This book will allow naturalists, nature stewards, and graduate students to appreciate and comprehend basic statistical concepts as a bridge to more complex themes relevant to their daily work. Although there are excellent sources on more specialized analytical topics relevant to naturalists, this introductory book makes a connection with the experience and needs of field practitioners. It uses aspects of the natural history of the Florida scrub relevant for conservation and management as examples of analytical issues pertinent to the naturalist in a broader context. Each chapter identifies important ecological questions and then provides approaches to evaluate data, focusing on the analytical decision-making process. The book guides the reader on frequently overlooked aspects such as the understanding of model assumptions, alternative model specifications, model output interpretation, and model limitations.
The study of ecological systems is often impeded by components that escape perfect observation, such as the trajectories of moving animals or the status of plant seed banks. These hidden components can be efficiently handled with statistical modeling by using hidden variables, which are often called latent variables. Notably, the hidden variables framework enables us to model an underlying interaction structure between variables (including random effects in regression models) and perform data clustering, which are useful tools in the analysis of ecological data. This book provides an introduction to hidden variables in ecology, through recent works on statistical modeling as well as on estimation in models with latent variables. All models are illustrated with ecological examples involving different types of latent variables at different scales of organization, from individuals to ecosystems. Readers have access to the data and R codes to facilitate understanding of the model and to adapt inference tools to their own data.
Applied Statistical Modelling for Ecologists provides a gentle introduction to the essential models of applied statistics: linear models, generalized linear models, mixed and hierarchical models. All models are fit with both a likelihood and a Bayesian approach, using several powerful software packages widely used in research publications: JAGS, NIMBLE, Stan, and TMB. In addition, the foundational method of maximum likelihood is explained in a manner that ecologists can really understand. This book is the successor of the widely used Introduction to WinBUGS for Ecologists (Kéry, Academic Press, 2010). Like its parent, it is extremely effective for both classroom use and self-study, allowing students and researchers alike to quickly learn, understand, and carry out a very wide range of statistical modelling tasks. The examples in Applied Statistical Modelling for Ecologists come from ecology and the environmental sciences, but the underlying statistical models are very widely used by scientists across many disciplines. This book will be useful for anybody who needs to learn and quickly become proficient in statistical modelling, with either a likelihood or a Bayesian focus, and in the model-fitting engines covered, including the three latest packages NIMBLE, Stan, and TMB. - Contains a concise and gentle introduction to probability and applied statistics as needed in ecology and the environmental sciences - Covers the foundations of modern applied statistical modelling - Gives a comprehensive, applied introduction to what currently are the most widely used and most exciting, cutting-edge model fitting software packages: JAGS, NIMBLE, Stan, and TMB - Provides a highly accessible applied introduction to the two dominant methods of fitting parametric statistical models: maximum likelihood and Bayesian posterior inference - Details the principles of model building, model checking and model selection - Adopts a "Rosetta Stone" approach, wherein understanding of one software, and of its associated language, will be greatly enhanced by seeing the analogous code in other engines - Provides all code available for download for students, at https://www.elsevier.com/books-and-journals/book-companion/9780443137150
Models and likelihood are the backbone of modern statistics. This 2003 book gives an integrated development of these topics that blends theory and practice, intended for advanced undergraduate and graduate students, researchers and practitioners. Its breadth is unrivaled, with sections on survival analysis, missing data, Markov chains, Markov random fields, point processes, graphical models, simulation and Markov chain Monte Carlo, estimating functions, asymptotic approximations, local likelihood and spline regressions as well as on more standard topics such as likelihood and linear and generalized linear models. Each chapter contains a wide range of problems and exercises. Practicals in the S language designed to build computing and data analysis skills, and a library of data sets to accompany the book, are available over the Web.
The environmental sciences are undergoing a revolution in the use of models and data. Facing ecological data sets of unprecedented size and complexity, environmental scientists are struggling to understand and exploit powerful new statistical tools for making sense of ecological processes. In Models for Ecological Data, James Clark introduces ecologists to these modern methods in modeling and computation. Assuming only basic courses in calculus and statistics, the text introduces readers to basic maximum likelihood and then works up to more advanced topics in Bayesian modeling and computation. Clark covers both classical statistical approaches and powerful new computational tools and describes how complexity can motivate a shift from classical to Bayesian methods. Through an available lab manual, the book introduces readers to the practical work of data modeling and computation in the language R. Based on a successful course at Duke University and National Science Foundation-funded institutes on hierarchical modeling, Models for Ecological Data will enable ecologists and other environmental scientists to develop useful models that make sense of ecological data. Consistent treatment from classical to modern Bayes Underlying distribution theory to algorithm development Many examples and applications Does not assume statistical background Extensive supporting appendixes Lab manual in R is available separately
The complexity of large-scale data sets (“Big Data”) has stimulated the development of advanced computational methods for analysing them. There are two different kinds of methods to aid this. The model-based method uses probability models and likelihood and Bayesian theory, while the model-free method does not require a probability model, likelihood or Bayesian theory. These two approaches are based on different philosophical principles of probability theory, espoused by the famous statisticians Ronald Fisher and Jerzy Neyman. Introduction to Statistical Modelling and Inference covers simple experimental and survey designs, and probability models up to and including generalised linear (regression) models and some extensions of these, including finite mixtures. A wide range of examples from different application fields are also discussed and analysed. No special software is used, beyond that needed for maximum likelihood analysis of generalised linear models. Students are expected to have a basic mathematical background in algebra, coordinate geometry and calculus. Features • Probability models are developed from the shape of the sample empirical cumulative distribution function (cdf) or a transformation of it. • Bounds for the value of the population cumulative distribution function are obtained from the Beta distribution at each point of the empirical cdf. • Bayes’s theorem is developed from the properties of the screening test for a rare condition. • The multinomial distribution provides an always-true model for any randomly sampled data. • The model-free bootstrap method for finding the precision of a sample estimate has a model-based parallel – the Bayesian bootstrap – based on the always-true multinomial distribution. • The Bayesian posterior distributions of model parameters can be obtained from the maximum likelihood analysis of the model. This book is aimed at students in a wide range of disciplines including Data Science. The book is based on the model-based theory, used widely by scientists in many fields, and compares it, in less detail, with the model-free theory, popular in computer science, machine learning and official survey analysis. The development of the model-based theory is accelerated by recent developments in Bayesian analysis.
Here, biologists and statisticians come together in an interdisciplinary synthesis with the aim of developing new methods to overcome the most significant challenges and constraints faced by quantitative biologists seeking to model demographic rates.
The existing theories on the evolution of senescence assume that senescence is inevitable in all organisms. However, recent studies have shown that this is not necessarily true. A better understanding of senescence and its underlying mechanisms could have far-reaching consequences for conservation and eco-evolutionary research. This book is the first to offer interdisciplinary perspectives on the evolution of senescence in many species, setting the stage for further developments. It brings together new insights from a wide range of scientific fields and cutting-edge research done on a multitude of different animals (including humans), plants and microbes, giving the reader a complete overview of recent developments and of the controversies currently surrounding the topic. Written by specialists from a variety of disciplines, this book is a valuable source of information for students and researchers interested in ageing and life history traits and populations.
