Problems using Anova functions 'type = 2' or 'type = 3' from car package with lme

Hi Mario,


Glad to hear you found the solution.  Unfortunately I can not validate it,
since I am not a stats expert. I was  thinking that maybe the emmeans
package could help you for the post-hoc contrasts, and the interaction
analysis:

https://cran.rstudio.com/web/packages/emmeans/vignettes/interactions.html


P.D. The statistician from my dept.  encourages us to work always
with ANOVA type II.  Maybe further information about it might be found not
here,  but in another list, such as stack overflow.


Best,

Julian Gaviria
Neurology and Imaging of cognition lab (Labnic)
University of Geneva. Campus Biotech.
9 Chemin des Mines, 1202 Geneva, CH
Tel: +41 22 379 0380
Email: Julian.GaviriaLopez at unige.ch
------------------------------
*From:* R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on
behalf of Mario Garrido <gaadio at post.bgu.ac.il>
*Sent:* Monday, October 28, 2019 11:18:44 AM
*To:* r-sig-mixed-models at r-project.org
*Subject:* Re: [R-sig-ME] Problems using Anova functions 'type = 2' or
'type = 3' from car package with lme

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 at post.bgu.ac.il>)
escribi?:

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

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