Preface

This book grew out of exercises used for the computer lab portion of ENS 495:Design & Analysis, an ecological statistics course I taught for two years as and adjunct with the Department of Department of Biological & Environmental Sciences at California University of Pennsylvania. The goal is to walk students step by step through the process of working with data in R.

A major influence in how this book is written is th online book Program MARK: a gentle introduction, edited Evan Cooch and Gary White. MARK is one of the most important pieces of software ever written for ecologists and implements a vast number of mark-recapture and occupancy-type models for understanding population processes such as population size, survival, migration, occupancy, and meta-population dynamics. The book patiently walks users through the basic of these models step by step, concept by concept, and click by click. I have sought to adopt a similar thorough and holistic approach in this book.

In Part I of this book I’ll introduce why the role of data science in ecology is important and lay out the scope of this book. I’ll also walk through the basic steps of getting R and RStudio up and running on your comptuer, walk through a basic R section, and discuss the various ways we’ll interact with R using code and script files. I’ll also introduce rmarkdown, a way of integrating the R code of scripts with basic capabilities of word processing and web developement. Scripts organized in rmarkdown are a handy way to organize and annotate code, store and disseminate your work, and structure your analyses and data presensations so that the computations behind them are fully reproducible.