[R-sig-ME] Problems using Anova functions 'type = 2' or 'type = 3' from car package with lme

[Mario Garrido]

Hi,
I think I have found the solution using:
anova.lme(model,type = "sequential") # same results as anova(model); it
seems logical, since Type I is sequential
anova.lme(model,type = "marginal") # as far as I know, sorry of Im wrong,
Type III is also called marginal

Cheers!

El lun., 28 oct. 2019 a las 10:33, Mario Garrido (<gaadio using post.bgu.ac.il>)
escribió:

> Hello,
> I use lme to create a linear mixed effects model with three fixed factors
> (Treatment, species and Period) and one random factor (individual identity,
> ExpID).
> After creating the model, I tried to apply Anova from car package to
> compute results with both Type II and III Sum of Squares, but I get the
> error stated below:
> I have UNBALANCED data, more data from sp1 than for the others
> These are the data types.
>
> > str(Data)
> 'data.frame':   496 obs. of  27 variables:
>  $ Trtmnt2     : Factor w/ 2 levels "Control","Treated": 2 2 2 2 2 2 2 2 1
> 1 ...
>  $ ExpID       : Factor w/ 62 levels "EA1","EA10","EA11",..: 1 1 1 1 1 1 1
> 1 10 10 ...
>  $ sp          : Factor w/ 3 levels "sp1","sp2","sp3": 2 2 2 2 2 2 2 2 2 2
> ...
>  $ Period      : Factor w/ 5 levels "Before","earlypeak",..: 1 5 2 4 3 5 4
> 3 1 2 ...
>  $ StdzDiff    : num  -51.1 -53.2 -49 22.9 ...
>
> Here is the code to generate the model
> > library(car)
> > options(contrasts = c("contr.sum", "contr.poly"))
>
> > model<- lme(StdzDiff ~ Trtmnt2*sp*Period, data = Data, random = ~
> 1|factor(ExpID))
> > Anova(model, type=2)  #with type = 3, I have the same problems
> Error in I.p[subs.relatives, , drop = FALSE] :
>   subscript out of bounds
>
> I have no problems with 'default' anova. But, I get the same error
> working with the following code
> model<- lme(StdzDiff ~ Trtmnt2*sp*Period, data =
> DataFreqDark_StdzDiff_peakAll, random = ~
> 1|factor(ExpID),contrasts=list(Trtmnt2=contr.sum, sp=contr.sum,
> Period=contr.sum))
>
> My questions:
> 1) What is my error?
> 2) If Anova from car cannot deal with lme, how can I apply Type III to my
> model?
> 3) To confirm, if I define nothing, anova with lme, is type I by default?
>
> Thanks!
>


-- 
Mario Garrido Escudero, PhD
Dr. Hadas Hawlena Lab
Mitrani Department of Desert Ecology
Jacob Blaustein Institutes for Desert Research
Ben-Gurion University of the Negev
Midreshet Ben-Gurion 84990 ISRAEL

gaiarrido using gmail.com; gaadio using post.bgu.ac.il
phone: (+972) 08-659-6854

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