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I have two dependent variable Prime Type (five levels), and Prime Relatedness (two levels), and one dependent variable; Reaction Time (RT). I have ran a linear mixed-effect model in R using the following formula for lme4 package:

data.mod1=lmer(RT~Related*PrimeType*(1|Subject)+(1|Item),mydata)

Then I ran a similar formula for nlme package

data.mod1.lme=lme(RT~Related*PrimeType, random=~1|Subject/Item,mydata)

Considering that these models are analyzing the same data set using linear mixed effect models, the t-test show different values! In fact, for one of the variables it shows a significant p-value in nlme model but not in lme4 package:

nlme.variable t=-1.98707 p-value=0.0470
lme4.variable t=-1.14    p-value=0.2917866* 

The p-value in lme4 is not calculated and sampMCMC is no longer available, I had to calculated using the following formula 2(1 - pt(abs(x), df)) --> 2*(1 - pt(abs(-1.14), 7))

My question is that why are the t-values differ between the two packages. Do I need to change or add something in R to have both models show the same t-values? Also, is my calculation of the p-value wrong? If yes, what is the correct way for it to be calculated it?

EDIT: nlme experts - what is the correct code for the above mentioned formula to add cross random effect?

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You haven't given a reproducible example, but:

library(lme4)
library(nlme)
library(pbkrtest)

fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
## see definition of KRSumFun below, taken from ?drop1.merMod:
## requires recent [development?] version of `lme4`:

packageVersion("lme4")  ## 1.1.2
drop1(fm1,test="user",sumFun=KRSumFun)

## Model: Reaction ~ Days + (Days | Subject)
## Method: Kenward-Roger via pbkrtest package
## 
## 
##        ndf ddf  Fstat    p.value F.scaling
## <none>                                    
## Days     1  17 45.853 3.2638e-06         1

fm2 <- lme(Reaction ~ Days , random = ~Days | Subject, sleepstudy)
anova(fm2)
##             numDF denDF   F-value p-value
##(Intercept)      1   161 1454.0766  <.0001
## Days            1   161   45.8534  <.0001

Note that this is a case (random-slopes model) where lme actually gets the wrong answer for the denominator degrees of freedom.

KRSumFun <- function(object, objectDrop, ...) {
       krnames <- c("ndf","ddf","Fstat","p.value","F.scaling")
       r <- if (missing(objectDrop)) {
           setNames(rep(NA,5),krnames)
       } else {
          krtest <- KRmodcomp(object,objectDrop)
          unlist(krtest$stats[krnames])
       }
       attr(r,"method") <- c("Kenward-Roger via pbkrtest package")
       r
    }
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  • $\begingroup$ library(lme4) # I updated it and it is on version'1.0.4' library(pbkrtest) mydata.mod1=lmer(RT~Related*PrimeType*(1|Item)+(1|Subject),mydata) drop1(mydata.mod1,test="user",sumFun=KRSumFun) # I recieved the following message "Error in match.arg(test) : 'arg' should be one of "none", "Chisq"" # @BenBolker what do you think the issue is? $\endgroup$ – ama Dec 23 '13 at 19:53
  • $\begingroup$ artax.karlin.mff.cuni.cz/r-help/library/afex/html/mixed.html $\endgroup$ – ama Dec 23 '13 at 19:59
  • $\begingroup$ # Also, I have tried the following the above post: mixed(mydata.mod1, mydata, type = 3, method = c("KR")) # and m1 <- mixed(RT~Related*PrimeType*(1|Item)+(1|Subject), data = mydata) # but it keeps telling me that "could not find function "mixed"" # am I missing the right package? $\endgroup$ – ama Dec 23 '13 at 19:59
  • $\begingroup$ mixed is from the afex package -- you need to install and load it. You need a more recent version of lme4 (are you running R < 3.0?); try install.packages("lme4",repos="http://lme4.r-forge.r-project.org/repos") (if you are running R >3.0 -- if not this will be more difficult) $\endgroup$ – Ben Bolker Dec 23 '13 at 20:58
  • $\begingroup$ You were right, I had to update R and re-install lme4. Both the mixed function from afex package and drop1 function worked well. Thank you! $\endgroup$ – ama Dec 29 '13 at 13:26
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I primarily use lme4, so you'll have to excuse me if this answer is incorrect. I believe you specified crossed-random effects in the lmer function call, but nested random effects in the lme function call. I'm not sure how to do crossed-random effects in lme, but perhaps this or this might yield some insight.

One other thing (unrelated), is that RTs usually possess a distribution with positive skew and could benefit from an inverse transformation. See my answer here for a little more info.

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  • $\begingroup$ I see, then I will look more into how the crossed-random effect is written in lme. @dmartin Since you use lme4, could you tell me how do you calculate the p-values? Also, what are the terms used in lme4 package to included nested random effects? I really appreciate it. $\endgroup$ – ama Dec 22 '13 at 21:19
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    $\begingroup$ 1) Lme4 doesn't give you p-values, because for unbalanced, multi-level data, denominator degrees of freedom are unknown. Most packages give an approximation. Douglas Bates (lme4 author) instead chooses not to. More information found here 2) Nested effects really depend on the structure of the data, so it's hard for me to see what you want to specify from the example. Here would be a good place to start $\endgroup$ – dmartin Dec 23 '13 at 16:54

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