[prev in list] [next in list] [prev in thread] [next in thread]
List: r-sig-mixed-models
Subject: Re: [R-sig-ME] making predictions with MCMCglmm
From: "=?utf-8?B?WUE=?=" <xinxi813 () 126 ! com>
Date: 2020-05-30 1:54:21
Message-ID: tencent_0C3B982AC4872050E7C33CA4742F5A36D607 () qq ! com
[Download RAW message or body]
Hi guys,
Thank you very much for the response.
Sree:
MathAch is different from mathach, these are two different variables. The continuous \
'MathAch' in the orignial dataset was used for the linear model m1, whereas the \
multinomial categorical 'mathach' I intentionally created was used for the subsequent \
multinomial logistic regression m3. Any other ideas?
Tom:
I tried add both value of Sex and created a value of 0 for the outcome MathAch in m1, \
I still got errors. It looks like MCMCglmm prediction has a different logic than the \
glm prediction? Please see the codes and errors blow:
> predict(m1,data.frame(Sex='Male',SES=c(0.3,-0.8),MathAch=0),type='response')
Error in buildZ(rmodel.terms[r], data = data, nginverse = names(ginverse)) :
object School not found
> predict(m1,data.frame(Sex=c('Male','Female'),SES=c(0.3,-0.8),MathAch=0,School='1288'),type='response')
Error in predict.MCMCglmm(m1, data.frame(Sex = c("Male", "Female"), SES = \
c(0.3, : model for newdata has fixed effects not present in original \
model
> predict(m1,data.frame(Sex=c('Male'),SES=c(0.3,-0.8),MathAch=0,School='1288'),type='response')
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
> predict(m1,data.frame(Sex=c('Male','Female'),SES=c(0.3,-0.8),School='1288'),type='response')
Error in FUN(X[[i]], ...) : object 'MathAch' not found
Cheers,
YA
------------------ Original ------------------
From: "sree datta"<sreedta8@gmail.com>;
Date: Sat, May 30, 2020 00:21 AM
To: "Tom Houslay"<houslay@gmail.com>;
Cc: "r-sig-mixed-models"<r-sig-mixed-models@r-project.org>;"xinxi813"<xinxi813@126.com>;
Subject: Re: [R-sig-ME] making predictions with MCMCglmm
Dear YA
I noticed the following in your code:
> &gt; dat$mathach[dat$MathAch&gt;=15]=2
> &gt; dat$mathach=as.factor(dat$mathach
the dat$MathAch variable in line 1 will be processed as a variable different from \
dat$mathach on line 2 - Is this what you planned for? Since R is case-sensitive, \
this can create the problems you are seeing - The error "object mathach \
not found" is likely a direct result of that.
Sree
On Fri, May 29, 2020 at 7:39 AM Tom Houslay <houslay@gmail.com> wrote:
Hi YA,
In your new data frame you just need to add a column for the response
variable as well (set it to 0 or similar). You may have additional issues
but that should get you over that first hurdle.
Speaking of which, I've found when predicting from MCMCglmm that it doesn't
like it when you only have a single value for any of your fixed effects --
so you may want to expand your prediction data frames, for example for m1
you could predict on those 2 SES values for both sexes (even if you are
only interested in males, you can simply subset the predictions afterwards).
Cheers
Tom
On Fri, 29 May 2020 at 11:01, <r-sig-mixed-models-request@r-project.org>
wrote:
>
>
>
> Message: 1
> Date: Fri, 29 May 2020 17:25:16 +0800
> From: "YA" <xinxi813@126.com>
> To: "r-sig-mixed-models" <r-sig-mixed-models@r-project.org>
> Subject: [R-sig-ME] making predictions with MCMCglmm
> Message-ID: <tencent_5701AD3CAB070C10E27910A2F3481E517A06@qq.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear list,
>
>
> I am still working on the MCMCglmm predictions. I realized that I didnt
provide a reproducible code in my last email, which makes people here lack
of clues for helping me. I am providing a reproducible example this time
using datasets from the nlme package, so if you have any experience on this
package, please give me some advice on programming the predictions. As you
can see below, same error occured on different models, I guess something is
wrong with my code. Thank you very much.
>
>
> &gt; library(MCMCglmm)
> &gt; library(nlme)
> &gt; data(MathAchieve,package='nlme')
> &gt; data(MathAchSchool,package='nlme')
> &gt; dat=merge(MathAchSchool,MathAchieve,by='School')
> &gt; dat$mathach[dat$MathAch<5]=0
> &gt; dat$mathach[dat$MathAch&gt;=5 &amp; dat$MathAch<15]=1
> &gt; dat$mathach[dat$MathAch&gt;=15]=2
> &gt; dat$mathach=as.factor(dat$mathach)
> &gt; str(dat)
>
>
> # prediction on a continous outcome 'MathAch'
>
> &gt; m1=MCMCglmm(MathAch~Sex+SES,random=~School+SES,dat=dat,verbose=F)
> &gt; summary(m1)
> &gt; predict(m1,data.frame(Sex='Male',SES=c(0.3,-0.8)),type='response')
> Error in FUN(X[[i]], ...) : object 'MathAch' not found
>
>
> # prediction on a binary outcome 'Sex'
> &gt;
m2=MCMCglmm(Sex~SES,random=~School+SES,data=dat,family='categorical',verbose=F)
> &gt; summary(m2)
> &gt;
predict(m2,data.frame(SES=0.5,School='1224'),marginal=NULL,type='response')
> Error in FUN(X[[i]], ...) : object 'Sex' not found
>
>
>
> # prediction on a three category unordered multinomial outcome 'mathach'
>
> &gt;
m3=MCMCglmm(mathach~SES,random=~School+SES,data=dat,rcov=~us(trait):units,family='categorical',verbose=F)
> &gt; summary(m3)
> &gt;
predict(m3,data.frame(SES=0.5,School='1224'),marginal=NULL,type='response')
> Error in FUN(X[[i]], ...) : object 'mathach' not found
>
>
> Best regards,
>
>
> YA
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> R-sig-mixed-models mailing list
> R-sig-mixed-models@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
> ------------------------------
>
> End of R-sig-mixed-models Digest, Vol 161, Issue 44
> ***************************************************
[[alternative HTML version deleted]]
_______________________________________________
R-sig-mixed-models@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
[[alternative HTML version deleted]]
_______________________________________________
R-sig-mixed-models@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
[prev in list] [next in list] [prev in thread] [next in thread]
Configure |
About |
News |
Add a list |
Sponsored by KoreLogic