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1 : bates 10 @BOOK{R:Venables+Ripley:2000,
2 :     AUTHOR = {William N. Venables and Brian D. Ripley},
3 :     TITLE = {S Programming},
4 :     PUBLISHER = {Springer},
5 :     YEAR = 2000,
6 :     NOTE = {ISBN 0-387-98966-8},
7 :     URL = {http://www.stats.ox.ac.uk/pub/MASS3/Sprog/},
8 :     ABSTRACT = {This provides an in-depth guide to writing software
9 :     in the S language which forms the basis of both the
10 :     commercial S-PLUS and the Open Source R data
11 :     analysis software systems.}
12 :     }
13 :    
14 :    
15 :     @BOOK{R:Chambers+Hastie:1992,
16 :     AUTHOR = {John M. Chambers and Trevor J. Hastie},
17 :     TITLE = {Statistical Models in {S}},
18 :     PUBLISHER = {Chapman \& Hall},
19 :     YEAR = 1992,
20 :     ADDRESS = {London},
21 :     ISBN = {0-412-83040-X},
22 :     ABSTRACT = {This is also called the ``\emph{White Book}'', and
23 :     introduced S version 3, which added structures to
24 :     facilitate statistical modeling in S. }
25 :     }
26 :    
27 :    
28 :     @Article{Rnews:Gentleman+Carey:2002,
29 :     author = {Robert Gentleman and Vincent Carey},
30 :     title = {Bioconductor},
31 :     journal = {R News},
32 :     year = 2002,
33 :     volume = 2,
34 :     number = 1,
35 :     pages = {11--16},
36 :     month = {March},
37 :     url = {http://CRAN.R-project.org/doc/Rnews/}
38 :     }
39 :    
40 :     @article{Ke:Wang:2001,
41 :     author = {Ke, Chunlei and Wang, Yuedong},
42 :     title = {Semiparametric nonlinear mixed-effects models and
43 :     their applications},
44 :     year = {2001},
45 :     journal = {Journal of the American Statistical Association},
46 :     volume = {96},
47 :     number = {456},
48 :     pages = {1272--1298},
49 :     keywords = {NONLINEAR MIXED EFFECTS MODEL; Penalized likelihood;
50 :     Repeated measures; SELF-MODELING NONLINEAR
51 :     REGRESSION; Smoothing spline}
52 :     }
53 :    
54 :     @Article{Lind:Bate:1988,
55 :     author = {Lindstrom, Mary J. and Bates, Douglas M.},
56 :     title = {Newton-{R}aphson and {EM} algorithms for linear
57 :     mixed-effects models for repeated-measures data
58 :     ({C}orr: 94{V}89 p1572)},
59 :     year = {1988},
60 :     journal = {Journal of the American Statistical Association},
61 :     volume = {83},
62 :     pages = {1014--1022},
63 :     keywords = {Growth curve; Longitudinal data}
64 :     }
65 :    
66 :    
67 :     @ARTICLE{Atlas,
68 :     AUTHOR = "R. Clint Whaley and Antoine Petitet and Jack J. Dongarra",
69 :     TITLE = "Automated Empirical Optimization of Software and the
70 :     {ATLAS} Project",
71 :     JOURNAL = "Parallel Computing",
72 :     VOLUME = "27",
73 :     NUMBER = "1--2",
74 :     PAGES = "3--35",
75 :     YEAR = 2001,
76 :     NOTE = "Also available as University of Tennessee LAPACK Working
77 :     Note \#147, UT-CS-00-448, 2000
78 :     ({\tt www.netlib.org/lapack/lawns/lawn147.ps})"
79 :     }
80 :    
81 :     @TechReport{GotosBLAS,
82 :     author = {Kazushige Goto and Robert van de Geijn},
83 :     title = {On Reducing TLB Misses in Matrix Multiplication},
84 :     institution = {Department of Computer Sciences, U. of Texas at Austin},
85 :     year = 2002,
86 :     number = {TR02-55}
87 :     }
88 :    
89 :     @Misc{Taucs,
90 :     author = {Sivan Toledo},
91 :     title = {Taucs: A Library of Sparse Linear Solvers},
92 :     howpublished = {http://www.tau.ac.il/~stoledo/taucs/},
93 :     year = 2003
94 :     }
95 :    
96 :     @Misc{Umfpack,
97 :     author = {Tim Davis},
98 :     title = {UMFPACK: Unified Multifrontal Package},
99 :     howpublished = {http://www.cise.ufl.edu/research/sparse/umfpack},
100 :     year = 2003
101 :     }
102 :    
103 :     @Misc{Metis,
104 :     author = {George Karapis},
105 :     title = {Metis: Family of Multilevel Partioning Algorithms},
106 :     howpublished = {http://www-users.cs.umn.edu/~karypis/metis/},
107 :     year = 2003
108 :     }
109 :    
110 :     @Book{Linpack,
111 :     author = {Jack Dongarra and Cleve Moler and Bunch and G.W. Stewart},
112 :     title = {Linpack Users' Guide},
113 :     publisher = {SIAM},
114 :     year = 1979
115 :     }
116 :    
117 :     @Book{Lapack,
118 :     author = {E. Anderson and Z. Bai and C. Bischof and
119 :     S. Blackford and J. Demmel and J. Dongarra and J. Du
120 :     Croz and A. Greenbaum and S. Hammarling and
121 :     A. McKenney and D. Sorensen},
122 :     title = {LAPACK Users' Guide},
123 :     chapter = {},
124 :     publisher = {SIAM},
125 :     year = 1999,
126 :     address = {Philadelphia, PA},
127 :     edition = {3rd}
128 :     }
129 :    
130 :     @Book{bryk00:_hlm,
131 :     author = {A. S. Bryk and S. W. Raudenbush and R. Congdon},
132 :     title = {{HLM} version 5},
133 :     publisher = {Scientific Software International, Inc.},
134 :     year = 2000,
135 :     address = {Chicago}
136 :     }
137 :    
138 :     @Article{demp:lair:rubi:1977,
139 :     Journal = JRSSB,
140 :     Volume = 39,
141 :     Pages = {1--22},
142 :     Keywords = {Posterior mode},
143 :     Author = {A. P. Dempster and N. M. Laird and D. B. Rubin},
144 :     Title = {Maximum Likelihood From Incomplete Data Via the {EM}
145 :     Algorithm},
146 :     Year = 1977
147 :     }
148 :    
149 :     @Book{denn:schn:1983,
150 :     author = {J. E. Dennis and R. B. Schnabel},
151 :     title = {Numerical Methods for Unconstrained Optimization and
152 :     Nonlinear Equations},
153 :     publisher = {Prentice-Hall},
154 :     year = 1983,
155 :     address = {Englewood Cliffs, NJ}
156 :     }
157 :    
158 :     @Book{dong:bunc:mole:stew:1979,
159 :     publisher = "SIAM",
160 :     address = "Philadelphia",
161 :     author = "J. J. Dongarra and J. R. Bunch and C. B. Moler and
162 :     G. W. Stewart",
163 :     title = "Linpack Users' Guide",
164 :     year = 1979
165 :     }
166 :    
167 :     @Book{goldstein98:_mlwin,
168 :     author = {H. Goldstein and J. Rasbash and I. Plewis and
169 :     D. Draper and W. Browne and M. Wang},
170 :     title = {A user's guide to {MLwiN}},
171 :     publisher = {University of London, Institute of Education},
172 :     year = 1998,
173 :     address = {London}
174 :     }
175 :    
176 :     @Book{golu:vanl:1996,
177 :     author = {Golub, Gene H. and van Loan, Charles F.},
178 :     title = {Matrix Computations},
179 :     publisher = {Johns Hopkins},
180 :     year = 1996,
181 :     edition = {3rd}
182 :     }
183 :    
184 :     @Article{ harv:1974,
185 :     author = {Harville, David A.},
186 :     title = {Bayesian Inference for Variance Components Using
187 :     Only Error Contrasts},
188 :     journal = {Biometrika},
189 :     year = 1974,
190 :     volume = 61,
191 :     pages = {383--385},
192 :     keywords = {Maximum likelihood}
193 :     }
194 :    
195 :     @Article{ lair:ware:1982,
196 :     author = {Laird, Nan M. and Ware, James H.},
197 :     title = {Random-effects Models for Longitudinal Data},
198 :     journal = {Biometrics},
199 :     year = 1982,
200 :     volume = 38,
201 :     pages = {963--974},
202 :     keywords = {Variance components; Repeated measurements;
203 :     Empirical Bayes; EM algorithm}
204 :     }
205 :    
206 :     @Book{lapack:1992,
207 :     publisher = "SIAM",
208 :     address = "Philadelphia",
209 :     author = "E. Anderson and Z. Bai and C. Bischof and J. Demmel
210 :     and J. Dongarra and J. Du Croz and A. Greenbaum and
211 :     S. Hammaring and A. McKenney and S. Ostrouchov and
212 :     D. Sorensen",
213 :     title = "Lapack Users' Guide",
214 :     year = 1992
215 :     }
216 :    
217 :     @Article{liu:rubi:1994,
218 :     author = {Liu, Chuanhai and Rubin, Donald B.},
219 :     title = {The {ECME} algorithm: {A} simple extension of {EM}
220 :     and {ECM} with faster monotone convergence},
221 :     year = {1994},
222 :     journal = {Biometrika},
223 :     volume = {81},
224 :     pages = {633--648},
225 :     keywords = {Markov chain monte carlo; Incomplete data}
226 :     }
227 :    
228 :     @article{patt:thom:1971,
229 :     Author = {Patterson, H. D. and Thompson, R.},
230 :     Title = {Recovery of Interblock Information When Block Sizes
231 :     Are Unequal},
232 :     Year = 1971,
233 :     Journal = {Biometrika},
234 :     Volume = 58,
235 :     Pages = {545--554},
236 :     Keywords = {Incomplete block design; Components of variance;
237 :     Maximum likelihood; Design of experiments}
238 :     }
239 :    
240 :     @phdthesis{pinh:1994,
241 :     author = {Jos\'{e} C. Pinheiro},
242 :     title = {Topics in Mixed-Effects Models},
243 :     school = {University of Wisconsin},
244 :     year = 1994,
245 :     address = {Madison, WI}
246 :     }
247 :    
248 :     @Article{pinh:bate:1995,
249 :     author = "Jos\'{e} C. Pinheiro and Douglas M. Bates",
250 :     title = "Approximations to the Log-Likelihood Function in the
251 :     Nonlinear Mixed-Effects Model",
252 :     year = 1995,
253 :     journal = "Journal of Computational and Graphical Statistics",
254 :     volume = 4,
255 :     number = 1,
256 :     pages = "12--35"
257 :     }
258 :    
259 :     @Article{ pinh:bate:1996,
260 :     author = {Jos\'{e} C. Pinheiro and Douglas M. Bates},
261 :     title = {Unconstrained Parameterizations for Variance-Covariance
262 :     Matrices},
263 :     journal = {Statistics and Computing},
264 :     year = 1996,
265 :     volume = 6,
266 :     pages = {289--296}
267 :     }
268 :    
269 :     @Book{pinh:bate:2000,
270 :     author = {Jos\'{e} C. Pinheiro and Douglas M. Bates},
271 :     title = {Mixed-Effects Models in {S} and {S-PLUS}},
272 :     year = 2000,
273 :     pages = {528},
274 :     ISBN = {0-387-98957-9},
275 :     publisher = {Springer}
276 :     }
277 :    
278 :     @Article{schn:koon:1985,
279 :     Journal = {ACM Trans. Math. Software},
280 :     Volume = 11,
281 :     Pages = {419--440},
282 :     Author = {R. B. Schnabel and J. E. Koontz and B. E. Weiss},
283 :     Title = {A modular system of algorithms for unconstrained
284 :     minimization},
285 :     Year = 1985
286 :     }
287 :    
288 :     @book{snijders99:_multil_analy,
289 :     author = {Tom Snijders and Roel Bosker},
290 :     title = {Multilevel Analysis: An introduction to basic and
291 :     advanced multilevel analysis},
292 :     publisher = {Sage},
293 :     year = 1999,
294 :     address = {London}
295 :     }
296 :    
297 :     @book{this:1988,
298 :     Author = {Thisted, R. A.},
299 :     Title = {Elements of Statistical Computing},
300 :     Year = 1988,
301 :     Publisher = {Chapman \& Hall},
302 :     address = {London}
303 :     }
304 :    
305 :     @Article{van:2000,
306 :     author = {van Dyk, David A.},
307 :     title = {Fitting mixed-effects models using efficient
308 :     {EM}-type algorithms},
309 :     year = {2000},
310 :     journal = {Journal of Computational and Graphical Statistics},
311 :     volume = {9},
312 :     number = {1},
313 :     pages = {78--98},
314 :     keywords = {EM algorithm; ECME algorithm; Gaussian hierarchical
315 :     models; Posterior inference; PXEM algorithm;
316 :     random-effects models; Reml; variance-component
317 :     models; working parameters}
318 :     }
319 :    
320 :     @misc{jfox:2002,
321 :     author = {Fox, John},
322 :     title = {Linear Mixed Models --
323 :     Appendix to {An R and S-PLUS Companion to
324 :     Applied Regression}},
325 :     year = 2002,
326 :     month= {May},
327 :     url = {http://www.socsci.mcmaster.ca/jfox/Books/companion/appendix-mixed-models.pdf}
328 :     }
329 :    
330 :     @book{roge:1980,
331 :     Author = {Rogers, Gerald S.},
332 :     Title = {Matrix Derivatives},
333 :     Year = 1980,
334 :     Publisher = {Marcell Dekker, Inc.},
335 :     address = {New York and Basel}
336 :     }
337 :    
338 :     @TechReport{DebRoy:Bates:2003a,
339 :     author = {Saikat DebRoy and Douglas M. Bates},
340 :     title = {Computational Methods for Single Level Linear
341 :     Mixed-effects Models},
342 :     institution = {Department of Statistics, University of Wisconsin-Madison},
343 :     number = {1073},
344 :     year = 2003
345 :     }
346 :    
347 :     @TechReport{DebRoy:Bates:2003b,
348 :     author = {Saikat DebRoy and Douglas M. Bates},
349 :     title = {Computational Methods for Multiple Level Linear
350 :     Mixed-effects Models},
351 :     institution = {Department of Statistics, University of Wisconsin-Madison},
352 :     number = {1076},
353 :     year = 2003
354 :     }
355 :    
356 :     @Article{RaudenbushYangYosef:2000,
357 :     author = {Stephen W. Raudenbush and Meng-Li Yang and Matheos Yosef},
358 :     title = {Maximum Likelihood for Generalized Linear Models
359 :     With Nested Random Effects via High-Order,
360 :     Multivariate {L}aplace Approximation},
361 :     journal = {J. Comput. Graph. Statist.},
362 :     year = 2000,
363 :     volume = 9,
364 :     number = 1,
365 :     pages = {141--157}
366 :     }
367 :    
368 :     @Book{goldstein87:_multil,
369 :     author = {Goldstein, Harvey},
370 :     title = {Multilevel models in education and social research},
371 :     publisher = {Oxford University Press},
372 :     year = 1987
373 :     }
374 :    
375 :     @Book{raudenbush02:_hierar_linear_model,
376 :     author = {Stephen W. Raudenbush and Anthony S. Bryk},
377 :     title = {Hierarchical Linear Models: Applications and Data Analysis Methods},
378 :     publisher = {Sage},
379 :     year = 2002,
380 :     edition = {second},
381 :     ISBN = {0-7619-1904-X}
382 :     }
383 :    
384 :     @BOOK{R:Chambers:1998,
385 :     AUTHOR = {John M. Chambers},
386 :     TITLE = {Programming with Data},
387 :     PUBLISHER = {Springer},
388 :     YEAR = 1998,
389 :     ADDRESS = {New York},
390 :     ISBN = {0-387-98503-4},
391 :     ABSTRACT = {This ``\emph{Green Book}'' describes version 4 of S, a
392 :     major revision of S designed by John Chambers to
393 :     improve its usefulness at every stage of the
394 :     programming process.}
395 :     }
396 :    
397 :     @article{Rodriguez:Goldman:1995,
398 :     author = {Germ\'an Rodriguez and Noreen Goldman},
399 :     title = {An assessment of estimation procedures for multilevel
400 :     models with binary responses},
401 :     year = {1995},
402 :     journal = {Journal of the Royal Statistical Society, Series A, General},
403 :     volume = {158},
404 :     pages = {73--89},
405 :     keywords = {Logistic regression; Random effects model; Software;
406 :     Variance component}
407 :     }
408 :    
409 :     @Article{koen:ng:2003,
410 :     author = {Roger Koenker and Pin Ng},
411 :     title = {{SparseM}: A Sparse Matrix Package for {R}},
412 :     journal = {J. of Statistical Software},
413 :     year = 2003,
414 :     volume = 8,
415 :     number = 6
416 :     }
417 :    
418 :     @Book{Eispack,
419 :     author = {Smith, B. T. and Boyle, J. M. and Dongarra, J. J. and Garbow, B. S. and Ikebe, Y. and Klema, V. C. and Moler, C. B.},
420 :     title = {Matrix Eigensystem Routines. EISPACK Guide},
421 :     publisher = {Springer-Verlag},
422 :     year = 1976,
423 :     volume = 6,
424 :     series = {Lecture Notes in Computer Science},
425 :     address = {New York}
426 :     }
427 :    
428 :     @Article{bate:debr:2004,
429 :     author = {Douglas M. Bates and Saikat DebRoy},
430 :     title = {Linear Mixed Models and Penalized Least Squares},
431 :     journal = {J. of Multivariate Analysis},
432 :     year = 2004,
433 :     note = {to appear}
434 :     }
435 :    
436 :     @Article{Rnews:Lockwood+Doran+Mccaffrey:2003,
437 :     author = {J.R. Lockwood and Harold Doran and Daniel
438 :     F. McCaffrey},
439 :     title = {Using R for Estimating Longitudinal Student
440 :     Achievement Models},
441 :     journal = {R News},
442 :     year = 2003,
443 :     volume = 3,
444 :     number = 3,
445 :     pages = {17--23},
446 :     month = {December},
447 :     url = {http://CRAN.R-project.org/doc/Rnews/}
448 :     }
449 :    
450 :     @Article{Paterson:1991,
451 :     author = {L. Paterson},
452 :     title = {Socio economic status and educational attainment:
453 :     a multidimensional and multilevel study},
454 :     journal = {Evaluation and Research in Education},
455 :     year = 1991,
456 :     volume = 5,
457 :     pages = {97--121}
458 :     }
459 :    

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