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R-SIG-mixed-models March 2013

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2 correlated random effects with quadrature?

5 msgs
Ross Boylan 2 correlated random effects with quadrature? Mar 11, 2013 Ben Bolker 2 correlated random effects with quadrature? Mar 12, 2013 Joshua Wiley 2 correlated random effects with quadrature? Mar 12, 2013 David Duffy 2 correlated random effects with quadrature? Mar 12, 2013 Ross Boylan 2 correlated random effects with quadrature? Mar 13, 2013

About glmmADMB Control Options...

1 msg
MARTINEZ GUTIERREZ, PATRICIA GUADALUPE About glmmADMB Control Options... Mar 19, 2013

Breeding Values of Parentals (pedigreemm)

3 msgs
Felipe Vargas Reeve Breeding Values of Parentals (pedigreemm) Mar 15, 2013 David Duffy Breeding Values of Parentals (pedigreemm) Mar 16, 2013 Felipe Vargas Reeve Breeding Values of Parentals (pedigreemm) Mar 18, 2013

Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size?

11 msgs
Chris Howden Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Feb 28, 2013 Emmanuel Curis Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 1, 2013 Ben Bolker Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 1, 2013 Steve Taylor Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 3, 2013 Chris Howden Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 3, 2013 Luca Borger Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 3, 2013 Ben Bolker Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 3, 2013 Chris Howden Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 3, 2013 Chris Howden Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 3, 2013 Chris Howden Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 3, 2013 Emmanuel Curis Can AIC be approximated by -2ln(L) i.e. the deviance, at very large sample size? Mar 4, 2013

Can I compare different models - with and without random effects - across different packages?

3 msgs
Antonio P. Ramos Can I compare different models - with and without random effects - across different packages? Mar 13, 2013 Antonio P. Ramos Can I compare different models - with and without random effects - across different packages? Mar 13, 2013 David Duffy Can I compare different models - with and without random effects - across different packages? Mar 13, 2013

Changes of estimate sign when interaction effects are highly significant

3 msgs
MORAN LOPEZ, TERESA Changes of estimate sign when interaction effects are highly significant Mar 5, 2013 Adam Smith Changes of estimate sign when interaction effects are highly significant Mar 5, 2013 Ben Bolker Changes of estimate sign when interaction effects are highly significant Mar 5, 2013

Cholesky factor discrepancy

1 msg
Pantelis Hadjipantelis Cholesky factor discrepancy Mar 19, 2013

Choosing nlme or lme4?

2 msgs
Filipe Carvalho Choosing nlme or lme4? Mar 5, 2013 Ben Bolker Choosing nlme or lme4? Mar 5, 2013

Cluster analysis in the setting of repeated measures

1 msg
John Sorkin Cluster analysis in the setting of repeated measures Mar 10, 2013

Comparing linear and ordinal model random effects

1 msg
Stuart Luppescu Comparing linear and ordinal model random effects Mar 8, 2013

Data frame size limits in MCMCglmm?

1 msg
Jarrod Hadfield Data frame size limits in MCMCglmm? Mar 6, 2013

Dispersion parameter calculation for Poisson glmer

1 msg
John Maindonald Dispersion parameter calculation for Poisson glmer Feb 28, 2013

Error :

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Ben Bolker Error : Mar 18, 2013

Error : "contrasts apply only to factors" in post-hoc analysis afer lmer fitting.

1 msg
shao chunxuan Error : "contrasts apply only to factors" in post-hoc analysis afer lmer fitting. Mar 11, 2013

Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model?

10 msgs
PALACIO BLASCO, SARA Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 4, 2013 Ben Bolker Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 4, 2013 PALACIO BLASCO, SARA Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 4, 2013 Ben Bolker Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 4, 2013 PALACIO BLASCO, SARA Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 4, 2013 Emmanuel Curis Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 4, 2013 PALACIO BLASCO, SARA Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 5, 2013 Emmanuel Curis Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 5, 2013 PALACIO BLASCO, SARA Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 5, 2013 PALACIO BLASCO, SARA Error en mer_finalize(ans) : Downdated X'X is not positive definite, 1. What is wrong with my model? Mar 6, 2013

Evaluating Z matrix

3 msgs
Pantelis Hadjipantelis Evaluating Z matrix Mar 14, 2013 Ben Bolker Evaluating Z matrix Mar 15, 2013 Pantelis Hadjipantelis Evaluating Z matrix Mar 16, 2013

False convergence

3 msgs
Nick Isaac False convergence Mar 1, 2013 Ben Bolker False convergence Mar 2, 2013 Nick Isaac False convergence Mar 4, 2013

Finding r^2 value and plotting regression lines and CIs from gls

1 msg
Ben Bolker Finding r^2 value and plotting regression lines and CIs from gls Mar 10, 2013

Finding r^2 value and plotting regression lines and CIs from gls

1 msg
Margie Mathewson Finding r^2 value and plotting regression lines and CIs from gls Mar 7, 2013

GAM and MCMCglmm - extracting splines from GAM to use in another package

1 msg
Antonio P. Ramos GAM and MCMCglmm - extracting splines from GAM to use in another package Mar 29, 2013

Help needed: Fitting and Simulating multilevel model in R.

1 msg
Robin Pritchard Help needed: Fitting and Simulating multilevel model in R. Mar 29, 2013

How does lmer obtain ML estimates that are not stationary points?

1 msg
Ben Bolker How does lmer obtain ML estimates that are not stationary points? Mar 14, 2013

How does lmer obtain ML estimates that are not stationary points?

1 msg
Asaf Weinstein How does lmer obtain ML estimates that are not stationary points? Mar 14, 2013

Is a mixed effects appropriate?

2 msgs
Ross Ahmed Is a mixed effects appropriate? Mar 16, 2013 Ben Bolker Is a mixed effects appropriate? Mar 16, 2013

Is it possible to run MCMCglmm without varying effects?

2 msgs
Jonathan Salerno Is it possible to run MCMCglmm without varying effects? Mar 5, 2013 Jarrod Hadfield Is it possible to run MCMCglmm without varying effects? Mar 6, 2013

Is there any way to model nested random effects in MCMCglmm?

2 msgs
Ivain MARTINOSSI--ALLIBERT Is there any way to model nested random effects in MCMCglmm? Mar 29, 2013 Jarrod Hadfield Is there any way to model nested random effects in MCMCglmm? Mar 29, 2013

MCMCglmm error message - data.frame subscripts

2 msgs
Liz Hare MCMCglmm error message - data.frame subscripts Mar 29, 2013 Jarrod Hadfield MCMCglmm error message - data.frame subscripts Mar 30, 2013

MCMCglmm ordinal: clarification on estimating an intercepts only model and interpreting cutpoints

2 msgs
Jonathan Salerno MCMCglmm ordinal: clarification on estimating an intercepts only model and interpreting cutpoints Mar 13, 2013 Jarrod Hadfield MCMCglmm ordinal: clarification on estimating an intercepts only model and interpreting cutpoints Mar 14, 2013

MCMCglmm predictions with fixed effects Splines

8 msgs
Antonio P. Ramos MCMCglmm predictions with fixed effects Splines Mar 25, 2013 Antonio P. Ramos MCMCglmm predictions with fixed effects Splines Mar 25, 2013 Joshua Wiley MCMCglmm predictions with fixed effects Splines Mar 25, 2013 Antonio P. Ramos MCMCglmm predictions with fixed effects Splines Mar 25, 2013 Jarrod Hadfield MCMCglmm predictions with fixed effects Splines Mar 26, 2013 Antonio P. Ramos MCMCglmm predictions with fixed effects Splines Mar 26, 2013 Jarrod Hadfield MCMCglmm predictions with fixed effects Splines Mar 26, 2013 Joshua Wiley MCMCglmm predictions with fixed effects Splines Mar 27, 2013

MCMCglmm:interaction bt continuous variable and categorical random effect

5 msgs
john benson MCMCglmm:interaction bt continuous variable and categorical random effect Mar 31, 2013 Joshua Wiley MCMCglmm:interaction bt continuous variable and categorical random effect Mar 31, 2013 john benson MCMCglmm:interaction bt continuous variable and categorical random effect Mar 31, 2013 Joshua Wiley MCMCglmm:interaction bt continuous variable and categorical random effect Mar 31, 2013 john benson MCMCglmm:interaction bt continuous variable and categorical random effect Mar 31, 2013

Make a 'between-and-within-factors' ANOVA with lmer function

1 msg
Ben Bolker Make a 'between-and-within-factors' ANOVA with lmer function Mar 24, 2013

Make a 'between-and-within-factors' ANOVA with lmer function

5 msgs
Vanni Rovera Make a 'between-and-within-factors' ANOVA with lmer function Mar 24, 2013 iwhite@staffmail.ed.ac.uk Make a 'between-and-within-factors' ANOVA with lmer function Mar 24, 2013 Vanni Rovera Make a 'between-and-within-factors' ANOVA with lmer function Mar 26, 2013 guillaume chaumet Make a 'between-and-within-factors' ANOVA with lmer function Mar 27, 2013 iwhite@staffmail.ed.ac.uk Make a 'between-and-within-factors' ANOVA with lmer function Mar 27, 2013

Model selection in GAMM

7 msgs
Mari Laine Model selection in GAMM Mar 17, 2013 Ben Bolker Model selection in GAMM Mar 17, 2013 Andrew Robinson Model selection in GAMM Mar 17, 2013 Ben Bolker Model selection in GAMM Mar 18, 2013 Joshua Wiley Model selection in GAMM Mar 18, 2013 Joshua Wiley Model selection in GAMM Mar 18, 2013 Mari Laine Model selection in GAMM Mar 27, 2013

Nested Effects and Correlation

3 msgs
Pantelis H Nested Effects and Correlation Mar 7, 2013 Ben Bolker Nested Effects and Correlation Mar 10, 2013 Ben Bolker Nested Effects and Correlation Mar 11, 2013

Nested fixed factors in glmer: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1.

6 msgs
Rolf Turner Nested fixed factors in glmer: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1. Feb 28, 2013 Rolf Turner Nested fixed factors in glmer: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1. Feb 28, 2013 Rolf Turner Nested fixed factors in glmer: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1. Feb 28, 2013 Andrew Robinson Nested fixed factors in glmer: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1. Feb 28, 2013 Andrew Robinson Nested fixed factors in glmer: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1. Feb 28, 2013 Emmanuel Curis Nested fixed factors in glmer: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 1. Mar 1, 2013

Nested random effects meta-analysis using nlme?

2 msgs
Masca, Nicholas Nested random effects meta-analysis using nlme? Mar 1, 2013 Shinichi Nakagawa Nested random effects meta-analysis using nlme? Mar 1, 2013

New book "Generalized Linear Mixed Models" by Walter Stroup

1 msg
Douglas Bates New book "Generalized Linear Mixed Models" by Walter Stroup Mar 2, 2013

Non-convergence error for GLMM with LME4?

2 msgs
Leanna Jones Non-convergence error for GLMM with LME4? Mar 23, 2013 Ben Bolker Non-convergence error for GLMM with LME4? Mar 24, 2013

Partial effects in mixed models

4 msgs
v_coudrain at voila.fr Partial effects in mixed models Mar 1, 2013 Steven J. Pierce Partial effects in mixed models Mar 1, 2013 Thompson,Paul Partial effects in mixed models Mar 1, 2013 v_coudrain at voila.fr Partial effects in mixed models Mar 1, 2013

Question about gls R function

1 msg
Douglas Bates Question about gls R function Mar 4, 2013

R2 from mixed models

1 msg
Alan Haynes R2 from mixed models Mar 21, 2013

R: Re: R: Re: GLMM family=binomial, link identity

1 msg
maggenga at libero.it R: Re: R: Re: GLMM family=binomial, link identity Mar 1, 2013

Random Effect Variance of Zero

2 msgs
Kevin E. Thorpe Random Effect Variance of Zero Mar 21, 2013 Ben Bolker Random Effect Variance of Zero Mar 21, 2013

Request for large data sets for linear mixed models

3 msgs
Douglas Bates Request for large data sets for linear mixed models Mar 25, 2013 Kevin Wright Request for large data sets for linear mixed models Mar 25, 2013 Douglas Bates Request for large data sets for linear mixed models Mar 25, 2013

adjusting convergence tolerance

1 msg
Roger Levy adjusting convergence tolerance Mar 29, 2013

cAIC

2 msgs
Oliver Soong cAIC Mar 15, 2013 Ben Bolker cAIC Mar 16, 2013

complete separation problem lmer

2 msgs
Giovanni Mancuso complete separation problem lmer Mar 25, 2013 Steve Walker complete separation problem lmer Mar 25, 2013

confidence interval for the SD of random effects

1 msg
Iasonas Lamprianou confidence interval for the SD of random effects Mar 28, 2013

data grouping and fitting mixed model with lme function

1 msg
KAYIS Seyit Ali data grouping and fitting mixed model with lme function Mar 2, 2013

determining whether factor is significant in linear mixed models

1 msg
Luca Borger determining whether factor is significant in linear mixed models Mar 25, 2013

determining whether factor is significant in linear mixed models

2 msgs
Brad Buran determining whether factor is significant in linear mixed models Mar 25, 2013 Steven Brady determining whether factor is significant in linear mixed models Mar 25, 2013

glmer: Downdated X'X is not positive definite [related to nAGQ] fixed?

1 msg
Ross Boylan glmer: Downdated X'X is not positive definite [related to nAGQ] fixed? Mar 13, 2013

glmmADMB Warning: Estimated covariance matrix may not be positive definite

2 msgs
angela.boag at alumni.ubc.ca glmmADMB Warning: Estimated covariance matrix may not be positive definite Mar 13, 2013 Ben Bolker glmmADMB Warning: Estimated covariance matrix may not be positive definite Mar 14, 2013

glmmADMB troubles

3 msgs
Ben Bolker glmmADMB troubles Mar 2, 2013 Ross Boylan glmmADMB troubles Mar 3, 2013 Ross Boylan glmmADMB troubles Mar 6, 2013

glmmADMB troubles [diagnosed + worked around]

1 msg
Ross Boylan glmmADMB troubles [diagnosed + worked around] Mar 28, 2013

glmmADMB truncated distributions

2 msgs
Ross Boylan glmmADMB truncated distributions Mar 28, 2013 Ben Bolker glmmADMB truncated distributions Mar 28, 2013

glmmadmb

2 msgs
Kevin Burls glmmadmb Mar 24, 2013 dave fournier glmmadmb Mar 24, 2013

gls error

2 msgs
Benjamin Gillespie gls error Mar 13, 2013 Ben Bolker gls error Mar 13, 2013

how to impose same variance for two random effects with fixed correlation patterns?

1 msg
Gabriel Baud-Bovy how to impose same variance for two random effects with fixed correlation patterns? Mar 28, 2013

lme heteroscedasticity

3 msgs
Iasonas Lamprianou lme heteroscedasticity Mar 31, 2013 Joshua Wiley lme heteroscedasticity Mar 31, 2013 Iasonas Lamprianou lme heteroscedasticity Mar 31, 2013

lme4 help

1 msg
Ludovico Frate lme4 help Mar 25, 2013

lme4 versions

3 msgs
Ross Boylan lme4 versions Mar 11, 2013 Ross Boylan lme4 versions Mar 11, 2013 Ben Bolker lme4 versions Mar 11, 2013

mixed effects model - log likelihood test

1 msg
Thomas Devlin mixed effects model - log likelihood test Mar 28, 2013

mixed model negative bionomial

3 msgs
Andrew McFadden (Andy) mixed model negative bionomial Mar 25, 2013 Ben Bolker mixed model negative bionomial Mar 27, 2013 Philippi, Tom mixed model negative bionomial Mar 29, 2013

new "Generalized Linear Mixed Models" book - #2

1 msg
Carl Von Ende new "Generalized Linear Mixed Models" book - #2 Mar 2, 2013

optimizers for mixed models

8 msgs
Ross Boylan optimizers for mixed models Mar 13, 2013 Ben Bolker optimizers for mixed models Mar 14, 2013 Douglas Bates optimizers for mixed models Mar 14, 2013 Ross Boylan optimizers for mixed models Mar 14, 2013 Ross Boylan optimizers for mixed models Mar 14, 2013 Ben Bolker optimizers for mixed models Mar 16, 2013 Pantelis Hadjipantelis optimizers for mixed models Mar 16, 2013 Ben Bolker optimizers for mixed models Mar 21, 2013

optimplus? (was Re: optimizers for mixed models)

2 msgs
Ross Boylan optimplus? (was Re: optimizers for mixed models) Mar 14, 2013 Ben Bolker optimplus? (was Re: optimizers for mixed models) Mar 14, 2013

partially crossed model

2 msgs
Alexej Siren partially crossed model Mar 13, 2013 Ben Bolker partially crossed model Mar 14, 2013

predictions for MCMCglmm

8 msgs
Antonio P. Ramos predictions for MCMCglmm Mar 18, 2013 Jarrod Hadfield predictions for MCMCglmm Mar 19, 2013 Antonio P. Ramos predictions for MCMCglmm Mar 19, 2013 Antonio P. Ramos predictions for MCMCglmm Mar 19, 2013 Joshua Wiley predictions for MCMCglmm Mar 19, 2013 Jarrod Hadfield predictions for MCMCglmm Mar 22, 2013 Antonio P. Ramos predictions for MCMCglmm Mar 22, 2013 Jarrod Hadfield predictions for MCMCglmm Mar 22, 2013

profile

2 msgs
KAYIS Seyit Ali profile Mar 22, 2013 Ben Bolker profile Mar 22, 2013

random effects with covariance matrix depending on a group characteristic

1 msg
Gabriel Baud-Bovy random effects with covariance matrix depending on a group characteristic Mar 27, 2013

semicontinuous variables: what likelihoods are available?

5 msgs
Aurelie Cosandey Godin semicontinuous variables: what likelihoods are available? Mar 18, 2013 Ben Bolker semicontinuous variables: what likelihoods are available? Mar 18, 2013 Aurelie Cosandey Godin semicontinuous variables: what likelihoods are available? Mar 18, 2013 George Wang semicontinuous variables: what likelihoods are available? Mar 18, 2013 Aurelie Cosandey Godin semicontinuous variables: what likelihoods are available? Mar 19, 2013

spatial/temporal correlation in gamm with binomial data

1 msg
Filipe Carvalho spatial/temporal correlation in gamm with binomial data Mar 13, 2013

syntax for partially crossed model

1 msg
Alexej Siren syntax for partially crossed model Mar 8, 2013

updated sourceforge repository

1 msg
Ben Bolker updated sourceforge repository Mar 2, 2013

variance of fixed effects

1 msg
Iasonas Lamprianou variance of fixed effects Mar 28, 2013