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Two Wrongs Make a Right: Addressing Underreporting in Binary Data from Multiple Sources
- Scott J. Cook, Betsabe Blas, Raymond J. Carroll, Samiran Sinha
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- Journal:
- Political Analysis / Volume 25 / Issue 2 / April 2017
- Published online by Cambridge University Press:
- 11 April 2017, pp. 223-240
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Media-based event data—i.e., data comprised from reporting by media outlets—are widely used in political science research. However, events of interest (e.g., strikes, protests, conflict) are often underreported by these primary and secondary sources, producing incomplete data that risks inconsistency and bias in subsequent analysis. While general strategies exist to help ameliorate this bias, these methods do not make full use of the information often available to researchers. Specifically, much of the event data used in the social sciences is drawn from multiple, overlapping news sources (e.g., Agence France-Presse, Reuters). Therefore, we propose a novel maximum likelihood estimator that corrects for misclassification in data arising from multiple sources. In the most general formulation of our estimator, researchers can specify separate sets of predictors for the true-event model and each of the misclassification models characterizing whether a source fails to report on an event. As such, researchers are able to accurately test theories on both the causes of and reporting on an event of interest. Simulations evidence that our technique regularly outperforms current strategies that either neglect misclassification, the unique features of the data-generating process, or both. We also illustrate the utility of this method with a model of repression using the Social Conflict in Africa Database.
10 - Bayesian Models for Flexible Integrative Analysis of Multi-Platform Genomics Data
- from Part B - Vertical Integrative Analysis (General Methods)
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- By Elizabeth J. McGuffey, United States Naval Academy, Annapolis, MD, Jeffrey S. Morris, UT MD Anderson Cancer Center, Houston, TX, Ganiraju C. Manyam, UT MD Anderson Cancer Center, Houston, TX, Raymond J. Carroll, Texas A&M University, College Station, TX, Veerabhadran Baladandayuthapani, UT MD Anderson Cancer Center, Houston, TX
- George Tseng, University of Pittsburgh, Debashis Ghosh, Pennsylvania State University, Xianghong Jasmine Zhou, University of Southern California
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- Book:
- Integrating Omics Data
- Published online:
- 05 September 2015
- Print publication:
- 23 September 2015, pp 221-241
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Contributors
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- By Mitchell Aboulafia, Frederick Adams, Marilyn McCord Adams, Robert M. Adams, Laird Addis, James W. Allard, David Allison, William P. Alston, Karl Ameriks, C. Anthony Anderson, David Leech Anderson, Lanier Anderson, Roger Ariew, David Armstrong, Denis G. Arnold, E. J. Ashworth, Margaret Atherton, Robin Attfield, Bruce Aune, Edward Wilson Averill, Jody Azzouni, Kent Bach, Andrew Bailey, Lynne Rudder Baker, Thomas R. Baldwin, Jon Barwise, George Bealer, William Bechtel, Lawrence C. Becker, Mark A. Bedau, Ernst Behler, José A. Benardete, Ermanno Bencivenga, Jan Berg, Michael Bergmann, Robert L. Bernasconi, Sven Bernecker, Bernard Berofsky, Rod Bertolet, Charles J. Beyer, Christian Beyer, Joseph Bien, Joseph Bien, Peg Birmingham, Ivan Boh, James Bohman, Daniel Bonevac, Laurence BonJour, William J. Bouwsma, Raymond D. Bradley, Myles Brand, Richard B. Brandt, Michael E. Bratman, Stephen E. Braude, Daniel Breazeale, Angela Breitenbach, Jason Bridges, David O. Brink, Gordon G. Brittan, Justin Broackes, Dan W. Brock, Aaron Bronfman, Jeffrey E. Brower, Bartosz Brozek, Anthony Brueckner, Jeffrey Bub, Lara Buchak, Otavio Bueno, Ann E. Bumpus, Robert W. Burch, John Burgess, Arthur W. Burks, Panayot Butchvarov, Robert E. Butts, Marina Bykova, Patrick Byrne, David Carr, Noël Carroll, Edward S. Casey, Victor Caston, Victor Caston, Albert Casullo, Robert L. Causey, Alan K. L. Chan, Ruth Chang, Deen K. Chatterjee, Andrew Chignell, Roderick M. Chisholm, Kelly J. Clark, E. J. Coffman, Robin Collins, Brian P. Copenhaver, John Corcoran, John Cottingham, Roger Crisp, Frederick J. Crosson, Antonio S. Cua, Phillip D. Cummins, Martin Curd, Adam Cureton, Andrew Cutrofello, Stephen Darwall, Paul Sheldon Davies, Wayne A. Davis, Timothy Joseph Day, Claudio de Almeida, Mario De Caro, Mario De Caro, John Deigh, C. F. Delaney, Daniel C. Dennett, Michael R. DePaul, Michael Detlefsen, Daniel Trent Devereux, Philip E. Devine, John M. Dillon, Martin C. Dillon, Robert DiSalle, Mary Domski, Alan Donagan, Paul Draper, Fred Dretske, Mircea Dumitru, Wilhelm Dupré, Gerald Dworkin, John Earman, Ellery Eells, Catherine Z. Elgin, Berent Enç, Ronald P. Endicott, Edward Erwin, John Etchemendy, C. Stephen Evans, Susan L. Feagin, Solomon Feferman, Richard Feldman, Arthur Fine, Maurice A. Finocchiaro, William FitzPatrick, Richard E. Flathman, Gvozden Flego, Richard Foley, Graeme Forbes, Rainer Forst, Malcolm R. Forster, Daniel Fouke, Patrick Francken, Samuel Freeman, Elizabeth Fricker, Miranda Fricker, Michael Friedman, Michael Fuerstein, Richard A. Fumerton, Alan Gabbey, Pieranna Garavaso, Daniel Garber, Jorge L. A. Garcia, Robert K. Garcia, Don Garrett, Philip Gasper, Gerald Gaus, Berys Gaut, Bernard Gert, Roger F. Gibson, Cody Gilmore, Carl Ginet, Alan H. Goldman, Alvin I. Goldman, Alfonso Gömez-Lobo, Lenn E. Goodman, Robert M. Gordon, Stefan Gosepath, Jorge J. E. Gracia, Daniel W. Graham, George A. Graham, Peter J. Graham, Richard E. Grandy, I. Grattan-Guinness, John Greco, Philip T. Grier, Nicholas Griffin, Nicholas Griffin, David A. Griffiths, Paul J. Griffiths, Stephen R. Grimm, Charles L. Griswold, Charles B. Guignon, Pete A. Y. Gunter, Dimitri Gutas, Gary Gutting, Paul Guyer, Kwame Gyekye, Oscar A. Haac, Raul Hakli, Raul Hakli, Michael Hallett, Edward C. Halper, Jean Hampton, R. James Hankinson, K. R. Hanley, Russell Hardin, Robert M. Harnish, William Harper, David Harrah, Kevin Hart, Ali Hasan, William Hasker, John Haugeland, Roger Hausheer, William Heald, Peter Heath, Richard Heck, John F. Heil, Vincent F. Hendricks, Stephen Hetherington, Francis Heylighen, Kathleen Marie Higgins, Risto Hilpinen, Harold T. Hodes, Joshua Hoffman, Alan Holland, Robert L. Holmes, Richard Holton, Brad W. Hooker, Terence E. Horgan, Tamara Horowitz, Paul Horwich, Vittorio Hösle, Paul Hoβfeld, Daniel Howard-Snyder, Frances Howard-Snyder, Anne Hudson, Deal W. Hudson, Carl A. Huffman, David L. Hull, Patricia Huntington, Thomas Hurka, Paul Hurley, Rosalind Hursthouse, Guillermo Hurtado, Ronald E. Hustwit, Sarah Hutton, Jonathan Jenkins Ichikawa, Harry A. Ide, David Ingram, Philip J. Ivanhoe, Alfred L. Ivry, Frank Jackson, Dale Jacquette, Joseph Jedwab, Richard Jeffrey, David Alan Johnson, Edward Johnson, Mark D. Jordan, Richard Joyce, Hwa Yol Jung, Robert Hillary Kane, Tomis Kapitan, Jacquelyn Ann K. Kegley, James A. Keller, Ralph Kennedy, Sergei Khoruzhii, Jaegwon Kim, Yersu Kim, Nathan L. King, Patricia Kitcher, Peter D. Klein, E. D. Klemke, Virginia Klenk, George L. Kline, Christian Klotz, Simo Knuuttila, Joseph J. Kockelmans, Konstantin Kolenda, Sebastian Tomasz Kołodziejczyk, Isaac Kramnick, Richard Kraut, Fred Kroon, Manfred Kuehn, Steven T. Kuhn, Henry E. Kyburg, John Lachs, Jennifer Lackey, Stephen E. Lahey, Andrea Lavazza, Thomas H. Leahey, Joo Heung Lee, Keith Lehrer, Dorothy Leland, Noah M. Lemos, Ernest LePore, Sarah-Jane Leslie, Isaac Levi, Andrew Levine, Alan E. Lewis, Daniel E. Little, Shu-hsien Liu, Shu-hsien Liu, Alan K. L. Chan, Brian Loar, Lawrence B. Lombard, John Longeway, Dominic McIver Lopes, Michael J. Loux, E. J. Lowe, Steven Luper, Eugene C. Luschei, William G. Lycan, David Lyons, David Macarthur, Danielle Macbeth, Scott MacDonald, Jacob L. Mackey, Louis H. Mackey, Penelope Mackie, Edward H. Madden, Penelope Maddy, G. B. Madison, Bernd Magnus, Pekka Mäkelä, Rudolf A. Makkreel, David Manley, William E. Mann (W.E.M.), Vladimir Marchenkov, Peter Markie, Jean-Pierre Marquis, Ausonio Marras, Mike W. Martin, A. P. Martinich, William L. McBride, David McCabe, Storrs McCall, Hugh J. McCann, Robert N. McCauley, John J. McDermott, Sarah McGrath, Ralph McInerny, Daniel J. McKaughan, Thomas McKay, Michael McKinsey, Brian P. McLaughlin, Ernan McMullin, Anthonie Meijers, Jack W. Meiland, William Jason Melanson, Alfred R. Mele, Joseph R. Mendola, Christopher Menzel, Michael J. Meyer, Christian B. Miller, David W. Miller, Peter Millican, Robert N. Minor, Phillip Mitsis, James A. Montmarquet, Michael S. Moore, Tim Moore, Benjamin Morison, Donald R. Morrison, Stephen J. Morse, Paul K. Moser, Alexander P. D. Mourelatos, Ian Mueller, James Bernard Murphy, Mark C. Murphy, Steven Nadler, Jan Narveson, Alan Nelson, Jerome Neu, Samuel Newlands, Kai Nielsen, Ilkka Niiniluoto, Carlos G. Noreña, Calvin G. Normore, David Fate Norton, Nikolaj Nottelmann, Donald Nute, David S. Oderberg, Steve Odin, Michael O’Rourke, Willard G. Oxtoby, Heinz Paetzold, George S. Pappas, Anthony J. Parel, Lydia Patton, R. P. Peerenboom, Francis Jeffry Pelletier, Adriaan T. Peperzak, Derk Pereboom, Jaroslav Peregrin, Glen Pettigrove, Philip Pettit, Edmund L. Pincoffs, Andrew Pinsent, Robert B. Pippin, Alvin Plantinga, Louis P. Pojman, Richard H. Popkin, John F. Post, Carl J. Posy, William J. Prior, Richard Purtill, Michael Quante, Philip L. Quinn, Philip L. Quinn, Elizabeth S. Radcliffe, Diana Raffman, Gerard Raulet, Stephen L. Read, Andrews Reath, Andrew Reisner, Nicholas Rescher, Henry S. Richardson, Robert C. Richardson, Thomas Ricketts, Wayne D. Riggs, Mark Roberts, Robert C. Roberts, Luke Robinson, Alexander Rosenberg, Gary Rosenkranz, Bernice Glatzer Rosenthal, Adina L. Roskies, William L. Rowe, T. M. Rudavsky, Michael Ruse, Bruce Russell, Lilly-Marlene Russow, Dan Ryder, R. M. Sainsbury, Joseph Salerno, Nathan Salmon, Wesley C. Salmon, Constantine Sandis, David H. Sanford, Marco Santambrogio, David Sapire, Ruth A. Saunders, Geoffrey Sayre-McCord, Charles Sayward, James P. Scanlan, Richard Schacht, Tamar Schapiro, Frederick F. Schmitt, Jerome B. Schneewind, Calvin O. Schrag, Alan D. Schrift, George F. Schumm, Jean-Loup Seban, David N. Sedley, Kenneth Seeskin, Krister Segerberg, Charlene Haddock Seigfried, Dennis M. Senchuk, James F. Sennett, William Lad Sessions, Stewart Shapiro, Tommie Shelby, Donald W. Sherburne, Christopher Shields, Roger A. Shiner, Sydney Shoemaker, Robert K. Shope, Kwong-loi Shun, Wilfried Sieg, A. John Simmons, Robert L. Simon, Marcus G. Singer, Georgette Sinkler, Walter Sinnott-Armstrong, Matti T. Sintonen, Lawrence Sklar, Brian Skyrms, Robert C. Sleigh, Michael Anthony Slote, Hans Sluga, Barry Smith, Michael Smith, Robin Smith, Robert Sokolowski, Robert C. Solomon, Marta Soniewicka, Philip Soper, Ernest Sosa, Nicholas Southwood, Paul Vincent Spade, T. L. S. Sprigge, Eric O. Springsted, George J. Stack, Rebecca Stangl, Jason Stanley, Florian Steinberger, Sören Stenlund, Christopher Stephens, James P. Sterba, Josef Stern, Matthias Steup, M. A. Stewart, Leopold Stubenberg, Edith Dudley Sulla, Frederick Suppe, Jere Paul Surber, David George Sussman, Sigrún Svavarsdóttir, Zeno G. Swijtink, Richard Swinburne, Charles C. Taliaferro, Robert B. Talisse, John Tasioulas, Paul Teller, Larry S. Temkin, Mark Textor, H. S. Thayer, Peter Thielke, Alan Thomas, Amie L. Thomasson, Katherine Thomson-Jones, Joshua C. Thurow, Vzalerie Tiberius, Terrence N. Tice, Paul Tidman, Mark C. Timmons, William Tolhurst, James E. Tomberlin, Rosemarie Tong, Lawrence Torcello, Kelly Trogdon, J. D. Trout, Robert E. Tully, Raimo Tuomela, John Turri, Martin M. Tweedale, Thomas Uebel, Jennifer Uleman, James Van Cleve, Harry van der Linden, Peter van Inwagen, Bryan W. Van Norden, René van Woudenberg, Donald Phillip Verene, Samantha Vice, Thomas Vinci, Donald Wayne Viney, Barbara Von Eckardt, Peter B. M. Vranas, Steven J. Wagner, William J. Wainwright, Paul E. Walker, Robert E. Wall, Craig Walton, Douglas Walton, Eric Watkins, Richard A. Watson, Michael V. Wedin, Rudolph H. Weingartner, Paul Weirich, Paul J. Weithman, Carl Wellman, Howard Wettstein, Samuel C. Wheeler, Stephen A. White, Jennifer Whiting, Edward R. Wierenga, Michael Williams, Fred Wilson, W. Kent Wilson, Kenneth P. Winkler, John F. Wippel, Jan Woleński, Allan B. Wolter, Nicholas P. Wolterstorff, Rega Wood, W. Jay Wood, Paul Woodruff, Alison Wylie, Gideon Yaffe, Takashi Yagisawa, Yutaka Yamamoto, Keith E. Yandell, Xiaomei Yang, Dean Zimmerman, Günter Zoller, Catherine Zuckert, Michael Zuckert, Jack A. Zupko (J.A.Z.)
- Edited by Robert Audi, University of Notre Dame, Indiana
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- Book:
- The Cambridge Dictionary of Philosophy
- Published online:
- 05 August 2015
- Print publication:
- 27 April 2015, pp ix-xxx
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Validating an FFQ for intake of episodically consumed foods: application to the National Institutes of Health–AARP Diet and Health Study
- Douglas Midthune, Arthur Schatzkin, Amy F Subar, Frances E Thompson, Laurence S Freedman, Raymond J Carroll, Marina A Shumakovich, Victor Kipnis
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- Journal:
- Public Health Nutrition / Volume 14 / Issue 7 / 09 June 2011
- Published online by Cambridge University Press:
- 13 April 2011, pp. 1212-1221
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Objective
To develop a method to validate an FFQ for reported intake of episodically consumed foods when the reference instrument measures short-term intake, and to apply the method in a large prospective cohort.
DesignThe FFQ was evaluated in a sub-study of cohort participants who, in addition to the questionnaire, were asked to complete two non-consecutive 24 h dietary recalls (24HR). FFQ-reported intakes of twenty-nine food groups were analysed using a two-part measurement error model that allows for non-consumption on a given day, using 24HR as a reference instrument under the assumption that 24HR is unbiased for true intake at the individual level.
SettingThe National Institutes of Health–AARP Diet and Health Study, a cohort of 567 169 participants living in the USA and aged 50–71 years at baseline in 1995.
SubjectsA sub-study of the cohort consisting of 2055 participants.
ResultsEstimated correlations of true and FFQ-reported energy-adjusted intakes were 0·5 or greater for most of the twenty-nine food groups evaluated, and estimated attenuation factors (a measure of bias in estimated diet–disease associations) were 0·4 or greater for most food groups.
ConclusionsThe proposed methodology extends the class of foods and nutrients for which an FFQ can be evaluated in studies with short-term reference instruments. Although violations of the assumption that the 24HR is unbiased could be inflating some of the observed correlations and attenuation factors, results suggest that the FFQ is suitable for testing many, but not all, diet–disease hypotheses in a cohort of this size.
Performance of a food-frequency questionnaire in the US NIH–AARP (National Institutes of Health–American Association of Retired Persons) Diet and Health Study
- Frances E Thompson, Victor Kipnis, Douglas Midthune, Laurence S Freedman, Raymond J Carroll, Amy F Subar, Charles C Brown, Matthew S Butcher, Traci Mouw, Michael Leitzmann, Arthur Schatzkin
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- Journal:
- Public Health Nutrition / Volume 11 / Issue 2 / February 2008
- Published online by Cambridge University Press:
- 01 February 2008, pp. 183-195
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Objective
We evaluated the performance of the food-frequency questionnaire (FFQ) administered to participants in the US NIH–AARP (National Institutes of Health–American Association of Retired Persons) Diet and Health Study, a cohort of 566 404 persons living in the USA and aged 50–71 years at baseline in 1995.
DesignThe 124-item FFQ was evaluated within a measurement error model using two non-consecutive 24-hour dietary recalls (24HRs) as the reference.
SettingParticipants were from six states (California, Florida, Pennsylvania, New Jersey, North Carolina and Louisiana) and two metropolitan areas (Atlanta, Georgia and Detroit, Michigan).
SubjectsA subgroup of the cohort consisting of 2053 individuals.
ResultsFor the 26 nutrient constituents examined, estimated correlations with true intake (not energy-adjusted) ranged from 0.22 to 0.67, and attenuation factors ranged from 0.15 to 0.49. When adjusted for reported energy intake, performance improved; estimated correlations with true intake ranged from 0.36 to 0.76, and attenuation factors ranged from 0.24 to 0.68. These results compare favourably with those from other large prospective studies. However, previous biomarker-based studies suggest that, due to correlation of errors in FFQs and self-report reference instruments such as the 24HR, the correlations and attenuation factors observed in most calibration studies, including ours, tend to overestimate FFQ performance.
ConclusionThe performance of the FFQ in the NIH–AARP Diet and Health Study, in conjunction with the study’s large sample size and wide range of dietary intake, is likely to allow detection of moderate (≥1.8) relative risks between many energy-adjusted nutrients and common cancers.
Bias in dietary-report instruments and its implications for nutritional epidemiology
- Victor Kipnis, Douglas Midthune, Laurence Freedman, Sheila Bingham, Nicholas E Day, Elio Riboli, Pietro Ferrari, Raymond J Carroll
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- Journal:
- Public Health Nutrition / Volume 5 / Issue 6a / December 2002
- Published online by Cambridge University Press:
- 22 December 2006, pp. 915-923
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Objective:
To evaluate measurement error structure in dietary assessment instruments and to investigate its implications for nutritional studies, using urinary nitrogen excretion as a reference biomarker for protein intake.
Design:The dietary assessment methods included different food-frequency questionnaires (FFQs) and such conventional dietary-report reference instruments as a series of 24-hour recalls, 4-day weighed food records or 7-day diaries.
Setting:Six original pilot validation studies within the European Prospective Investigation of Cancer (EPIC), and two validation studies conducted by the British Medical Research Council (MRC) within the Norfolk cohort that later joined as a collaborative component cohort of EPIC.
Subjects:A sample of approximately 100 to 200 women and men, aged 35–74 years, from each of eight validation studies.
Results:In assessing protein intake, all conventional dietary-report reference methods violated the critical requirements for a valid reference instrument for evaluating, and adjusting for, dietary measurement error in an FFQ. They displayed systematic bias that depended partly on true intake and partly was person-specific, correlated with person-specific bias in the FFQ. Using the dietary-report methods as reference instruments produced substantial overestimation (up to 230%) of the FFQ correlation with true usual intake and serious underestimation (up to 240%) of the degree of attenuation of FFQ-based log relative risks.
Conclusion:The impact of measurement error in dietary assessment instruments on the design, analysis and interpretation of nutritional studies may be much greater than has been previously estimated, at least regarding protein intake.
6 - Modeling Nonlinear Gene Interactions Using Bayesian MARS
- Edited by Kim-Anh Do, University of Texas, MD Anderson Cancer Center, Peter Müller, Swiss Federal Institute of Technology, Zürich, Marina Vannucci, Rice University, Houston
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- Book:
- Bayesian Inference for Gene Expression and Proteomics
- Published online:
- 23 November 2009
- Print publication:
- 24 July 2006, pp 116-136
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Summary
Abstract
DNA microarray technology enables us to monitor the expression levels of thousands of genes simultaneously, and hence helps to obtain a better picture of the interactions between the genes. In order to understand the biological structure underlying these gene interactions, we present here a statistical approach to model the functional relationship between genes and also between genes and disease status. We suggest a hierarchical Bayesian model based on multivariate adaptive regression splines (MARS) to model these complex nonlinear interaction functions. The novelty of the approach lies in the fact that we attempt to capture the complex nonlinear dependencies between the genes which otherwise would have been missed by linear approaches. Owing to the large number of genes (variables) and the complexity of the data, we use Markov Chain Monte Carlo (MCMC) based stochastic search algorithms to choose among models. The Bayesian model is flexible enough to identify significant genes as well as model the functional relationships between them. The effectiveness of the proposed methodology is illustrated using two publicly available microarray data sets: leukemia and hereditary breast cancer.
Introduction
DNA microarray technology has revolutionized biological and medical research. The use of DNA microarrays allows simultaneous monitoring of the expressions of thousands of genes (Schena et al. 1995; Duggan et al. 1999), and has emerged as a tool for disease diagnosis. This technology promises to monitor the whole genome on a single chip so that researchers can have a better picture of the interactions among thousands of genes simultaneously.
ESTIMATION IN AN ADDITIVE MODEL WHEN THE COMPONENTS ARE LINKED PARAMETRICALLY
- Raymond J. Carroll, Wolfgang Härdle, Enno Mammen
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- Journal:
- Econometric Theory / Volume 18 / Issue 4 / August 2002
- Published online by Cambridge University Press:
- 17 May 2002, pp. 886-912
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Motivated by a nonparametric GARCH model we consider nonparametric additive autoregression models in the special case that the additive components are linked parametrically. We show that the parameter can be estimated with parametric rate and give the normal limit. Our procedure is based on two steps. In the first step nonparametric smoothers are used for the estimation of each additive component without taking into account the parametric link of the functions. In a second step the parameter is estimated by using the parametric restriction between the additive components. Interestingly, our method needs no undersmoothing in the first step.