habitat suitability of a threatened species. This is the _rst `real' application of this approach in ecology. Lastly, sensitivity analysis of the priors in Bayesian classi_cation trees are examined for a real case study. Previously, sensitivity analysis of this approach to priors has not been examined. To address the second aim, expert elicitation methods are developed, extended and compared in this thesis. In particular, one elicitation approach is extended from previous research, there is a comparison of three elicitation methods, and one new elicitation approach is proposed. These approaches are illustrated for habitat suitability modelling of a rare species and the opinions of one or two experts are elicited. The _rst approach utilises a simple questionnaire, in which expert opinion is elicited on whether increasing values of a covariate either increases, decreases or does not substantively impact on a response. This approach is extended to express this information as a mixture of three normally distributed prior distributions, which are then combined with available presence/absence data in a logistic regression. This is one of the _rst elicitation approaches within the habitat suitability modelling literature that is appropriate for experts with limited statistical knowledge and can be used to elicit information from single or multiple experts. Three relatively new approaches to eliciting expert knowledge in a form suitable for Bayesian logistic regression are compared, one of which is the questionnaire approach. Included in this comparison of three elicitation methods are a summary of the advantages and disadvantages of these three methods, the results from elicitations and comparison of the prior and posterior distributions. An expert elicitation approach is developed for classi_cation trees, in which the size and structure of the tree is elicited. There have been numerous elicitation approaches proposed for logistic regression, however no approaches have been suggested for classi_cation trees. The last aim of this thesis is addressed in all chapters, since the statistical approaches proposed and extended in this thesis have been applied to real case studies. Two case studies have been examined in this thesis. The _rst is the rare native Australian thistle (Stemmacantha australis), in which the dataset contains a large number of absences distributed over the majority of Queensland, and a small number of presence sites that are only within South-East Queensland. This case study motivated the multilevel modelling framework. The second case study is the threatened Australian brush-tailed rock-wallaby (Petrogale penicillata). The application and sensitivity analysis of Bayesian classi_cation trees, and all expert elicitation approaches investigated in this thesis are applied to this case study. This work has several implications for conservation and management of rare and threatened species. Novel statistical approaches addressing the _rst aim provide extensions to currently existing methods, or propose a new approach, for identi _cation of current and potential habitat. We demonstrate that better model predictions can be achieved using each method, compared to standard techniques. Elicitation approaches addressing the second aim ensure expert knowledge in various forms can be harnessed for habitat modelling, a particular bene_t for rare and threatened species which typically have limited data. Throughout, innovations in statistical methodology are both motivated and illustrated via habitat modelling for two rare and threatened species: the native thistle Stemmacantha australis and the brush-tailed rock wallaby Petrogale penicillata.

Dizertační práce se zabývá predikcí vysokodimenzionálních dat genových expresí. Množství dostupných genomických dat významně vzrostlo v průběhu posledního desetiletí. Kombinování dat genových expresí s dalšími daty nachází uplatnění v mnoha oblastech. Například v klinickém řízení rakoviny (clinical cancer management) může přispět k přesnějšímu určení prognózy nemocí. Hlavní část této dizertační práce je zaměřena na kombinování dat genových expresí a klinických dat. Používáme logistické regresní modely vytvořené prostřednictvím různých regularizačních technik. Generalizované lineární modely umožňují kombinování modelů s různou strukturou dat. V dizertační práci je ukázáno, že kombinování modelu dat genových expresí a klinických dat může vést ke zpřesnění výsledku predikce oproti vytvoření modelu pouze z dat genových expresí nebo klinických dat. Navrhované postupy přitom nejsou výpočetně náročné.  Testování je provedeno nejprve se simulovanými datovými sadami v různých nastaveních a následně s~reálnými srovnávacími daty. Také se zde zabýváme určením přídavné hodnoty microarray dat. Dizertační práce obsahuje porovnání příznaků vybraných pomocí klasifikátoru genových expresí na pěti různých sadách dat týkajících se rakoviny prsu. Navrhujeme také postup výběru příznaků, který kombinuje data genových expresí a znalosti z genových ontologií.

當母體中有部份對象因被治癒或免疫而不會失敗時，需考慮這群對象所佔的比率，即存活分率。本文主要在探討如何以貝氏方法對含存活分率之治癒率模式進行分析，並特別針對兩種含存活分率的迴歸模式，分別是Weibull迴歸模式以及對數邏輯斯迴歸模式，導出概似函數與各參數之完全條件後驗分配及其性質。由於聯合後驗分配相當複雜，各參數之邊際後驗分配之解析形式很難表達出。所以，我們採用了馬可夫鏈蒙地卡羅方法（MCMC）中的Gibbs抽樣法及Metropolis法，模擬產生參數值，以進行貝氏分析。實證部份，我們分析了黑色素皮膚癌的資料，這是由美國Eastern Cooperative Oncology Group所進行的第三階段臨床試驗研究。有關模式選取的部份，我們先分別求出各對象在每個模式之下的條件預測指標（CPO），再據以算出各模式的對數擬邊際概似函數值（LPML），以比較各模式之適合性。 / When we face the problem that part of subjects have been cured or are immune so they never fail, we need to consider the fraction of this group among the whole population, which is the so called survival fraction. This article discuss that how to analyze cure rate models containing survival fraction based on Bayesian method. Two cure rate models containing survival fraction are focused; one is based on the Weibull regression model and the other is based on the log-logistic regression model. Then, we derive likelihood functions and full conditional posterior distributions under these two models. Since joint posterior distributions are both complicated, and marginal posterior distributions don’t have closed form, we take Gibbs sampling and Metropolis sampling of Markov Monte Carlo chain method to simulate parameter values. We illustrate how to conduct Bayesian analysis by using the data from a melanoma clinical trial in the third stage conducted by Eastern Cooperative Oncology Group. To do model selection, we compute the conditional predictive ordinate (CPO) for every subject under each model, then the goodness is determined by the comparing the value of log of pseudomarginal likelihood (LPML) of each model.