[R-sig-ME] multinomial model with MCMCglmm
Cate Ferrari
caterinaww at gmail.com
Sat Dec 16 14:31:22 CET 2017
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
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