[R-sig-ME] multinomial model with MCMCglmm

[Cate Ferrari]

Dear members of the list
 I am writing you about a multinomial model I am currently trying to run
using  MCMCglmm.
 My data are about time budget behaviors, so I have different behaviors on
different individuals collected during a scan. In my model I added some
fxed effects as age, season, area, and Id of the animal as random term.
The model run but when I have the summary I see that instead of having the
6 behaviors that I have in the dataset, I have 5; so I guess the first (in
alphabetic order) is retained as reference. But I don't want this to
happen, where am I wrong?

Also I would need to back transform the estimates for each behavior given
in the summary , but I don't know how to do it.

Can anyone give me some advices?
Thanks a lot in advance!
Caterina


Behaviors in the model:
Agonistic, affiliative, others, foraging, looking, moving


Model

MarmotTB3.mcmc<-MCMCglmm(ATTIVITA2~trait-1+trait:ETA+trait:ZONA+trait:
PERIODO,random=~us(trait)

                         :MARMOTTA,rcov = ~ us(trait):units, family=
"categorical",

                         prior=prior, data=alta.dat,verbose=TRUE,nitt=130000,
thin=100, burnin=30000)


Iterations = 30001:129901

Thinning interval = 100

Number of chains = 1

Sample size per chain = 1000


1. Empirical mean and standard deviation for each variable,

plus standard error of the mean:



  Mean     SD Naive SE Time-series SE

traitATTIVITA2.AGONISTICO           -5.1953780 0.9464 0.029928
0.23713

traitATTIVITA2.ALTRO                -6.2860308 0.8939 0.028268
0.19988

traitATTIVITA2.FORAGING              0.9998039 0.3022 0.009555
0.03373

traitATTIVITA2.LOOKING               0.7450175 0.3297 0.010425
0.03146

traitATTIVITA2.MOVING               -0.9486360 0.3775 0.011938
0.04533


traitATTIVITA2.AGONISTICO:ETA1       1.4235583 1.0277 0.032499
0.27793

traitATTIVITA2.ALTRO:ETA1            0.3434346 0.8574 0.027113
0.21602

traitATTIVITA2.FORAGING:ETA1        -0.2241162 0.2880 0.009107
0.02506

traitATTIVITA2.LOOKING :ETA1        -0.6997858 0.3096 0.009792
0.02601

traitATTIVITA2.MOVING:ETA1          -0.7655606 0.3917 0.012388
0.05077

traitATTIVITA2.AGONISTICO:ETA2+      3.9285262 0.9196 0.029080
0.24008

traitATTIVITA2.ALTRO:ETA2+           1.8530251 0.9014 0.028504
0.23861

traitATTIVITA2.FORAGING:ETA2+        0.4938721 0.2772 0.008766
0.02789

traitATTIVITA2.LOOKING :ETA2+        0.3984561 0.3102 0.009808
0.02788

traitATTIVITA2.MOVING:ETA2+          0.5437561 0.3356 0.010612
0.03101

traitATTIVITA2.AGONISTICO:ZONABASSA -0.7366481 0.6147 0.019437
0.11113

traitATTIVITA2.ALTRO:ZONABASSA       1.5733998 0.5394 0.017056
0.12034

traitATTIVITA2.FORAGING:ZONABASSA    0.1929651 0.2218 0.007013
0.01844

traitATTIVITA2.LOOKING :ZONABASSA    0.2431249 0.2522 0.007975
0.02239

traitATTIVITA2.MOVING:ZONABASSA      0.2652439 0.3282 0.010380
0.05740

traitATTIVITA2.AGONISTICO:PERIODOB   0.8002443 0.3524 0.011143
0.04702

traitATTIVITA2.ALTRO:PERIODOB        1.4053954 0.5840 0.018467
0.14606

traitATTIVITA2.FORAGING:PERIODOB     0.4976160 0.1958 0.006192
0.03157

traitATTIVITA2.LOOKING :PERIODOB     0.6249756 0.2100 0.006640
0.02844

traitATTIVITA2.MOVING:PERIODOB       0.3089387 0.2710 0.008570
0.04932

traitATTIVITA2.AGONISTICO:PERIODOC   0.7986439 0.4134 0.013073
0.06651

traitATTIVITA2.ALTRO:PERIODOC        1.2147869 0.7173 0.022683
0.20310

traitATTIVITA2.FORAGING:PERIODOC     1.5504290 0.1906 0.006029
0.02575

traitATTIVITA2.LOOKING :PERIODOC     0.9520809 0.2049 0.006478
0.02630

traitATTIVITA2.MOVING:PERIODOC      -0.0004336 0.2828 0.008943
0.05482

	[[alternative HTML version deleted]]