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List:       r-sig-mixed-models
Subject:    [R-sig-ME] questions on MCMCglmm
From:       "=?gb18030?B?WUE=?=" <xinxi813 () 126 ! com>
Date:       2020-05-25 9:43:42
Message-ID: tencent_6108C57938AF2DDD8036849507C60B312405 () qq ! com
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Dear list,


I am using MCMCglmm package in R for my multilevel multinomial logistic regression \
model. I have a three category level1 unordered multinomial outcome 'nomial', which \
was coded as 0,1,2, a level1 continuous predictor 'IT1', and a level2 continuous \
predictor 'age', the ID variable is 'ID'. My questions are:


1. The regression coeffecient of IT1 is 0.120220, but which category of 'nomial' does \
the coefficient concern? how to interpret it? 

2.  Although I have got the model run properly, I dont quite understand  what the \
'rcov = ~us(trait):units' do in the model, only that the model  cant run without this \
part. I have read the coursenote on the website  several times, but still have not \
figured it out. 

3. What  does 'us','idh', 'ihv' stands for (the author uses them to refer to  \
covariance structure, are they initials of some terminologies)? 

4. I tried to make predictions with IT1=3 and age=23, I got error suggesting "object \
'nomial' not found", but 'nomial' is exactly what I am trying to predict. How to \
understand the logic behind this?



 So the model fit and prediction are as below:


&gt; m10=MCMCglmm(as.factor(nomial)~IT1+age,random=~ID,data=dat,rcov = \
~us(trait):units,family='categorical')  &gt; summary(m10)

&nbsp;Iterations = 3001:12991
&nbsp;Thinning interval&nbsp; = 10
&nbsp;Sample size&nbsp; = 1000 

&nbsp;DIC: 358.2906 

&nbsp;G-structure:&nbsp; ~ID

&nbsp;&nbsp; post.mean l-95% CI u-95% CI eff.samp
ID&nbsp;&nbsp; &nbsp; 28.75&nbsp; &nbsp; 18.64&nbsp; &nbsp; 38.81&nbsp; &nbsp; 767.4

&nbsp;R-structure:&nbsp; ~us(trait):units

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n \
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; \
&nbsp; post.mean l-95% CI u-95% CI eff.samp traitnomial.1:traitnomial.1.units &nbsp; \
0.04237&nbsp; 0.01597&nbsp; 0.13210&nbsp; &nbsp; 10.77 \
traitnomial.2:traitnomial.1.units&nbsp; -0.21941 -0.39132 -0.07699&nbsp;&nbsp; &nbsp; \
6.04 traitnomial.1:traitnomial.2.units&nbsp; -0.21941 -0.39132 -0.07699&nbsp;&nbsp; \
&nbsp; 6.04 traitnomial.2:traitnomial.2.units &nbsp; 1.69265&nbsp; 1.21517&nbsp; \
2.21141&nbsp; &nbsp; 23.81

&nbsp;Location effects: as.factor(nomial) ~ IT1 + age 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; post.mean &nbsp; \
l-95% CI &nbsp; u-95% CI eff.samp pMCMC&nbsp; &nbsp; (Intercept)&nbsp; 34.541008 \
-15.319976&nbsp; 78.613352&nbsp; 931.637 0.120&nbsp; &nbsp; \
IT1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; 0.120220 &nbsp; 0.009121 \
&nbsp; 0.343275&nbsp; &nbsp; 6.204 0.004 ** \
age&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; -1.404272&nbsp; -3.267662 &nbsp; \
                0.659993&nbsp; 931.605 0.130&nbsp; &nbsp;
---
Signif. codes:&nbsp; 0 ¡®***¡¯ 0.001 ¡®**¡¯ 0.01 ¡®*¡¯ 0.05 ¡®.¡¯ 0.1 ¡® ¡¯ 1


&gt; predict.MCMCglmm(m10,data.frame(IT1=3,age=23),type='response')
Error in eval(inp, data, env) : object 'nomial' not found


Thank you very much.


Best regards,


YA
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