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references.bib
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@article{knuth84,
author = {Knuth, Donald E.},
title = {Literate Programming},
year = {1984},
issue_date = {May 1984},
publisher = {Oxford University Press, Inc.},
address = {USA},
volume = {27},
number = {2},
issn = {0010-4620},
url = {https://doi.org/10.1093/comjnl/27.2.97},
doi = {10.1093/comjnl/27.2.97},
journal = {Comput. J.},
month = may,
pages = {97–111},
numpages = {15}
}
@Article{baayen.vasishth.etal:2017jml,
author = {Baayen, Harald and Vasishth, Shravan and Kliegl, Reinhold and Bates, Douglas},
title = {The cave of shadows: Addressing the human factor with generalized additive mixed models},
doi = {10.1016/j.jml.2016.11.006},
pages = {206--234},
volume = {94},
abstract = {Abstract Generalized additive mixed models are introduced as an extension of the generalized linear mixed model which makes it possible to deal with temporal autocorrelational structure in experimental data. This autocorrelational structure is likely to be a consequence of learning, fatigue, or the ebb and flow of attention within an experiment (the `human factor'). Unlike molecules or plots of barley, subjects in psycholinguistic experiments are intelligent beings that depend for their survival on constant adaptation to their environment, including the environment of an experiment. Three data sets illustrate that the human factor may interact with predictors of interest, both factorial and metric. We also show that, especially within the framework of the generalized additive model, in the nonlinear world, fitting maximally complex models that take every possible contingency into account is ill-advised as a modeling strategy. Alternative modeling strategies are discussed for both confirmatory and exploratory data analysis.},
date-added = {2020-03-24},
date-modified = {2017-02-14 02:16:15 +0000},
file = {baayen.vasishth.etal\:2017jml - cave shadows_ Addressing.pdf:2017/baayen.vasishth.etal_2017jml - cave shadows_ Addressing.pdf:PDF},
file2 = {/Documents/Papers/2017/baayen.vasishth.etal2017jml - The cave of shadows Addressing the human factor with generalized additive mixed modelsa.pdf},
groups = {Methods, GAMMs},
journal = {Journal of Memory and Language},
keywords = {Generalized additive mixed models, Within-experiment adaptation, Autocorrelation, Experimental time series, Confirmatory versus exploratory data analysis, Model selection},
month = jun,
year = {2017},
}
@Article{bates.kliegl.etal:2015a,
author = {Bates, Douglas and Kliegl, Reinhold and Vasishth, Shravan and Baayen, Harald},
title = {Parsimonius Mixed Models},
pages = {1506.04967v1},
date-added = {2020-03-24},
date-modified = {2015-06-25 03:21:03 +0000},
file = {bates.kliegl.etal\:2015a - Parsimonius Mixed Models.pdf:2015/bates.kliegl.etal_2015a - Parsimonius Mixed Models.pdf:PDF},
journal = {arXiv},
year = {2015},
}
@Article{bates.maechler.etal:2015,
author = {Bates, Douglas and Maechler, Martin and Bolker, Benjamin M. and Walker, Steven},
title = {Fitting Linear Mixed-Effects Models using lme4},
doi = {10.18637/jss.v067.i01},
number = {1},
pages = {1--48},
volume = {67},
date-added = {2020-03-24},
date-modified = {2016-02-12 06:52:06 +0000},
file = {:2015/bates.maechler.etal_2015 - Fitting Linear Mixed.pdf:PDF},
journal = {Journal of Statistical Software},
year = {2015},
}
@Article{matuschek.kliegl.etal:2017jml,
author = {Matuschek, Hannes and Kliegl, Reinhold and Vasishth, Shravan and Baayen, Harald and Bates, Douglas},
title = {Balancing Type I error and power in linear mixed models},
doi = {10.1016/j.jml.2017.01.001},
pages = {305--315},
volume = {94},
abstract = {Abstract Linear mixed-effects models have increasingly replaced mixed-model analyses of variance for statistical inference in factorial psycholinguistic experiments. Although LMMs have many advantages over ANOVA, like ANOVAs, setting them up for data analysis also requires some care. One simple option, when numerically possible, is to fit the full variance-covariance structure of random effects (the maximal model; Barr, Levy, Scheepers & Tily, 2013), presumably to keep Type I error down to the nominal α in the presence of random effects. Although it is true that fitting a model with only random intercepts may lead to higher Type I error, fitting a maximal model also has a cost: it can lead to a significant loss of power. We demonstrate this with simulations and suggest that for typical psychological and psycholinguistic data, higher power is achieved without inflating Type I error rate if a model selection criterion is used to select a random effect structure that is supported by the data.},
date-added = {2020-03-24},
date-modified = {2017-02-14 02:15:14 +0000},
file = {matuschek.kliegl.etal\:2017jml - Balancing Type I.pdf:2017/matuschek.kliegl.etal_2017jml - Balancing Type I.pdf:PDF},
journal = {Journal of Memory and Language},
keywords = {Power, Linear mixed effect model, Hypothesis testing},
month = jun,
year = {2017},
}
@Article{bates2019n,
author = {Bates, Douglas},
title = {Complexity in fitting Linear Mixed Models},
doi = {10.33016/nextjournal.100002},
date-added = {2020-03-24},
journal = {Nextjournal},
month = {aug},
publisher = {Nextjournal},
year = {2019},
}
@Article{barr2013a,
author = {Barr, Dale J.},
title = {Random Effects Structure for Testing Interactions in Linear Mixed-effects Models},
doi = {10.3389/fpsyg.2013.00328},
number = {328},
volume = {4},
date-added = {2020-03-24},
date-modified = {2015-02-06 17:10:55 +0000},
file = {barr2013a - Random Effects Structure.pdf:2013/barr2013a - Random Effects Structure.pdf:PDF},
journal = {Frontiers in Psychology},
year = {2013},
}
@Article{barrlevyscheepers2013a,
author = {Barr, Dale J. and Levy, Roger and Scheepers, Christoph and Tily, Harry J.},
title = {Random Effects Structure for Confirmatory Hypothesis Testing: Keep It Maximal},
doi = {10.1016/j.jml.2012.11.001},
pages = {255--278},
volume = {68},
date-added = {2020-03-24},
date-modified = {2015-02-06 17:10:37 +0000},
file = {barrlevyscheepers2013a - Random Effects Structure.pdf:2013/barrlevyscheepers2013a - Random Effects Structure.pdf:PDF},
journal = {Journal of Memory and Language},
keywords = {mixed effects models},
year = {2013},
}
@Article{mb1,
author = {{ManyBabiesConsortium}},
date = {in press},
journaltitle = {Advances in Methods and Practices in Psychological Science},
title = {Quantifying sources of variability in infancy research using the infant-directed speech preference},
date-added = {2020-03-24},
}
@Article{baayendavidsonbates2008a,
author = {Baayen, R. H. and Davidson, D. J. and Bates, D. M.},
title = {Mixed-effects Modeling with Crossed Random Effects for Subjects and Items},
pages = {390--412},
volume = {59},
date-added = {2020-03-24},
date-modified = {2015-02-06 17:11:33 +0000},
file = {baayendavidsonbates2008a - Mixed effects Modeling.pdf:2008/baayendavidsonbates2008a - Mixed effects Modeling.pdf:PDF},
journal = {Journal of Memory and Language},
keywords = {statistics, mixed effects models},
year = {2008},
}
@Article{alday.etal:mixedmodels.jl,
author = {Alday, Phillip M. and Kleinschmidt, David and Kliegl, Reinhold and Bates, D.},
date = {in prep},
journaltitle = {Journal of Statistical Software},
title = {An efficient derivation of the profiled log likelihood for linear mixed-effects models.},
date-added = {2020-03-25},
}
@WWW{frank.blog.maximal,
author = {Michael Frank},
date = {2019},
title = {Mixed effects models: Is it time to go Bayesian by default?},
url = {https://web.archive.org/web/20190601175639/https://babieslearninglanguage.blogspot.com/2019/05/its-random-effects-stupid.html},
urldate = {2019-06-01},
date-added = {2020-03-29},
}
@WWW{frank.blog.bayes,
author = {Michael Frank},
date = {2018},
title = {It's the random effects, stupid!},
url = {https://web.archive.org/web/20190715193907/https://babieslearninglanguage.blogspot.com/2018/02/mixed-effects-models-is-it-time-to-go.html},
urldate = {2019-07-15},
date-added = {2020-03-29},
}
@Book{box73:_bayes_infer_statis_analy,
author = {Box, G.E.P. and Tiao, G.C.},
title = {Bayesian Inference in Statistical Analysis},
publisher = {Addison-Wesley},
year = 1973,
address = {Reading, MA}
}
@Book{milliken09:_analy_messy_data,
author = {George A. Milliken and Dallas E. Johnson},
title = {Analysis of Messy Data: Volume 1, Designed Experiments},
publisher = {CRC Press},
year = 2009,
edition = {2nd}}
@Book{cleveland93:_visual_data,
author = {Bill Cleveland},
title = {Visualizing Data},
publisher = {Hobart Press},
year = 1993,
address = {Summit, NJ}}
@Article{Burchinal:1997,
author = {Burchinal, M.R. and Campbell, F.A and Bryant, D.M. and Wasik, B.H. and Ramey, C.T.},
title = {Early intervention and mediating processes in cognitive performance of children of low income {A}frican {A}merican families},
pages = {935--954},
volume = {68},
journal = {Child Development},
year = {1997},
}
@Article{Burchinal:2000,
author = {Burchinal, M.R. and Roberts, J.E and Riggins, R. and
Zeisel, S.A. and Neebe, E. and Bryant, D.},
title = {Relating quality of center child care to early
cognitive and language development longitudinally},
journal = {Child Development},
year = 2000,
volume = 71,
pages = {339--357}
}
@Book{Rcpp,
title = {Seamless {R} and {C++} Integration with {Rcpp}},
author = {Dirk Eddelbuettel},
publisher = {Springer},
address = {New York},
year = {2013},
note = {ISBN 978-1-4614-6867-7},
doi = {10.1007/978-1-4614-6868-4},
}
@Book{davies72:_statis_method_in_resear_and_produc,
editor = {Owen L. Davies and Peter L. Goldsmith},
title = {Statistical Methods in Research and Production},
publisher = {Hafner},
year = 1972,
edition = {4th}}
@Book{Sing:Will:2003,
author = {Judith D. Singer and John B. Willett},
title = {Applied Longitudinal Data Analysis},
publisher = {Oxford University Press},
year = 2003,
ISBN = {0-19-515296-4}
}
@Book{Rauden:Bryk:2002,
author = {Stephen W. Raudenbush and Anthony S. Bryk},
title = {Hierarchical Linear Models: Applications and Data
Analysis Methods},
publisher = {Sage},
year = 2002,
edition = {2nd},
ISBN = {0-7619-1904-X}
}
@Article{belenky03:_patter,
author = {Gregory Belenky and Nancy J. Wesensten and David
R. Thorne and Maria L. Thomas and Helen C. Sing and
Daniel P. Redmond and Michael B. Russo and Thomas
J. Balkin},
title = {Patterns of performance degradation and restoration
during sleep restriction and subsequent recovery: a
sleep dose-response study},
journal = {Journal of Sleep Research},
year = 2003,
volume = 12,
pages = {1--12}
}
@Article{henderson50:_estim,
author = {C.R. Henderson},
title = {Estimation of genetic parameters},
journal = {Annals of Mathematical Statistics},
year = 1950,
volume = 21,
pages = 309
}
@Article{Rnews:Bates:2005,
author = {Douglas Bates},
title = {Fitting Linear Mixed Models in {R}},
journal = {R News},
year = 2005,
volume = 5,
number = 1,
pages = {27--30},
month = {May},
url = {http://CRAN.R-project.org/doc/Rnews/},
}
@Article{bates04:_linear,
author = {Douglas M. Bates and Saikat DebRoy},
title = {Linear mixed models and penalized least squares},
journal = {Journal of Multivariate Analysis},
year = 2004,
volume = 91,
number = 1,
pages = {1--17}
}
@Book{henderson84:_applic_model_animal_breed,
author = {C. Henderson},
title = {Applications of Linear Models in Animal Breeding},
publisher = {University of Guelph},
year = 1984,
address = {Ontario, Canada}
}
@Book{davis06:csparse_book,
author = {Tim Davis},
title = {Direct Methods for Sparse Linear Systems},
publisher = {SIAM},
address = {Philadelphia, PA},
year = 2006}
@TechReport{huq:cleland:1990,
author = {N. M. Huq and J. Cleland},
title = {Bangladesh Fertility Survey 1989 (Main Report)},
institution = {National Institute of Population Research and Training},
year = 1990,
address = {Dhaka, Bangladesh}}
@Article{spiegelhalter02:_bayes_measur_of_model_compl,
author = {David J. Spiegelhalter and Nicola G. Best and
Bradley P. Carlin and Angelika van der Linde},
title = {Bayesian measures of model complexity and fit (with
discussion)},
journal = {Journal of the Royal Statistical Society, Series B},
year = 2002,
volume = 64,
number = 4,
pages = {583--639}}
@Book{sarkar08:_lattic,
author = {Deepayan Sarkar},
title = {Lattice: Multivariate Data Visualization with R},
publisher = {Springer},
year = 2008}
@inproceedings{lmucs-papers:Leisch:2002,
author = {Friedrich Leisch},
title = {Sweave: Dynamic Generation of Statistical Reports Using
Literate Data Analysis},
booktitle = {Compstat 2002 --- Proceedings in Computational
Statistics},
pages = {575--580},
year = 2002,
editor = {Wolfgang H{\"a}rdle and Bernd R{\"o}nz},
publisher = {Physica Verlag, Heidelberg},
note = {ISBN 3-7908-1517-9},
url = {http://www.stat.uni-muenchen.de/~leisch/Sweave}
}
@Book{saka:ishi:kita:1986,
publisher = "Reidel",
address = "Dordrecht, Holland",
pages = "290",
keywords = "information criterion statistics",
author = "Y. Sakamoto and M. Ishiguro and G. Kitagawa",
title = "Akaike Information Criterion Statistics",
year = "1986",
}
@Article{schw:1978,
author = {Schwarz, G.},
title = {Estimating the Dimension of a Model},
journal = {Annals of Statistics},
year = {1978},
volume = {6},
pages = {461--464},
}
@Article{Davis:1996,
author = {Tim Davis},
title = {An approximate minimal degree ordering algorithm},
journal = {SIAM J. Matrix Analysis and Applications},
year = 1996,
volume = 17,
number = 4,
pages = {886-905}
}
@Book{west07:_linear_mixed_model,
author = {Brady T. West and Kathleen B. Welch and Andrzej
T. Ga\l{}ecki},
title = {Linear Mixed Models: A Practical Guide Using
Statistical Software},
publisher = {Chapman and Hall/CRC},
ISBN = {1-58488-480-0},
year = 2007,
address = {Boca Raton, FL}
}
@Book{bateswatts88:_nonlin,
author = {Douglas M. Bates and Donald G. Watts},
title = {Nonlinear Regression Analysis and Its Applications},
publisher = {Wiley},
year = 1988,
ISBN = {0-471-81643-4},
address = {Hoboken, NJ}}
@misc{Cholmod,
author = {Tim Davis},
title = {{CHOLMOD}: sparse supernodal {Cholesky} factorization
and update/downdate},
url = {http://www.cise.ufl.edu/research/sparse/cholmod},
year = 2005
}
@book{R:Chambers:2008,
author = {John M. Chambers},
title = {Software for Data Analysis: Programming with {R}},
publisher = {Springer},
year = 2008,
address = {New York},
note = {ISBN 978-0-387-75935-7},
url = {http://stat.stanford.edu/~jmc4/Rbook/},
publisherurl = {http://www.springer.com/statistics/computational/book/978-0-387-75935-7},
abstract = {The R version of S4 and other R techniques. This book
guides the reader in programming with R, from
interactive use and writing simple functions to the
design of R packages and intersystem interfaces.},
orderinfo = {springer.txt}
}
@Book{MLwiNUser:2000,
author = {J. Rasbash and W. Browne and H. Goldstein and M. Yang and I. Plewis},
title = {A User's Guide to {MLwiN}},
publisher = {Multilevel Models Project, Institute of Education, University of London},
year = 2000,
address = {London}
}
@Book{Rcpp,
title = {Seamless {R} and {C++} Integration with {Rcpp}},
author = {Dirk Eddelbuettel},
publisher = {Springer},
address = {New York},
year = {2013},
note = {ISBN 978-1-4614-6867-7},
doi = {10.1007/978-1-4614-6868-4},
}
@article{DanischKrumbiegel2021,
doi = {10.21105/joss.03349},
url = {https://doi.org/10.21105/joss.03349},
year = {2021},
publisher = {The Open Journal},
volume = {6},
number = {65},
pages = {3349},
author = {Simon Danisch and Julius Krumbiegel},
title = {Makie.jl: Flexible high-performance data visualization for {J}ulia},
journal = {Journal of Open Source Software}
}
@Book{davis2002,
author = {Charles S. {Davis}},
date = {2002},
title = {Statistical methods for the analysis of repeated measurements},
doi = {10.1007/b97287},
isbn = {0-387-95370-1},
language = {English},
pages = {xxiv + 415},
publisher = {New York, NY: Springer},
issn = {1431-875X},
journaltitle = {Springer Texts in Statistics},
keywords = {62-01 62J10},
zbl = {0985.62002},
}
@Article{elstongrizzle1962,
author = {R. C. {Elston} and J. E. {Grizzle}},
date = {1962},
journaltitle = {Biometrics},
title = {Estimation of time-response curves and their confidence bands},
doi = {10.2307/2527453},
issn = {0006-341X},
language = {English},
pages = {148--159},
volume = {18},
publisher = {Wiley (Wiley-Blackwell), Malden, MA; International Biometric Society, Washington, DC},
zbl = {0104.38101},
}
@Book{pinheirobates2000,
author = {Jos\'e C. {Pinheiro} and Douglas M. {Bates}},
date = {2000},
title = {Mixed-effects models in {S} and {S-Plus}},
doi = {10.1007/b98882},
isbn = {0-387-98957-9},
language = {English},
pages = {xvi + 528},
publisher = {New York, NY: Springer},
issn = {1431-8784},
series = {Statistics and Computing (Cham)},
keywords = {62J10 62-01 62-04 62J02 62J05 62J99},
zbl = {0953.62065},
}
@Article{box1950,
author = {G. E. P. Box},
date = {1950},
journaltitle = {Biometrics},
title = {Problems in the Analysis of Growth and Wear Curves},
doi = {10.2307/3001781},
number = {4},
pages = {362},
volume = {6},
publisher = {{JSTOR}},
}
@Article{Balota_2007,
author = {David A. Balota and Melvin J. Yap and Keith A. Hutchison and Michael J. Cortese and Brett Kessler and Bjorn Loftis and James H. Neely and Douglas L. Nelson and Greg B. Simpson and Rebecca Treiman},
date = {2007-08},
journaltitle = {Behavior Research Methods},
title = {The {E}nglish Lexicon Project},
doi = {10.3758/bf03193014},
number = {3},
pages = {445--459},
volume = {39},
publisher = {Springer Science and Business Media {LLC}},
}
@Article{Box1964,
author = {G. E. P. Box and D. R. Cox},
date = {1964-07},
journaltitle = {Journal of the Royal Statistical Society: Series B (Methodological)},
title = {An Analysis of Transformations},
doi = {10.1111/j.2517-6161.1964.tb00553.x},
number = {2},
pages = {211--243},
volume = {26},
publisher = {Wiley},
}
@Article{Bezanson2017,
author = {Jeff Bezanson and Alan Edelman and Stefan Karpinski and Viral B. Shah},
date = {2017-01},
journaltitle = {{SIAM} Review},
title = {Julia: A Fresh Approach to Numerical Computing},
doi = {10.1137/141000671},
number = {1},
pages = {65--98},
volume = {59},
publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
}
@Article{Brauer2018,
author = {Markus Brauer and John J. Curtin},
date = {2018-09},
journaltitle = {Psychological Methods},
title = {Linear mixed-effects models and the analysis of nonindependent data: A unified framework to analyze categorical and continuous independent variables that vary within-subjects and/or within-items.},
doi = {10.1037/met0000159},
number = {3},
pages = {389--411},
volume = {23},
publisher = {American Psychological Association ({APA})},
}
@Article{Harper2016,
author = {F. Maxwell Harper and Joseph A. Konstan},
date = {2016-01},
journaltitle = {{ACM} Transactions on Interactive Intelligent Systems},
title = {The {MovieLens} Datasets},
doi = {10.1145/2827872},
number = {4},
pages = {1--19},
volume = {5},
publisher = {Association for Computing Machinery ({ACM})},
}
@Book{Kaminski2023,
author = {Kamiński, Bogumił},
date = {2023},
title = {Julia for Data Analysis},
location = {Shelter Island, NY},
publisher = {Manning},
}
@article{TierneyKadane1986,
author = {Luke Tierney and Joseph B. Kadane },
title = {Accurate Approximations for Posterior Moments and Marginal Densities},
journal = {Journal of the American Statistical Association},
volume = {81},
number = {393},
pages = {82-86},
year = {1986},
publisher = {Taylor & Francis},
doi = {10.1080/01621459.1986.10478240},
URL = {https://www.tandfonline.com/doi/abs/10.1080/01621459.1986.10478240}
}
@article{powell2009bobyqa,
title={The BOBYQA algorithm for bound constrained optimization without derivatives},
author={Powell, Michael JD},
journal={Cambridge NA Report NA2009/06, University of Cambridge, Cambridge},
volume={26},
year={2009}
}
@article{Wickham2011,
title={The Split-Apply-Combine Strategy for Data Analysis},
volume={40},
url={https://www.jstatsoft.org/index.php/jss/article/view/v040i01},
doi={10.18637/jss.v040.i01},
abstract={Many data analysis problems involve the application of a split-apply-combine strategy, where you break up a big problem into manageable pieces, operate on each piece independently and then put all the pieces back together. This insight gives rise to a new R package that allows you to smoothly apply this strategy, without having to worry about the type of structure in which your data is stored. The paper includes two case studies showing how these insights make it easier to work with batting records for veteran baseball players and a large 3d array of spatio-temporal ozone measurements.},
number={1},
journal={Journal of Statistical Software},
author={Wickham, Hadley},
year={2011},
pages={1–29}
}
@article{JSSv107i04,
title={DataFrames.jl: Flexible and Fast Tabular Data in {J}ulia},
volume={107},
url={https://www.jstatsoft.org/index.php/jss/article/view/v107i04},
doi={10.18637/jss.v107.i04},
abstract={<p>DataFrames.jl is a package written for and in the Julia language offering flexible and efficient handling of tabular data sets in memory. Thanks to Julia’s unique strengths, it provides an appealing set of features: Rich support for standard data processing tasks and excellent flexibility and efficiency for more advanced and non-standard operations. We present the fundamental design of the package and how it compares with implementations of data frames in other languages, its main features, performance, and possible extensions. We conclude with a practical illustration of typical data processing operations.</p>},
number={4},
journal={Journal of Statistical Software},
author={Bouchet-Valat, Milan and Kamiński, Bogumił},
year={2023},
pages={1–32}
}
@Comment{jabref-meta: databaseType:biblatex;}