4. Denitions
Statistics
Computation
Software
Conclusions
References
(Generalized) linear mixed models
(G)LMMs: a statistical modeling framework incorporating:
Linear combinations of categorical and continuous
predictors, and interactions
Response distributions in the
exponential family
(binomial, Poisson, and extensions)
Any smooth, monotonic
link function
(e.g. logistic, exponential models)
Flexible combinations of
blocking factors
(clustering; random eects)
Applications in ecology, neurobiology, behaviour, epidemiology, real
estate, . . .
Ben Bolker
Mixed model software
5. Denitions
Statistics
Computation
Software
Conclusions
References
(Generalized) linear mixed models
(G)LMMs: a statistical modeling framework incorporating:
Linear combinations of categorical and continuous
predictors, and interactions
Response distributions in the
exponential family
(binomial, Poisson, and extensions)
Any smooth, monotonic
link function
(e.g. logistic, exponential models)
Flexible combinations of
blocking factors
(clustering; random eects)
Applications in ecology, neurobiology, behaviour, epidemiology, real
estate, . . .
Ben Bolker
Mixed model software
6. Denitions
Statistics
Computation
Software
Conclusions
References
(Generalized) linear mixed models
(G)LMMs: a statistical modeling framework incorporating:
Linear combinations of categorical and continuous
predictors, and interactions
Response distributions in the
exponential family
(binomial, Poisson, and extensions)
Any smooth, monotonic
link function
(e.g. logistic, exponential models)
Flexible combinations of
blocking factors
(clustering; random eects)
Applications in ecology, neurobiology, behaviour, epidemiology, real
estate, . . .
Ben Bolker
Mixed model software
7. Denitions
Statistics
Computation
Software
Conclusions
References
(Generalized) linear mixed models
(G)LMMs: a statistical modeling framework incorporating:
Linear combinations of categorical and continuous
predictors, and interactions
Response distributions in the
exponential family
(binomial, Poisson, and extensions)
Any smooth, monotonic
link function
(e.g. logistic, exponential models)
Flexible combinations of
blocking factors
(clustering; random eects)
Applications in ecology, neurobiology, behaviour, epidemiology, real
estate, . . .
Ben Bolker
Mixed model software
8. Denitions
Statistics
Computation
Software
Conclusions
References
Examples
ecology survival, predation, etc. (experimental plots)
genomics presence/absence of polymorphisms, gene expression
(individuals)
educational assessment student scores (students
×
teachers)
psychology/sensometrics decisions, responses to stimuli
(individuals)
epidemiology disease prevalence (postal codes, provinces, countries)
Ben Bolker
Mixed model software
9. Denitions
Statistics
Computation
Software
Conclusions
References
Examples
ecology survival, predation, etc. (experimental plots)
genomics presence/absence of polymorphisms, gene expression
(individuals)
educational assessment student scores (students
×
teachers)
psychology/sensometrics decisions, responses to stimuli
(individuals)
epidemiology disease prevalence (postal codes, provinces, countries)
Ben Bolker
Mixed model software
10. Denitions
Statistics
Computation
Software
Conclusions
References
Examples
ecology survival, predation, etc. (experimental plots)
genomics presence/absence of polymorphisms, gene expression
(individuals)
educational assessment student scores (students
×
teachers)
psychology/sensometrics decisions, responses to stimuli
(individuals)
epidemiology disease prevalence (postal codes, provinces, countries)
Ben Bolker
Mixed model software
11. Denitions
Statistics
Computation
Software
Conclusions
References
Examples
ecology survival, predation, etc. (experimental plots)
genomics presence/absence of polymorphisms, gene expression
(individuals)
educational assessment student scores (students
×
teachers)
psychology/sensometrics decisions, responses to stimuli
(individuals)
epidemiology disease prevalence (postal codes, provinces, countries)
Ben Bolker
Mixed model software
12. Denitions
Statistics
Computation
Software
Conclusions
References
Examples
ecology survival, predation, etc. (experimental plots)
genomics presence/absence of polymorphisms, gene expression
(individuals)
educational assessment student scores (students
×
teachers)
psychology/sensometrics decisions, responses to stimuli
(individuals)
epidemiology disease prevalence (postal codes, provinces, countries)
Ben Bolker
Mixed model software
21. Denitions
Statistics
Computation
Software
Problems of big data
How big is big?
Airline data: 12G
(G)LMM works on
moderately large problems,
e.g. student evaluations
(≈ 75K total, 3K students, 1K profs)
Fairly clever linear algebra
Possible improvements?
Chunking/parallelization
Out-of-memory operation
Ben Bolker
Mixed model software
Conclusions
References
22. Denitions
Statistics
Computation
Sparse matrix algorithms
repeated decomposition of
large, matrices (especially Z )
ll-reducing permutation to
improve sparsity pattern
further improvements possible:
better matrix representation,
parallelization?
Ben Bolker
Mixed model software
Software
Conclusions
References
26. Denitions
Statistics
Computation
Software
Getting it right vs. getting it written
the curse of neophilia: Superiority
many versions:
nlme, lme4(a,b,Eigen)
The moral of the story is that if
you want to create a beautiful
language, for god's sake don't
make it useful
(Patrick Burns)
Ben Bolker
Mixed model software
...
Conclusions
References
27. Denitions
Statistics
Computation
Software
Conclusions
References
Sociological issues
Wide user base:
As usual when software for complicated statistical
inference procedures is broadly disseminated, there is
potential for abuse and misinterpretation.
(Breslow, 2004)
What if there is no good answer?
do no harm vs. better me than someone else
Diagnostics and warning messages
End users
Ben Bolker
Mixed model software
vs.
downstream developers
32. Denitions
Statistics
Computation
Software
Conclusions
References
Booth, J.G. and Hobert, J.P., 1999. Journal of the Royal Statistical Society. Series B, 61(1):265285.
doi:10.1111/1467- 9868.00176.
Breslow, N.E., 2004. In D.Y. Lin and P.J. Heagerty, editors, Proceedings of the second Seattle
symposium in biostatistics: Analysis of correlated data, pages 122. Springer. ISBN 0387208623.
McKeon, C.S., Stier, A., et al., 2012. Oecologia, 169(4):10951103. ISSN 0029-8549.
doi:10.1007/s00442- 012-2275-2.
Pinheiro, J.C. and Bates, D.M., 1996. Statistics and Computing, 6(3):289296.
doi:10.1007/BF00140873.
Ponciano, J.M., Taper, M.L., et al., 2009. Ecology, 90(2):356362. ISSN 0012-9658.
Sung, Y.J., 2007. The Annals of Statistics, 35(3):9901011. ISSN 0090-5364.
doi:10.1214/009053606000001389.
Ben Bolker
Mixed model software