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Foundational and Applied Statistics for Biologists Using R © 2008 Taylor & Francis Group, LLC K13403 FOUNDATIONAL and APPLIED STATISTICS f o r BIOLOGISTS USING R F O U N D A T IO N A L a n d A P P L IE D S T A T IS T IC S fo r B IO L O G IS T S U S IN G R FOUNDATIONAL and APPLIED STATISTICS f o r BIOLOGISTS USING R Ken A. Aho A h o Full of biological applications, exercises, and interactive graphical examples, Foundational and Applied Statistics for Biologists Using R presents comprehensive coverage of both modern analytical methods and statistical foundations. The author harnesses the inherent properties of the R environment to examine the code of complicated procedures step by step. The graphical capabilities of R are used to provide interactive demonstrations of simple to complex statistical concepts. The first seven chapters of the book address fundamental topics in statistics, such as the philosophy of science, probability, estimation, hypothesis testing, sampling, and experimental design. The remaining four chapters focus on applications involving correlation, regression, ANOVA, and tabular analyses. Features • Covers a wide range of analytical topics, including bootstrapping, Bayesian MCMC procedures, regression, model selection, GLMs, GAMs, nonlinear models, ANOVA designs, mixed effects models, and permutation • Emphasizes the understanding of statistical foundations • Provides R code for all analyses and uses R to generate most of the figures • Offers an introduction to R and R code for each chapter on the author’s website Unlike classic biometric texts, this book provides you with an understanding of the underlying statistics involved in the analysis of biological applications. It shows how a solid statistical foundation leads to the correct application of procedures, a clear understanding of analyses, and valid inferences concerning biological phenomena. Statistics K13403_Cover.indd 1 11/1/13 2:27 PM © 2008 Taylor & Francis Group, LLC FOUNDATIONAL and APPLIED STATISTICS f o r BIOLOGISTS USING R © 2008 Taylor & Francis Group, LLC Ken A. Aho Idaho State University Pocatel lo , Idaho, USA FOUNDATIONAL and APPLIED STATISTICS f o r BIOLOGISTS USING R Cover: View east from the Abiathar Peak in Northeastern Yellowstone National Park. Three mountain goats (Oreom- nos americanus) are visible at the edge of the summit plateau. Goat weights are approximately normally distributed with mean 90.5 kg and variance 225 kg2. This distribution is shown in the lower right hand corner of the cover. A ran- dom sample from this distribution is shown in the strip at the top. Photo credit: Scott Close. Goat illustration donated by Pearson Scott Foresman (an educational publisher) to Wikimedia Commons, http://commons.wikimedia.org/wiki/ Category:Pearson_Scott_Foresman_publisher; http://all-free-download.com. CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2014 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Version Date: 20131001 International Standard Book Number-13: 978-1-4398-7339-7 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the valid- ity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or uti- lized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopy- ing, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http:// www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com © 2008 Taylor & Francis Group, LLC To JEF and OAA who traveled on this journey vii© 2008 Taylor & Francis Group, LLC Contents Preface ........................................................................................................................................... xix Acknowledgments ...................................................................................................................... xxi Section I Foundations 1. Philosophical and Historical Foundations ........................................................................3 1.1 Introduction ...................................................................................................................3 1.2 Nature of Science ..........................................................................................................3 1.3 Scientific Principles .......................................................................................................4 1.3.1 Objectivity .........................................................................................................4 1.3.2 Realism ..............................................................................................................4 1.3.3 Communalism ..................................................................................................5 1.4 Scientific Method ......................................