[R] Plotting log transformed predicted values from lme

[Michael Dewey]

On 10/08/2017 13:48, Alina Vodonos Zilberg wrote:
> Thank you Michael,
> Curves for each level of the factor sounds  very interesting,
> Do you have a suggestion how to plot them?
>

Make your newdata matrix N times longer where your factor has N levels 
and replicate your log(x) down one column and repeat each factor level 
118 times.

Then plot the predicted values using lines separately for each subset of 
data corresponding to a level of your factor (choosing a different line 
type)

> Thank you!
> Alina
>
> *Alina Vodonos Zilberg*
>
>
>
>
> On Thu, Aug 10, 2017 at 7:39 AM, Michael Dewey <lists at dewey.myzen.co.uk
> <mailto:lists at dewey.myzen.co.uk>> wrote:
>
>     Dear Alina
>
>     If I understand you correctly you cannot just have a single
>     predicted curve but one for each level of your factor.
>
>
>     On 09/08/2017 16:24, Alina Vodonos Zilberg wrote:
>
>         Hi,
>
>         I am performing meta-regression using linear mixed-effect model
>         with the
>         lme() function  that has two fixed effect variables;one as a log
>         transformed variable (x)  and one as factor (y) variable, and
>         two nested
>         random intercept terms.
>
>         I want to save the predicted values from that model and show the
>         log curve
>         in a plot ; predicted~log(x)
>
>         mod<-lme(B~log(x)+as.factor(y), random=~1|cohort/Study,
>         weights=varFixed(~I(SE^2)), na.action=na.omit, data=subset(meta),
>                   control = lmeControl(sigma = 1, apVar = FALSE))
>         summary(mod)
>
>         newdat <- data.frame(x=seq(min(meta$x), max(meta$x),,118))  # I
>         have 118
>         observations. #How do I add the factor variable to my newdat?
>         newdat$pred <- predict(mod, newdat,level = 0,type="response")
>
>         plot(B ~ x, data=meta)
>         lines(B ~ x, data=newdat)
>
>         Can you please assist me ?
>
>         Thank you!
>
>         Alina
>
>                 [[alternative HTML version deleted]]
>
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Michael
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