====== GEM² - GRUPO DE ESTUDO EM MODELOS MISTOS ======


==== Objetivo ====
**Geral**
    - Estudar modelos misto em uma abordagem teórica e computacional

**Especificos, Abordodagem em:**
       - Experimentação Agropecuária
       - Genética 
       - Modelagem Ambiental

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==== Participantes: ====
    * [[pessoais:paulojus|Paulo Justiniano Ribeiro Jr]]
    * [[pessoais:silvia|Silvia Emiko Shimakura]]
    * [[pessoais:elias|Elias Teixeira Krainski]]
    * [[pessoais:wbonat|Wagner Hugo Bonat]]
    * [[pessoais:walmes|Walmes Marques Zeviani]]
    * [[pessoais:fernanda| Fernanda Bührer Rizzato]]
    * [[pessoais:cesar| Cesar Taconeli]]
    * [[pessoais:eder|Eder David Borges da Silva]] 
    * [[pessoais:Renato.oliveira|Renato Gonçalves de Oliveira]] 

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==== Scripts  & Códigos====
    * {{:pessoais:mixedeffects.r|Random Effects - Faraway}} 
    * {{:pessoais:reml.r|REML e ML}} Comparação entre verossimilhança (ML) e verossimilhança residual (REML) em modelos mistos
    * [[http://www.maths.bath.ac.uk/~jjf23/ELM/scripts/|Scritps]] Extending the Linear Model with R
    * [[http://www.maths.bath.ac.uk/~jjf23/ELM/mixchange.pdf| Random Effects]] Material Atualizado do livro
    * {{:pessoais:pql.r|PQL para dados Poisson com efeito aleatório individual não estruturado (Silvia)}}

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==== Artigos ====
  *{{http://www.jstor.org/stable/pdfplus/2527669.pdf|The Estimation of Environmental and Genetic Trends from Records Subject to Culling}}
  * {{http://www.sciencedirect.com/science/article/pii/S0022030278835905|Simulation of Examine Distributions of Estimators of Variances and Ratios of Variances}}
  * {{http://www.jstor.org/stable/3001853|Estimation of Variance and Covariance Components}}
  * {{http://www.sciencedirect.com/science/article/pii/S0022030291786013|C. R. Henderson: Contributions to Predicting Genetic Merit}}
  * {{http://download.journals.elsevierhealth.com/pdfs/journals/0022-0302/PIIS002203027584776X.pdf|Rapid Method for Computing the Inverse of a Relationship Matrix}}
  * {{http://www.jstor.org/pss/2529339|A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values}}
  * {{http://www.jstor.org/stable/2529430?&Search=yes&searchText=%22C.+R.+Henderson%22&list=hide&searchUri=%2Faction%2FdoBasicSearch%3FQuery%3Dau%253A%2522C.%2BR.%2BHenderson%2522%26wc%3Don&prevSearch=&item=3&ttl=373&returnArticleService=showFullText|Best Linear Unbiased Estimation and Prediction under a Selection Model}}
  * {{http://www.jstor.org/stable/2530609?&Search=yes&searchText=%22C.+R.+Henderson%22&list=hide&searchUri=%2Faction%2FdoBasicSearch%3FQuery%3Dau%253A%2522C.%2BR.%2BHenderson%2522%26wc%3Don&prevSearch=&item=5&ttl=373&returnArticleService=showFullText|Variance-Covariance Matrix of Estimators of Variances in Unweighted Means ANOVA}}
  * {{http://www.jstor.org/stable/2529264?seq=10|A Comparison of Variance Component Estimators}}
  

==== Slides, notas de aula e apostilas ====

  * {{http://socserv.mcmaster.ca/jfox/Courses/soc761/mixed-models-1.pdf|John Fox - Introduction to Mixed-Effects Models for Hierarchical and Longitudinal Data (I)}};
  * {{http://socserv.mcmaster.ca/jfox/Courses/soc761/mixed-models-2.pdf|John Fox - Introduction to Mixed-Effects Models for Hierarchical and Longitudinal Data (II)}};
  * {{http://www-m4.ma.tum.de/courses/WS09-10/glm/GLM_LecNotes.pdf|Claudia Czado - Lecture Notes on Linear Mixed Models}};
  * {{http://mcs.une.edu.au/~stat504/StudyGuide/UNEnotes.pdf|R. D. Murison - Mixed Models Lecture Notes}};
  * {{http://gbi.agrsci.dk/~ejo/publications/preprints/2001.04.i.pdf|Søren Højsgaard & Erik Jørgensen - Lecture Slides on Mixed Models}};
  * {{http://plantecology.syr.edu/fridley/bio793/nichenotes_portal.html|Jason Fridley - Lecture notes from Bio793: Plant Ecology/Niche modeling/Modeling in R}};
  * {{http://www.stat.uga.edu/~dhall/8630/lec1.pdf|Mixed-Effect Models and Longitudinal Data Analysis -- Lecture Notes}};
  * {{http://mypage.iu.edu/~ehouswor/Spring2006/Math761/LectureNotes.pdf|Elizabeth Ann Housworth - Lecture Notes for M761: Topics in Applied Statistics}};
  * {{http://idiom.ucsd.edu/~rlevy/lign251/fall2007/|Roger Levy - Linguistics 251: Probabilistic Methods in Linguistics}};
  * {{http://www.public.iastate.edu/~dnett/S511/lectures.shtml|Dan Nettleton - Statistics 511 Lecture Notes}};
  * {{https://www.stat.washington.edu/hoff/courses/560/LectureNotes/notes.pdf|Peter D. Hoff - CSSS-Statistics 560 Lecture Notes}};
  * {{http://joyx.joensuu.fi/~lamehtat/documents/lecture_notes.pdf|Lauri Mehtätalo - Forest biometrics with examples in R}};
  * {{http://www.stat.sc.edu/~hansont/stat771/stat771.html|Tim Hanson - Stat 771: Longitudinal Data Analysis}};
  * {{http://www.stat.rutgers.edu/home/mxie/stat587/glmm1.pdf|Lectures notes on generalized mixed models}};
  * {{http://rweb.stat.ucla.edu/lme4/|yeroon.net/lme4 R Web Application}};
  * {{http://www.unil.ch/webdav/site/ee/shared/WorkshopD.pdf|Douglas Bates - Mixed models in R using the lme4 package}};
  * {{http://www.stat.wisc.edu/~bates/PotsdamGLMM/LMMD.pdf|Douglas Bates - Fitting Linear Mixed-Effects Models Using the lme4 Package in R}};
  * {{http://www.stat.wisc.edu/~bates/PotsdamGLMM/GLMMD.pdf|Douglas Bates - Generalized Linear and Nonlinear Mixed-Effects Models}};
  * Douglas Bates Tour em {{http://lme4.r-forge.r-project.org/slides/2011-03-16-Amsterdam/|Amsterdam(2011)}}, {{http://lme4.r-forge.r-project.org/slides/2011-01-11-Madison/|Madson(2011)}}, {{http://lme4.r-forge.r-project.org/slides/2010-07-20-Gaithersburg/|Gaithersburg(2010)}}, {{http://lme4.r-forge.r-project.org/slides/2009-07-21-Seewiesen/|Seewiesen(2009)}}, {{http://lme4.r-forge.r-project.org/slides/2009-07-07-Rennes/|Rennes(2009)}}, {{http://lme4.r-forge.r-project.org/slides/2009-07-01-Lausanne/|Lausanne(2009)}};
  * {{http://maths.anu.edu.au/~johnm/r-book/xtras/mlm-ohp.pdf|John Maindonald - The Anatomy of a Mixed Model Analysis, with R's lme4 Package}};
  * {{http://kups.ku.edu/maillist/classes/ps707/2004/msg00038.html|[R] GLMM (lme4) vs. glmmPQL output (summary with lme4 revised)}};
  * {{http://www.meetup.com/LAarea-R-usergroup/messages/8429649/|Los Angeles area R users group (data analysis/statistics)}};
  * {{http://www.let.uu.nl/~Hugo.Quene/personal/multilevel/jml2008/x24lmerlog.html|Hugo Quené - Mixed-effects modeling with crossed random effects in R}};
  * {{http://www.let.uu.nl/~Hugo.Quene/personal/mixedeffects/|Hugo Quené - Mixed-Effects Modeling Multilevel Modeling}};
  * {{http://wiki.math.yorku.ca/index.php/R:_lmer|Using lmer and nlme at the same time}};
  * {{http://www.unt.edu/rss/class/Jon/R_SC/Module9/LMM_Examples.R|Brief Introduction to LINEAR MIXED MODELS in R}};
  * {{http://www.unt.edu/rss/class/Jon/R_SC/|Research and Statistical Support}};
  * {{http://cran.r-project.org/doc/contrib/Fox-Companion/appendix-mixed-models.pdf|Linear Mixed Models Appendix to An R and S-PLUS Companion to Applied Regression - John Fox}};
  * {{http://www.jstor.org/stable/3647633|Likelihood Ratio Tests in Linear Mixed Models with One Variance Component - Ciprian M. Crainiceanu and David Ruppert}};
  * {{http://www.jstor.org/stable/2291460|Maximum Likelihood Algorithms for Generalized Linear Mixed Models - Charles E. McCulloch}};
  * {{http://www.fcsm.gov/09papers/Lahiri_II-C.pdf|Generalized Maximum Likelihood Method in Linear Mixed Models with an Application in Small-Area Estimation - P.Lahiri and Huilin Li}};
  * {{http://www3.stat.sinica.edu.tw/statistica/oldpdf/A14n21.pdf|CONDITIONAL LIKELIHOOD INFERENCE IN GENERALIZED LINEAR MIXED MODELS N. Sartori and T. A. Severini}};
  * {{http://lme4.r-forge.r-project.org/slides/2011-01-11-Madison/6NLMMH.pdf|Mixed models in R using the lme4 package Part 6: Nonlinear mixed models Douglas Bates}};
  * {{http://arxiv.org/pdf/1010.0303|Likelihood Inference for Models with Unobservables: Another View - Youngjo Lee and John A. Nelder}};
  * {{http://www.jstor.org/stable/2958794|Asymptotic Properties of Maximum Likelihood Estimates in the Mixed Model of the Analysis of Variance}};
  * {{http://www.springerlink.com/content/4w32240527212732/|A direct derivation of the REML likelihood function}};
  * {{http://www.math.ku.dk/~erhansen/web/stat1/pinheiro.pdf|Topics in Mixed Effects Models - José Carlos Pinheiro}};
  * {{http://researchspace.ukzn.ac.za/xmlui/bitstream/handle/10413/2547/Hammujuddy_M_J_2004.pdf?sequence=1|A CLASSICAL APPROACH FOR THE ANALYSIS OF GENERALIZED LINEAR MIXED MODELS - MJ Hammujuddy}};
  * {{http://www.springerlink.com/content/72052208xwl2q362/|Marginal maximum likelihood estimation of variance components in Poisson mixed models using Laplacian integration}};
  * {{https://perswww.kuleuven.be/~u0018341/documents/ldasc06newjersey.pdf|Longitudinal data, mixed models and incomplete data - Geert}};
  * {{http://www.google.com/search?client=ubuntu&channel=fs&q=restricted+maximum+likelihood+estimation+of+variance+components+in+generalized+linear+mixed+models&ie=utf-8&oe=utf-8#hl=pt-BR&client=ubuntu&hs=tLi&channel=fs&q=restricted+maximum+likelihood+estimation+of+variance+components+in+generalized+linear+mixed+models+filetype:ps&aq=f&aqi=&aql=&oq=&pbx=1&bav=on.2,or.r_gc.r_pw.&fp=7992793a42cf0be6&biw=1760&bih=849|Thomas Kneib - Restricted maximum likelihood estimation of variance components in generalized linear mixed models}}; =)
  * {{http://research.utar.edu.my/CMS/ICMSA2010/ICMSA2010_Proceedings/files/poster/P-Rashidi.pdf|Fit generalized linear mixed models (GLMM), using of different likelihoods}};
  * {{http://www.ebah.com.br/content/ABAAAAG_sAC/modelos-lineares|Modelos Lineares - João Gil de Luna}};
  * {{http://nlp.stanford.edu/~manning/courses/ling289/GLMM.pdf|Generalized Linear Mixed Models (illustrated with R on Bresnan et al.’s datives data)}};

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==== Histórico ====
  * Em preto: conteúdo abordado no encontro;
  * Em <fc #008000>verde</fc>: conteúdo previsto para o próximo encontro;

^     Data  ^  Hora   ^   Acontecimento                                       ^ 
| 23/03/2011| 17:30   | Discussão inicial do grupo - Walmes, PJ , Éder, Renato|
| 20/05/2011| 16:00   | Discussão sobre separação de atividades (Derivação das expressões, ML, REML, PQL, Inferência em MM, exemplos em genética e experimentação )  |
| 17/06/2011| 16:00   | Procedimento REML de estimação de componentes de variância em LMM (PJ). Implementação de funções de verossimilhança para estimação de parâmetros em GLMM sem e com estrutura para um fator de efeito aleatório (WB). |
| 01/07/2011| 16:00   | Procedimentos PQL para modelos mistos na família exponencial (SS), métodos numéricos (Gauss-Hermite, Laplace, Quasi Monte Carlo) empregados para estimação em modelos mistos (WB).  |
| 08/07/2011| 16:00   |  <fc #008000>Implementação do procedimento REML (EB), PQL (SS) e predição de efeitos aleatórios (PJ).</fc>  |
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==== Lista de afazeres ====

  * (17/06/2011)
    * WB: disponibilizar os scripts apresentadas em 17/06;
    * WZ: preparar documento com a distribuição marginal em LMM;
    * PJ & WZ: preparar documento com a derivação e implementação (didática) do método REML;
  * (01/07/2011)
    * WZ: documentar os procedimentos de estimação empregando métodos numéricos para a integração dos efeitos aleatórios escritos por WB, rodar glmm.PQL(), glmer();
    * SS: implementar o PQL;
    * EB: implementar o REML;
    * PJ: procedimentos para predição dos efeitos aleatórios;



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==== Referências  ====

=== Livros ===
<bibtex>

@book{magalhaes,
	title = {Noções de Probabilidade e Estatística},
	publisher = {Edusp},
	author = {M N Magalhães and A C P Lima},
	year = {200?},
        edition = {1},
	pages = {540}
}

@TechReport{ribeiro_jr-leg,
	url = {http://www.leg.ufpr.br/~paulojus/embrapa/Rembrapa/Rembrapa.pdf},
	year = {2009},
	author = {Paulo Justiniano {Ribeiro Júnior}},
	title = {Introdução ao Ambiente Estatístico R}
}

@book{venables_modern_2002,
	title = {Modern applied statistics with S},
        url = {http://www.leg.ufpr.br/~walmes/docs/Modern%20Applied%20Statistical%20Methods%20with%20S%20plus.pdf},
	isbn = {9780387954578},
	publisher = {Birkhäuser},
	author = {William N. Venables and Brian D. Ripley},
	year = {2002},
	pages = {518}
}


@book{everitt_handbook_2009,
	edition = {2},
	title = {A Handbook of Statistical Analyses Using R, Second Edition},
        %url = {http://www.maths.bath.ac.uk/~jjf23/ELM/},
        url = {http://www.leg.ufpr.br/~walmes/docs/A%20handbook%20of%20statistical%20analyses%20using%20R.pdf},
	isbn = {1420079336},
	publisher = {Chapman \& Hall},
	author = {Brian S. Everitt and Torsten Hothorn},
	month = jul,
	year = {2009}
}

@book{dalgaard_introductory_2008,
	edition = {2nd},
	title = {Introductory Statistics with R},
        url = {http://www.leg.ufpr.br/~walmes/docs/Introductory%20Statistics%20with%20R.pdf},
	isbn = {0387790535},
	publisher = {Springer},
	author = {Peter Dalgaard},
	month = aug,
	year = {2008}
}

@book{sarkar_lattice:_2008,
	edition = {1},
	title = {Lattice: Multivariate Data Visualization with R},
        url = {http://www.leg.ufpr.br/~walmes/docs/Lattice%20Multivariate%20Data%20Visualization%20with%20R.pdf},
	isbn = {0387759689},
	shorttitle = {Lattice},
	publisher = {Springer},
	author = {Deepayan Sarkar},
	month = mar,
	year = {2008}
}
</bibtex>

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==== Software ====
  - [[http://www.r-project.org|The R project for Statistical Computing]]: página do programa **R**
      -[[http://cran.r-project.org/web/packages/nlme/index.html|nlme]] Linear and Nonlinear Mixed Effects Models
  - [[http://www.math.ilstu.edu/dhkim/Rstuff/Rtutor.html|Uma página interessante]] com um introdução ao R
  - O [[http://www.xemacs.org|Xemacs]] é uma outra opção de editor que facilita a edição de arquivos do   <latex>\LaTeX</latex> e **R** e disponível para plataformas Linux e Windows.
  - [[software:rbr|R-br]] é a lista de discussão em português sobre o uso do R

----