[R-sig-ME] Plotting predicted values mcmcglmm

[romunov]

Can you share your data (dput())?

Cheers,
Roman

On Mon, Nov 23, 2015 at 11:58 PM, Lotte van Boheemen <
lotte.van.boheemen at monash.edu> wrote:

> Hi,
>
> My goal is to plot the predicted values of the mcmcglmm model with
> variables: NoFeeds ~  offset(ObsDuration) + Month + AnnualInsects +
> TQc_Combined + NoOffspring + NoH*Status + Status*WatchType ,
> random=~idh(Status):BirdID + NestID:NestWatchID + Obs
>
> Predicted values are calculated as:
> mpred0 <- predict(model,interval="confidence")
> colnames(mpred0) <- paste("mpred0",c("fit","lwr","upr"),sep=".")
> mpred1 <- predict(model,interval="confidence",marginal=~ BirdID + MateID +
> NestID:NestWatchID + Year:Month + Obs)
> colnames(mpred1) <- paste("mpred1",c("fit","lwr","upr"),sep=".")
> dataf <- data.frame(data_UnID,mpred0,mpred1)
>
> g0 <- ggplot(dataf,aes(x=NoH,y=FeedsPerHour))+
>   stat_sum(aes(size=factor(..n..)),alpha=0.5)+
>   facet_grid(~Status+WatchType)+
>   scale_size_discrete(name="n",range=c(2,5))
> g0 + geom_line(aes(x=as.numeric(NoH),y=mpred0.fit),colour="red")+
>   geom_ribbon(aes(x=as.numeric(NoH),y=mpred0.fit,
>                   ymin=mpred0.lwr,ymax=mpred0.upr),fill="red",
>               alpha=0.3)
>
>
> However, the plots this results in show 'jagged' predictions for the model,
> e.g. it seems like at one particular value of NoH, the model predicts 2
> different values, which is not the case (figure attached).
>
> Lotte Anna van Boheemen
> PhD Research Candidate
> School of Biological Sciences
> Monash University
>
>    -
>
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>



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