-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathreferences.bib
executable file
·3194 lines (2859 loc) · 110 KB
/
references.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
@misc{ais,
title = {{AIDS Indicators Survey (AIS)}},
author = {{DHS Program}},
url = {https://dhsprogram.com/Methodology/Survey-Types/AIS.cfm},
note = {Accessed 17/05/2022}
}
@article{akaike1973information,
title = {{Information theory as an extension of the maximum likelihood principle--In: Second International Symposium on Information Theory (Eds) BN Petrov, F}},
author = {Akaike, Hirotugu},
year = 1973,
journal = {Csaki. BNPBF Csaki Budapest: Academiai Kiado}
}
@article{aldor2013power,
title = {{The power to see: A new graphical test of normality}},
author = {Aldor-Noiman, Sivan and Brown, Lawrence D and Buja, Andreas and Rolke, Wolfgang and Stine, Robert A},
year = 2013,
journal = {The American Statistician},
publisher = {Taylor \& Francis},
volume = 67,
number = 4,
pages = {249--260}
}
@article{amoah2020geostatistical,
title = {{A geostatistical framework for combining spatially referenced disease prevalence data from multiple diagnostics}},
author = {Amoah, Benjamin and Diggle, Peter J and Giorgi, Emanuele},
year = 2020,
journal = {Biometrics},
publisher = {Wiley Online Library},
volume = 76,
number = 1,
pages = {158--170}
}
@article{arambepola2022simulation,
title = {{A simulation study of disaggregation regression for spatial disease mapping}},
author = {Arambepola, Rohan and Lucas, Tim CD and Nandi, Anita K and Gething, Peter W and Cameron, Ewan},
year = 2022,
journal = {Statistics in Medicine},
publisher = {Wiley Online Library},
volume = 41,
number = 1,
pages = {1--16}
}
@article{auvert2005randomized,
title = {{Randomized, controlled intervention trial of male circumcision for reduction of HIV infection risk: the ANRS 1265 Trial}},
author = {Auvert, Bertran and Taljaard, Dirk and Lagarde, Emmanuel and Sobngwi-Tambekou, Joelle and Sitta, R{\'e}mi and Puren, Adrian},
year = 2005,
journal = {PLOS Medicine},
publisher = {Public Library of Science San Francisco, USA},
volume = 2,
number = 11,
pages = {e298}
}
@article{bachl2019inlabru,
title = {{inlabru: an R package for Bayesian spatial modelling from ecological survey data}},
author = {Bachl, Fabian E and Lindgren, Finn and Borchers, David L and Illian, Janine B},
year = 2019,
journal = {Methods in Ecology and Evolution},
publisher = {Wiley Online Library},
volume = 10,
number = 6,
pages = {760--766}
}
@article{bailey2007male,
title = {{Male circumcision for HIV prevention in young men in Kisumu, Kenya: a randomised controlled trial}},
author = {Bailey, Robert C and Moses, Stephen and Parker, Corette B and Agot, Kawango and Maclean, Ian and Krieger, John N and Williams, Carolyn FM and Campbell, Richard T and Ndinya-Achola, Jeckoniah O},
year = 2007,
journal = {The Lancet},
publisher = {Elsevier},
volume = 369,
number = 9562,
pages = {643--656}
}
@article{baker1994multinomial,
title = {{The multinomial-Poisson transformation}},
author = {Baker, Stuart G},
year = 1994,
journal = {Journal of the Royal Statistical Society: Series D (The Statistician)},
publisher = {Wiley Online Library},
volume = 43,
number = 4,
pages = {495--504}
}
@article{bao2012new,
title = {{A new infectious disease model for estimating and projecting HIV/AIDS epidemics}},
author = {Bao, Le},
year = 2012,
journal = {Sexually Transmitted Infections},
publisher = {BMJ Publishing Group Ltd},
volume = 88,
number = {Suppl 2},
pages = {i58--i64}
}
@article{baral2012burden,
title = {{Burden of HIV among female sex workers in low-income and middle-income countries: a systematic review and meta-analysis}},
author = {Baral, Stefan and Beyrer, Chris and Muessig, Kathryn and Poteat, Tonia and Wirtz, Andrea L and Decker, Michele R and Sherman, Susan G and Kerrigan, Deanna},
year = 2012,
journal = {{The Lancet Infectious Diseases}},
publisher = {Elsevier},
volume = 12,
number = 7,
pages = {538--549}
}
@article{barre1983isolation,
title = {{Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS)}},
author = {Barr{\'e}-Sinoussi, Fran{\c{c}}oise and Chermann, Jean-Claude and Rey, Fran and Nugeyre, Marie Therese and Chamaret, Sophie and Gruest, Jacqueline and Dauguet, Charles and Axler-Blin, Charles and V{\'e}zinet-Brun, Fran{\c{c}}oise and Rouzioux, Christine and others},
year = 1983,
journal = {Science},
publisher = {American Association for the Advancement of Science},
volume = 220,
number = 4599,
pages = {868--871}
}
@article{baydin2017automatic,
title = {{Automatic differentiation in machine learning: a survey}},
author = {Baydin, At{\i}l{\i}m G{\"u}nes and Pearlmutter, Barak A and Radul, Alexey Andreyevich and Siskind, Jeffrey Mark},
year = 2017,
journal = {The Journal of Machine Learning Research},
publisher = {JMLR. org},
volume = 18,
number = 1,
pages = {5595--5637}
}
@article{bell2012cppad,
title = {{CppAD: a package for C++ algorithmic differentiation}},
author = {Bell, Bradley M},
year = 2012,
journal = {Computational Infrastructure for Operations Research},
volume = 57,
number = 10
}
@article{bennett2019particulate,
title = {{Particulate matter air pollution and national and county life expectancy loss in the USA: A spatiotemporal analysis}},
author = {Bennett, James E and Tamura-Wicks, Helen and Parks, Robbie M and Burnett, Richard T and Pope III, C Arden and Bechle, Matthew J and Marshall, Julian D and Danaei, Goodarz and Ezzati, Majid},
year = 2019,
journal = {PLOS Medicine},
publisher = {Public Library of Science San Francisco, CA USA},
volume = 16,
number = 7,
pages = {e1002856}
}
@article{berger2006case,
title = {{The Case for objective Bayesian analysis}},
author = {Berger, James},
year = 2006,
journal = {Bayesian Analysis},
volume = 1,
number = 3,
pages = {385--402}
}
@incollection{berliner1996hierarchical,
title = {{Hierarchical Bayesian Time Series Models}},
author = {Berliner, L Mark},
year = 1996,
booktitle = {Maximum Entropy and Bayesian Methods},
publisher = {Springer},
pages = {15--22}
}
@book{bernardo2001bayesian,
title = {{Bayesian theory}},
author = {Bernardo, Jos{\'e} M and Smith, Adrian FM},
year = 2001,
publisher = {John Wiley \& Sons}
}
@article{besag1974spatial,
title = {{Spatial Interaction and the Statistical Analysis of Lattice Systems}},
author = {Besag, Julian},
year = 1974,
journal = {Journal of the Royal Statistical Society: Series B (Methodological)},
publisher = {Wiley Online Library},
volume = 36,
number = 2,
pages = {192--225}
}
@article{besag1991bayesian,
title = {{Bayesian image restoration, with two applications in spatial statistics}},
author = {Besag, Julian and York, Jeremy and Molli{\'e}, Annie},
year = 1991,
journal = {Annals of the Institute of Statistical Mathematics},
publisher = {Springer},
volume = 43,
number = 1,
pages = {1--20}
}
@inproceedings{best1999bayesian,
title = {{Bayesian models for spatially correlated disease and exposure data}},
author = {Best, N and Arnold, N and Thomas, A and Waller, L and Conlon, E},
year = 1999,
booktitle = {Bayesian Statistics 6: Proceedings of the Sixth Valencia International Meeting},
volume = 6,
pages = 131,
organization = {Oxford University Press}
}
@article{best2005comparison,
title = {{A comparison of Bayesian spatial models for disease mapping}},
author = {Best, Nicky and Richardson, Sylvia and Thomson, Andrew},
year = 2005,
journal = {Statistical Methods in Medical Research},
publisher = {Sage Publications Sage CA: Thousand Oaks, CA},
volume = 14,
number = 1,
pages = {35--59}
}
@misc{betancourt2017robust,
title = {{Robust Gaussian processes in Stan}},
author = {Betancourt, Michael},
year = 2017,
url = {https://betanalpha.github.io/assets/case\%5Fstudies/gp\%5Fpart3/part3.html}
}
@article{bhatt2015effect,
title = {{The effect of malaria control on Plasmodium falciparum in Africa between 2000 and 2015}},
author = {Bhatt, Samir and Weiss, DJ and Cameron, E and Bisanzio, D and Mappin, B and Dalrymple, U and Battle, KE and Moyes, CL and Henry, A and Eckhoff, PA and others},
year = 2015,
journal = {Nature},
publisher = {Nature Publishing Group UK London},
volume = 526,
number = 7572,
pages = {207--211}
}
@article{bilodeau2022stochastic,
title = {{Stochastic convergence rates and applications of adaptive quadrature in Bayesian inference}},
author = {Bilodeau, Blair and Stringer, Alex and Tang, Yanbo},
year = 2022,
journal = {Journal of the American Statistical Association},
publisher = {Taylor \& Francis},
pages = {1--11}
}
@book{bivand2008applied,
title = {{Applied spatial data analysis with R}},
author = {Bivand, Roger S and Pebesma, Edzer J and G{\'o}mez-Rubio, Virgilio and Pebesma, Edzer Jan},
year = 2008,
publisher = {Springer}
}
@article{blangiardo2013spatial,
title = {{Spatial and spatio-temporal models with R-INLA}},
author = {Marta Blangiardo and Michela Cameletti and Gianluca Baio and Håvard Rue},
year = 2013,
journal = {Spatial and Spatio-temporal Epidemiology},
volume = 4,
pages = {33--49}
}
@book{blangiardo2015spatial,
title = {{Spatial and spatio-temporal Bayesian models with R-INLA}},
author = {Blangiardo, Marta and Cameletti, Michela},
year = 2015,
publisher = {John Wiley \& Sons}
}
@article{blei2017variational,
title = {{Variational inference: A review for statisticians}},
author = {Blei, David M and Kucukelbir, Alp and McAuliffe, Jon D},
year = 2017,
journal = {Journal of the American Statistical Association},
publisher = {Taylor \& Francis},
volume = 112,
number = 518,
pages = {859--877}
}
@article{bolker2013strategies,
title = {{Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS}},
author = {Bolker, Benjamin M and Gardner, Beth and Maunder, Mark and Berg, Casper W and Brooks, Mollie and Comita, Liza and Crone, Elizabeth and Cubaynes, Sarah and Davies, Trevor and de Valpine, Perry and others},
year = 2013,
journal = {Methods in Ecology and Evolution},
publisher = {Wiley Online Library},
volume = 4,
number = 6,
pages = {501--512}
}
@article{bollhofer2020state,
title = {{State-of-the-art sparse direct solvers}},
author = {Bollh{\"o}fer, Matthias and Schenk, Olaf and Janalik, Radim and Hamm, Steve and Gullapalli, Kiran},
year = 2020,
journal = {Parallel Algorithms in Computational Science and Engineering},
publisher = {Springer},
pages = {3--33}
}
@misc{bosse2022scoringutils,
title = {{Evaluating Forecasts with scoringutils in R}},
author = {Bosse, Nikos I. and Gruson, Hugo and Cori, Anne and van Leeuwen, Edwin and Funk, Sebastian and Abbott, Sam},
year = 2022,
publisher = {arXiv},
url = {https://arxiv.org/abs/2205.07090},
copyright = {Creative Commons Attribution 4.0 International},
keywords = {Methodology (stat.ME), Applications (stat.AP), Computation (stat.CO), FOS: Computer and information sciences, FOS: Computer and information sciences}
}
@article{bosse2023scoring,
title = {{Scoring epidemiological forecasts on transformed scales}},
author = {Bosse, Nikos I and Abbott, Sam and Cori, Anne and van Leeuwen, Edwin and Bracher, Johannes and Funk, Sebastian},
year = 2023,
journal = {PLOS Computational Biology},
publisher = {Public Library of Science San Francisco, CA USA},
volume = 19,
number = 8,
pages = {e1011393}
}
@article{botswana2013botswana,
title = {{Botswana AIDS Impact Survey IV Statistical Report}},
author = {Botswana, Statistics},
year = 2013,
journal = {Government Printer, Gaborone, Republic of Botswana}
}
@incollection{box1992experimental,
title = {{On the experimental attainment of optimum conditions}},
author = {Box, George EP and Wilson, Kenneth B},
year = 1992,
booktitle = {Breakthroughs in Statistics: Methodology and Distribution},
publisher = {Springer},
pages = {270--310}
}
@inproceedings{bradley2023alsd,
title = {{Active Learning sampling design (A-LSD): a new adaptive survey design paradigm to improve representativeness for subpopulations}},
author = {Bradley, Valerie and Semenova, Elizaveta and Howes, Adam and Zhang, Mengyan and Eaton, Jeffrey and Sejdinovic, Dino and Flaxman, Seth},
year = 2023,
booktitle = {Proceedings of the 9th International Conference on Infectious Disease Dynamics}
}
@article{breslow1993approximate,
title = {{Approximate inference in generalized linear mixed models}},
author = {Breslow, Norman E and Clayton, David G},
year = 1993,
journal = {Journal of the American Statistical Association},
publisher = {Taylor \& Francis},
volume = 88,
number = 421,
pages = {9--25}
}
@manual{bridgestan,
title = {{bridgestan: BridgeStan, Accessing Stan Model Functions in R}},
author = {Brian Ward},
year = 2023,
note = {R package version 1.0.1}
}
@article{brier1950verification,
title = {{Verification of forecasts expressed in terms of probability}},
author = {Brier, Glenn W},
year = 1950,
journal = {Monthly Weather Review},
volume = 78,
number = 1,
pages = {1--3}
}
@article{brooks2017glmmtmb,
title = {{glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling}},
author = {Brooks, Mollie E and Kristensen, Kasper and Van Benthem, Koen J and Magnusson, Arni and Berg, Casper W and Nielsen, Anders and Skaug, Hans J and Machler, Martin and Bolker, Benjamin M},
year = 2017,
journal = {{The R Journal}},
publisher = {Technische Universitaet Wien},
volume = 9,
number = 2,
pages = {378--400}
}
@article{brown2015model,
title = {{Model-based geostatistics the easy way}},
author = {Brown, Patrick E},
year = 2015,
journal = {Journal of Statistical Software},
volume = 63,
pages = {1--24}
}
@article{broyles2023risk,
title = {{The risk of sexual transmission of HIV in individuals with low-level HIV viraemia: a systematic review}},
author = {Broyles, Laura N and Luo, Robert and Boeras, Debi and Vojnov, Lara},
year = 2023,
journal = {The Lancet},
publisher = {Elsevier}
}
@article{brugh2021characterizing,
title = {{Characterizing and mapping the spatial variability of HIV risk among adolescent girls and young women: A cross-county analysis of population-based surveys in Eswatini, Haiti, and Mozambique}},
author = {Brugh, Kristen N and Lewis, Quinn and Haddad, Cameron and Kumaresan, Jon and Essam, Timothy and Li, Michelle S},
year = 2021,
journal = {PLOS One},
publisher = {Public Library of Science San Francisco, CA USA},
volume = 16,
number = 12,
pages = {e0261520}
}
@article{carpenter2017stan,
title = {{Stan: A probabilistic programming language}},
author = {Carpenter, Bob and Gelman, Andrew and Hoffman, Matthew D and Lee, Daniel and Goodrich, Ben and Betancourt, Michael and Brubaker, Marcus and Guo, Jiqiang and Li, Peter and Riddell, Allen},
year = 2017,
journal = {Journal of Statistical Software},
publisher = {Columbia Univ., New York, NY (United States); Harvard Univ., Cambridge, MA~…},
volume = 76,
number = 1
}
@article{carpenter2017stan,
title = {{Stan: A probabilistic programming language}},
author = {Carpenter, Bob and Gelman, Andrew and Hoffman, Matthew D and Lee, Daniel and Goodrich, Ben and Betancourt, Michael and Brubaker, Marcus and Guo, Jiqiang and Li, Peter and Riddell, Allen},
year = 2017,
journal = {Journal of Statistical Software},
publisher = {Columbia Univ., New York, NY (United States); Harvard Univ., Cambridge, MA~…},
volume = 76,
number = 1
}
@article{casella1985introduction,
title = {{An introduction to empirical Bayes data analysis}},
author = {Casella, George},
year = 1985,
journal = {The American Statistician},
publisher = {Taylor \& Francis},
volume = 39,
number = 2,
pages = {83--87}
}
@article{chau2021deconditional,
title = {{Deconditional downscaling with Gaussian processes}},
author = {Chau, Siu Lun and Bouabid, Shahine and Sejdinovic, Dino},
year = 2021,
journal = {Advances in Neural Information Processing Systems},
volume = 34,
pages = {17813--17825}
}
@article{chen2014use,
title = {{The use of sampling weights in Bayesian hierarchical models for small area estimation}},
author = {Chen, Cici and Wakefield, Jon and Lumely, Thomas},
year = 2014,
journal = {Spatial and Spatio-temporal Epidemiology},
publisher = {Elsevier},
volume = 11,
pages = {33--43}
}
@book{chopin2020introduction,
title = {{An introduction to sequential Monte Carlo}},
author = {Chopin, Nicolas and Papaspiliopoulos, Omiros and others},
year = 2020,
publisher = {Springer},
volume = 4
}
@article{cleland2004monitoring,
title = {{Monitoring sexual behaviour in general populations: a synthesis of lessons of the past decade}},
author = {Cleland, John and Boerma, J Ties and Cara{\"e}l, Michel and Weir, Sharon S},
year = 2004,
journal = {Sexually Transmitted Infections},
publisher = {The Medical Society for the Study of Venereal Disease},
volume = 80,
number = {suppl 2},
pages = {ii1--ii7}
}
@article{cohen2011prevention,
title = {{Prevention of HIV-1 infection with early antiretroviral therapy}},
author = {Cohen, Myron S and Chen, Ying Q and McCauley, Marybeth and Gamble, Theresa and Hosseinipour, Mina C and Kumarasamy, Nagalingeswaran and Hakim, James G and Kumwenda, Johnstone and Grinsztejn, Beatriz and Pilotto, Jose HS and others},
year = 2011,
journal = {New England Journal of Medicine},
publisher = {Mass Medical Soc},
volume = 365,
number = 6,
pages = {493--505}
}
@article{conegan2022geostan,
title = {{geostan: An R package for Bayesian spatial analysis}},
author = {Connor Donegan},
year = 2022,
journal = {The Journal of Open Source Software},
volume = 7,
number = 79,
pages = 4716,
doi = {10.21105/joss.04716}
}
@misc{cppaddocumentation,
title = {{CppAD: a package for C++ algorithmic differentiation}},
author = {Bell, Bradley},
year = 2023,
note = {Accessed: September 25, 2023},
howpublished = {\url{http://www.coin-or.org/CppAD}}
}
@misc{cramb2018investigation,
title = {{Investigation of Bayesian spatial models}},
author = {Cramb, SM and Duncan, EW and Baade, PD and Mengersen, KL},
year = 2018,
publisher = {Cancer Council Queensland and Queensland University of Technology (QUT)}
}
@manual{cranlogs,
title = {{cranlogs: Download Logs from the 'RStudio' 'CRAN' Mirror}},
author = {Gábor Csárdi},
year = 2023,
note = {https://github.com/r-hub/cranlogs, https://r-hub.github.io/cranlogs}
}
@book{cressie2015statistics,
title = {{Statistics for spatio-temporal data}},
author = {Cressie, Noel and Wikle, Christopher K},
year = 2015,
publisher = {John Wiley \& Sons}
}
@inproceedings{cseke2010improving,
title = {{Improving posterior marginal approximations in latent Gaussian models}},
author = {Cseke, Botond and Heskes, Tom},
year = 2010,
booktitle = {Proceedings of the Thirteenth International Conference on Artificial Intelligence and Statistics},
pages = {121--128}
}
@book{davis1975methods,
title = {{Methods of numerical integration}},
author = {Davis, Philip J and Rabinowitz, Philip},
year = 1975,
publisher = {Academic Press}
}
@article{dawid1984present,
title = {{Present position and potential developments: Some personal views statistical theory the prequential approach}},
author = {Dawid, A Philip},
year = 1984,
journal = {Journal of the Royal Statistical Society: Series A (General)},
publisher = {Wiley Online Library},
volume = 147,
number = 2,
pages = {278--290}
}
@article{de2017programming,
title = {{Programming with models: writing statistical algorithms for general model structures with NIMBLE}},
author = {de Valpine, Perry and Turek, Daniel and Paciorek, Christopher J and Anderson-Bergman, Clifford and Lang, Duncan Temple and Bodik, Rastislav},
year = 2017,
journal = {Journal of Computational and Graphical Statistics},
publisher = {Taylor \& Francis},
volume = 26,
number = 2,
pages = {403--413}
}
@article{dean2001detecting,
title = {{Detecting interaction between random region and fixed age effects in disease mapping}},
author = {Dean, CB and Ugarte, MD and Militino, AF},
year = 2001,
journal = {Biometrics},
publisher = {Wiley Online Library},
volume = 57,
number = 1,
pages = {197--202}
}
@article{dempster1977maximum,
title = {{Maximum Likelihood from Incomplete Data Via the EM Algorithm}},
author = {Dempster, A. P. and Laird, N. M. and Rubin, D. B.},
year = 1977,
journal = {Journal of the Royal Statistical Society: Series B (Methodological)},
volume = 39,
number = 1,
pages = {1--22}
}
@article{dempster1977maximum,
title = {{Maximum likelihood from incomplete data via the EM algorithm}},
author = {Dempster, Arthur P and Laird, Nan M and Rubin, Donald B},
year = 1977,
journal = {Journal of the Royal Statistical Society: Series B (Methodological)},
publisher = {Wiley Online Library},
volume = 39,
number = 1,
pages = {1--22}
}
@article{dennis1981adaptive,
title = {{An adaptive nonlinear least-squares algorithm}},
author = {Dennis Jr, John E and Gay, David M and Walsh, Roy E},
year = 1981,
journal = {ACM Transactions on Mathematical Software (TOMS)},
publisher = {ACM New York, NY, USA},
volume = 7,
number = 3,
pages = {348--368}
}
@article{diaconis1988bayesian,
title = {{Bayesian numerical analysis}},
author = {Diaconis, Persi},
year = 1988,
journal = {Statistical Decision Theory and Related Topics IV},
volume = 1,
pages = {163--175}
}
@inproceedings{diaz2018openmp,
title = {{OpenMP 4.5 Validation and Verification Suite for Device Offload}},
author = {Diaz, Jose Monsalve and Pophale, Swaroop and Hernandez, Oscar and Bernholdt, David E and Chandrasekaran, Sunita},
year = 2018,
booktitle = {Evolving OpenMP for Evolving Architectures: 14th International Workshop on OpenMP, IWOMP 2018, Barcelona, Spain, September 26--28, 2018, Proceedings 14},
pages = {82--95},
organization = {Springer}
}
@article{diggle2013spatial,
title = {{Spatial and spatio-temporal log-Gaussian Cox processes: extending the geostatistical paradigm}},
author = {Diggle, Peter J and Moraga, Paula and Rowlingson, Barry and Taylor, Benjamin M and others},
year = 2013,
journal = {Statistical Science},
publisher = {Institute of Mathematical Statistics},
volume = 28,
number = 4,
pages = {542--563}
}
@article{diggle2016model,
title = {{Model-based geostatistics for prevalence mapping in low-resource settings}},
author = {Diggle, Peter J and Giorgi, Emanuele},
year = 2016,
journal = {Journal of the American Statistical Association},
publisher = {Taylor \& Francis},
volume = 111,
number = 515,
pages = {1096--1120}
}
@article{duane1987hybrid,
title = {{Hybrid Monte Carlo}},
author = {Duane, Simon and Kennedy, Anthony D and Pendleton, Brian J and Roweth, Duncan},
year = 1987,
journal = {Physics letters B},
publisher = {Elsevier},
volume = 195,
number = 2,
pages = {216--222}
}
@article{duncan2017spatial,
title = {{Spatial smoothing in Bayesian models: a comparison of weights matrix specifications and their impact on inference}},
author = {Duncan, Earl W and White, Nicole M and Mengersen, Kerrie},
year = 2017,
journal = {International Journal of Health Geographics},
publisher = {BioMed Central},
volume = 16,
number = 1,
pages = {1--16}
}
@article{durrande2019banded,
title = {{Banded matrix operators for Gaussian Markov models in the automatic differentiation era}},
author = {Durrande, Nicolas and Adam, Vincent and Bordeaux, Lucas and Eleftheriadis, Stefanos and Hensman, James},
year = 2019,
journal = {arXiv preprint arXiv:1902.10078}
}
@article{dwyer2015drinking,
title = {{Drinking patterns in US counties from 2002 to 2012}},
author = {Dwyer-Lindgren, Laura and Flaxman, Abraham D and Ng, Marie and Hansen, Gillian M and Murray, Christopher JL and Mokdad, Ali H},
year = 2015,
journal = {American Journal of Public Health},
publisher = {American Public Health Association},
volume = 105,
number = 6,
pages = {1120--1127}
}
@article{dwyer2019mapping,
title = {{Mapping HIV prevalence in sub-Saharan Africa between 2000 and 2017}},
author = {Dwyer-Lindgren, Laura and Cork, Michael A and Sligar, Amber and Steuben, Krista M and Wilson, Kate F and Provost, Naomi R and Mayala, Benjamin K and VanderHeide, John D and Collison, Michael L and Hall, Jason B and others},
year = 2019,
journal = {Nature},
publisher = {Nature Publishing Group},
volume = 570,
number = 7760,
pages = {189--193}
}
@article{eaton2019joint,
title = {{Joint small-area estimation of HIV prevalence, ART coverage and HIV incidence}},
author = {Eaton, Jeffrey W and Bajaj, Sumali and Jahn, Andreas and Kalua, Thokozani and Mganga, Andrew and Auld, Andrew F and Kim, Evelyn and Payne, Danielle and Shiraishi, Ray W and Gutreuter, Steve and Hallett, Timothy B and Johnson, Leigh F},
year = 2019,
journal = {Working paper}
}
@article{eaton2021naomi,
title = {{Naomi: a new modelling tool for estimating HIV epidemic indicators at the district level in sub-Saharan Africa}},
author = {Eaton, Jeffrey W and Dwyer-Lindgren, Laura and Gutreuter, Steve and O'Driscoll, Megan and Stevens, Oliver and Bajaj, Sumali and Ashton, Rob and Hill, Alexandra and Russell, Emma and Esra, Rachel and others},
year = 2021,
journal = {Journal of the International AIDS Society},
publisher = {Wiley Online Library},
volume = 24,
pages = {e25788}
}
@inproceedings{eaton2022aids,
title = {{Precision public health and infectious diseases}},
author = {Eaton, W Jeffrey},
year = 2022,
booktitle = {AIDS2022: Strengthening health systems session.}
}
@misc{economist2023triple,
title = {{A triple dividend: the health, social and economic gains from financing the HIV response in Africa}},
author = {{Economist Impact}},
year = 2023
}
@article{elliott1992small,
title = {{The Small Area Health Statistics Unit: a national facility for investigating health around point sources of environmental pollution in the United Kingdom.}},
author = {Elliott, Paul and Westlake, Andrew J and Hills, Michael and Kleinschmidt, Immo and Rodrigues, Laura and McGale, Paul and Marshall, Kay and Rose, Geoffrey},
year = 1992,
journal = {Journal of Epidemiology \& Community Health},
publisher = {BMJ Publishing Group Ltd},
volume = 46,
number = 4,
pages = {345--349}
}
@article{esra2024improved,
title={Improved Indicators for Subnational Unmet Antiretroviral Therapy Need in the Health System: Updates to the Naomi Model in 2023},
author={Esra, Rachel and Mmelesi, Mpho and Ketlogetswe, Akeem T. and Wolock, Timothy M. and Howes, Adam and Nong, Tlotlo and Matlhaga, Matshelo Tina and Ratladi, Siphiwe and Ramaabya, Dinah and Imai-Eaton, Jeffrey W.},
journal={Journal of Acquired Immune Deficiency Syndromes},
volume={95},
number={1S},
pages={e24-e33},
year={2024},
month={January 1},
doi={10.1097/QAI.0000000000003324},
}
@misc{fattah2022smart,
title = {{Smart gradient-an adaptive technique for improving gradient estimation}},
author = {Fattah, EA and Niekerk, JV and Rue, H},
year = 2022,
journal = {Foundations of Data Science},
volume = 4,
number = 1,
pages = {123--136}
}
@article{fay1979estimates,
title = {{Estimates of income for small places: an application of James-Stein procedures to census data}},
author = {Fay, Robert E and Herriot, Roger A},
year = 1979,
journal = {Journal of the American Statistical Association},
publisher = {Taylor \& Francis},
volume = 74,
number = {366a},
pages = {269--277}
}
@article{fisher1936design,
title = {{Design of experiments}},
author = {Fisher, Ronald Aylmer},
year = 1936,
journal = {British Medical Journal},
publisher = {BMJ Publishing Group},
volume = 1,
number = 3923,
pages = 554
}
@inproceedings{flaxman2015supported,
title = {{Who supported Obama in 2012? Ecological inference through distribution regression}},
author = {Flaxman, Seth R and Wang, Yu-Xiang and Smola, Alexander J},
year = 2015,
booktitle = {Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
pages = {289--298}
}
@article{flaxman2019bayesian,
title = {{Bayesian survey design: a new paradigm for social science research}},
author = {Seth Flaxman},
year = 2019,
journal = {CMStatistics Presentation}
}
@misc{follestad2003modelling,
title = {{Modelling spatial variation in disease risk using Gaussian Markov random field proxies for Gaussian random fields}},
author = {Follestad, Turid and Rue, H{\aa}vard},
year = 2003
}
@article{fournier2012ad,
title = {{AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models}},
author = {Fournier, David A and Skaug, Hans J and Ancheta, Johnoel and Ianelli, James and Magnusson, Arni and Maunder, Mark N and Nielsen, Anders and Sibert, John},
year = 2012,
journal = {Optimization Methods and Software},
publisher = {Taylor \& Francis},
volume = 27,
number = 2,
pages = {233--249}
}
@article{fournier2012ad,
title = {{AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models}},
author = {Fournier, David A and Skaug, Hans J and Ancheta, Johnoel and Ianelli, James and Magnusson, Arni and Maunder, Mark N and Nielsen, Anders and Sibert, John},
year = 2012,
journal = {Optimization Methods and Software},
publisher = {Taylor \& Francis},
volume = 27,
number = 2,
pages = {233--249}
}
@article{fournier2012ad,
title = {{AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models}},
author = {Fournier, David A and Skaug, Hans J and Ancheta, Johnoel and Ianelli, James and Magnusson, Arni and Maunder, Mark N and Nielsen, Anders and Sibert, John},
year = 2012,
journal = {Optimization Methods and Software},
publisher = {Taylor \& Francis},
volume = 27,
number = 2,
pages = {233--249}
}
@article{freni2018note,
title = {{A note on intrinsic conditional autoregressive models for disconnected graphs}},
author = {Freni-Sterrantino, Anna and Ventrucci, Massimo and Rue, H{\aa}vard},
year = 2018,
journal = {Spatial and Spatio-temporal Epidemiology},
publisher = {Elsevier},
volume = 26,
pages = {25--34}
}
@article{fuglstad2019constructing,
title = {{Constructing priors that penalize the complexity of Gaussian random fields}},
author = {Fuglstad, Geir-Arne and Simpson, Daniel and Lindgren, Finn and Rue, H{\aa}vard},
year = 2019,
journal = {Journal of the American Statistical Association},
publisher = {Taylor \& Francis},
volume = 114,
number = 525,
pages = {445--452}
}
@article{gaedke2023parallelized,
title = {{Parallelized integrated nested Laplace approximations for fast Bayesian inference}},
author = {Gaedke-Merzh{\"a}user, Lisa and van Niekerk, Janet and Schenk, Olaf and Rue, H{\aa}vard},
year = 2023,
journal = {Statistics and Computing},
publisher = {Springer},
volume = 33,
number = 1,
pages = 25
}
@inproceedings{gartner2002multi,
title = {{Multi-instance kernels}},
author = {G{\"a}rtner, Thomas and Flach, Peter A and Kowalczyk, Adam and Smola, Alexander J},
year = 2002,
booktitle = {ICML},
volume = 2,
number = 3,
pages = 7
}
@article{gelfand2001change,
title = {{On the change of support problem for spatio-temporal data}},
author = {Gelfand, Alan E and Zhu, Li and Carlin, Bradley P},
year = 2001,
journal = {Biostatistics},
publisher = {Oxford University Press},
volume = 2,
number = 1,
pages = {31--45}
}
@article{gelman1992inference,
title = {{Inference from iterative simulation using multiple sequences}},
author = {Gelman, Andrew and Rubin, Donald B},
year = 1992,
journal = {Statistical Science},
publisher = {JSTOR},
pages = {457--472}
}
@article{gelman2005analysis,
title = {{Analysis of variance—why it is more important than ever}},
author = {Gelman, Andrew},
year = 2005
}
@article{gelman2006prior,
author = {Andrew Gelman},
title = {{Prior distributions for variance parameters in hierarchical models (comment on article by Browne and Draper)}},
volume = {1},
journal = {Bayesian Analysis},
number = {3},
publisher = {International Society for Bayesian Analysis},
pages = {515 -- 534},
year = {2006}
}
@article{gelman2007struggles,
title = {{Struggles with survey weighting and regression modeling}},
author = {Gelman, Andrew},
year = 2007
}
@book{gelman2013bayesian,
title = {{Bayesian data analysis}},
author = {Gelman, Andrew and Carlin, John B and Stern, Hal S and Dunson, David B and Vehtari, Aki and Rubin, Donald B},
year = 2013,
publisher = {CRC press}
}
@article{gelman2014understanding,
title = {{Understanding predictive information criteria for Bayesian models}},
author = {Gelman, Andrew and Hwang, Jessica and Vehtari, Aki},
year = 2014,
journal = {Statistics and Computing},
publisher = {Springer},
volume = 24,
number = 6,
pages = {997--1016}
}
@article{gelman2017prior,
title = {{The prior can often only be understood in the context of the likelihood}},
author = {Gelman, Andrew and Simpson, Daniel and Betancourt, Michael},
year = 2017,
journal = {Entropy},
publisher = {MDPI},
volume = 19,
number = 10,
pages = 555
}
@article{gelman2020bayesian,
title = {{Bayesian workflow}},
author = {Gelman, Andrew and Vehtari, Aki and Simpson, Daniel and Margossian, Charles C and Carpenter, Bob and Yao, Yuling and Kennedy, Lauren and Gabry, Jonah and B{\"u}rkner, Paul-Christian and Modr{\'a}k, Martin},
year = 2020,
journal = {arXiv preprint arXiv:2011.01808}
}
@article{geman1984stochastic,
title = {{Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images}},
author = {Geman, Stuart and Geman, Donald},
year = 1984,
journal = {IEEE Transactions on pattern analysis and machine intelligence},
publisher = {IEEE},
number = 6,
pages = {721--741}
}
@article{giordano2018covariances,
title = {{Covariances, Robustness, and Variational Bayes}},
author = {Ryan Giordano and Tamara Broderick and Michael I. Jordan},
year = 2018,
journal = {Journal of Machine Learning Research},
volume = 19,
number = 51,
pages = {1--49},
url = {http://jmlr.org/papers/v19/17-670.html}
}
@article{giorgi2018bivariate,
title = {{Bivariate geostatistical modelling of the relationship between Loa loa prevalence and intensity of infection}},
author = {Giorgi, Emanuele and Schl{\"u}ter, Daniela K and Diggle, Peter J},
year = 2018,
journal = {Environmetrics},
publisher = {Wiley Online Library},
volume = 29,
number = {5-6},
pages = {e2447}
}
@manual{global2018measurement,