Nothing
## ----echo=FALSE---------------------------------------------------------------------------------------------
options(width=110)
## -----------------------------------------------------------------------------------------------------------
library(buildmer)
head(vowels)
## -----------------------------------------------------------------------------------------------------------
f <- f1 ~ vowel*timepoint*following * neighborhood*information*stress +
(vowel*timepoint*following * neighborhood+information+stress | participant) +
(timepoint | word)
## -----------------------------------------------------------------------------------------------------------
f <- f1 ~ vowel*timepoint*following +
(vowel*timepoint*following | participant) +
(timepoint | word)
## ----eval=FALSE---------------------------------------------------------------------------------------------
# library(lme4)
# m <- buildmer(f,data=vowels,buildmerControl=buildmerControl(direction='order',
# args=list(control=lmerControl(optimizer='bobyqa'))))
## ----echo=FALSE---------------------------------------------------------------------------------------------
cat('Determining predictor order
Fitting via lm: f1 ~ 1
Currently evaluating LRT for: following, timepoint, vowel
Fitting via lm: f1 ~ 1 + following
Fitting via lm: f1 ~ 1 + timepoint
Fitting via lm: f1 ~ 1 + vowel
Updating formula: f1 ~ 1 + vowel
Currently evaluating LRT for: following, timepoint
Fitting via lm: f1 ~ 1 + vowel + following
Fitting via lm: f1 ~ 1 + vowel + timepoint
Updating formula: f1 ~ 1 + vowel + timepoint
Currently evaluating LRT for: following, vowel:timepoint
Fitting via lm: f1 ~ 1 + vowel + timepoint + following
Fitting via lm: f1 ~ 1 + vowel + timepoint + vowel:timepoint
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint
Currently evaluating LRT for: following
Fitting via lm: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following
Currently evaluating LRT for: timepoint:following, vowel:following
Fitting via lm: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following
Fitting via lm: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + vowel:following
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following
Currently evaluating LRT for: vowel:following
Fitting via lm: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following
Currently evaluating LRT for: vowel:timepoint:following
Fitting via lm: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following
Fitting via gam, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following
Currently evaluating LRT for: 1 | participant, 1 | word
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 | participant)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 | word)
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following + (1 | participant)
Currently evaluating LRT for: following | participant, timepoint | participant, vowel |
participant, 1 | word
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + following |
participant)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint |
participant)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + vowel | participant)
boundary (singular) fit: see ?isSingular
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 | participant) + (1 |
word)
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following + (1 | participant) + (1 | word)
Currently evaluating LRT for: following | participant, timepoint | participant, vowel |
participant, timepoint | word
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + following |
participant) + (1 | word)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint |
participant) + (1 | word)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + vowel | participant)
+ (1 | word)
boundary (singular) fit: see ?isSingular
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 | participant) + (1 +
timepoint | word)
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following + (1 | participant) + (1 + timepoint | word)
Currently evaluating LRT for: following | participant, timepoint | participant, vowel |
participant
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + following |
participant) + (1 + timepoint | word)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint |
participant) + (1 + timepoint | word)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + vowel | participant)
+ (1 + timepoint | word)
boundary (singular) fit: see ?isSingular
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following + (1 + timepoint | participant) + (1 + timepoint |
word)
Currently evaluating LRT for: following | participant, vowel | participant
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint + following
| participant) + (1 + timepoint | word)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint + vowel |
participant) + (1 + timepoint | word)
boundary (singular) fit: see ?isSingular
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following + (1 + timepoint + following | participant) + (1 +
timepoint | word)
Currently evaluating LRT for: timepoint:following | participant, vowel | participant
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint + following
+ timepoint:following | participant) + (1 + timepoint | word)
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint + following
+ vowel | participant) + (1 + timepoint | word)
boundary (singular) fit: see ?isSingular
Updating formula: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following + timepoint:following +
vowel:following + vowel:timepoint:following + (1 + timepoint + following + timepoint:following
| participant) + (1 + timepoint | word)
Currently evaluating LRT for: vowel | participant
Fitting via lmer, with REML: f1 ~ 1 + vowel + timepoint + vowel:timepoint + following +
timepoint:following + vowel:following + vowel:timepoint:following + (1 + timepoint + following
+ timepoint:following + vowel | participant) + (1 + timepoint | word)
boundary (singular) fit: see ?isSingular
Ending the ordering procedure due to having reached the maximal feasible model - all higher models
failed to converge. The types of convergence failure are: Singular fit
Finalizing by converting the model to lmerTest')
## ----include=F----------------------------------------------------------------------------------------------
library(lme4)
#hack for consistency with actual output without actually fitting the model every time I change something in the vignette
m <- buildmer:::mkBuildmer(model=list(formula=(function () as.formula('f1 ~ following + vowel + timepoint + vowel:timepoint + following:timepoint + following:vowel + following:vowel:timepoint + (1 + timepoint + following + timepoint:following | participant) + (1 + timepoint | word)',.GlobalEnv))()))
## -----------------------------------------------------------------------------------------------------------
(f <- formula(m@model))
## ----eval=FALSE---------------------------------------------------------------------------------------------
# m <- buildmer(f,data=vowels,buildmerControl=list(direction='backward',
# args=list(control=lmerControl(optimizer='bobyqa'))))
## ----echo=FALSE---------------------------------------------------------------------------------------------
cat('Fitting ML and REML reference models
Fitting via lmer, with REML: f1 ~ following + vowel + timepoint + vowel:timepoint +
following:timepoint + following:vowel + following:vowel:timepoint + (1 + timepoint + following
+ timepoint:following | participant) + (1 + timepoint | word)
Fitting via lmer, with REML: f1 ~ following + vowel + timepoint + vowel:timepoint +
following:timepoint + following:vowel + following:vowel:timepoint + (1 + timepoint + following
+ timepoint:following | participant) + (1 + timepoint | word)
Testing terms
Fitting via lmer, with ML: f1 ~ 1 + following + vowel + timepoint + vowel:timepoint +
following:timepoint + following:vowel + (1 + timepoint + following + timepoint:following |
participant) + (1 + timepoint | word)
Fitting via lmer, with REML: f1 ~ 1 + following + vowel + timepoint + vowel:timepoint +
following:timepoint + following:vowel + following:vowel:timepoint + (1 + timepoint + following
| participant) + (1 + timepoint | word)
Fitting via lmer, with REML: f1 ~ 1 + following + vowel + timepoint + vowel:timepoint +
following:timepoint + following:vowel + following:vowel:timepoint + (1 + timepoint + following
+ timepoint:following | participant) + (1 | word)
grouping term block Iteration LRT
1 <NA> 1 NA NA 1 1 NA
2 <NA> following NA NA following 1 NA
3 <NA> vowel NA NA vowel 1 NA
4 <NA> timepoint NA NA timepoint 1 NA
5 <NA> vowel:timepoint NA NA vowel:timepoint 1 NA
6 <NA> following:timepoint NA NA following:timepoint 1 NA
7 <NA> following:vowel NA NA following:vowel 1 NA
8 <NA> following:vowel:timepoint NA NA following:vowel:timepoint 1 3.609316e-30
9 participant 1 NA participant 1 1 NA
10 participant timepoint NA participant timepoint 1 NA
11 participant following NA participant following 1 NA
12 participant timepoint:following NA participant timepoint:following 1 1.013211e-10
13 word 1 NA word 1 1 NA
14 word timepoint NA word timepoint 1 2.198802e-153
All terms are significant
Finalizing by converting the model to lmerTest')
## ----echo=FALSE,message=FALSE-------------------------------------------------------------------------------
f2 <- as.formula('f1 ~ following + vowel + timepoint + vowel:timepoint + following:timepoint + (1 + timepoint | word) + (1 + timepoint + following + timepoint:following | participant)',.GlobalEnv)
m <- buildmer(f2,vowels,buildmerControl=list(direction=NULL,args=list(control=lmerControl(optimizer='bobyqa'))))
## -----------------------------------------------------------------------------------------------------------
summary(m)
## -----------------------------------------------------------------------------------------------------------
tabulate.formula(f)
## -----------------------------------------------------------------------------------------------------------
vowels <- cbind(vowels,model.matrix(~vowel,vowels))
## -----------------------------------------------------------------------------------------------------------
form <- diag(f1 ~ (vowel1+vowel2+vowel3+vowel4)*timepoint*following +
((vowel1+vowel2+vowel3+vowel4)*timepoint*following | participant) +
(timepoint | word))
terms <- tabulate.formula(form,group='vowel[^:]')
## ----eval=FALSE---------------------------------------------------------------------------------------------
# m <- buildmer(terms,data=vowels,buildmerControl=buildmerControl(dep='f1',
# args=list(control=lmerControl(optimizer='bobyqa'))))
# ## (output not shown)
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