[R] Predicting complicated GAMMs on response scale

[William Paterson]

Creation of Animal category in p.d solved all problems. Plots fine now. The
smallest hurdles are often the hardest to get over.


Gavin Simpson wrote:
> 
> On Mon, 2009-05-18 at 11:48 -0700, William Paterson wrote:
>> Hi,
>> 
>> I am using GAMMs to show a relationship of temperature differential over
>> time with a model that looks like this:-
>> 
>> gamm(Diff~s(DaysPT)+AirToC,method="REML") 
>> 
>> where DaysPT is time in days since injury and Diff is repeat measures of
>> temperature differentials with regards to injury sites compared to
>> non-injured sites in individuals over the course of 0-24 days. I use the
>> following code to plot this model on the response scale with 95% CIs
>> which
>> works fine:-
>> 
>> g.m<-gamm(Diff~s(DaysPT)+AirToC,method="REML")
>> p.d<-data.frame(DaysPT=seq(min(DaysPT),max(DaysPT)))
>> p.d$AirToC<-(6.7)
>> b<-predict.gam(g.m$gam,p.d,se=TRUE)
>> range<-c(min(b$fit-2*b$se.fit),max(b$fit+2*b$se.fit))
>> plot(p.d$DaysPT,b$fit,ylim=c(-4,12),xlab="Days post-tagging",ylab="dTmax
>> (ºC)",type="l",lab=c(24,4,12),las=1,cex.lab=1.5, cex.axis=1,lwd=2)
>> lines(p.d$DaysPT,b$fit+b$se.fit*1.96,lty=2,lwd=1.5)
>> lines(p.d$DaysPT,b$fit-b$se.fit*1.96,lty=2,lwd=1.5)
>> points(DaysPT,Diff)
>> 
>> 
>> However, when I add a correlation structure and/or a variance structure
>> so
>> that the model may look like:- 
>> 
>> 
>> gamm(Diff~s(DaysPT3)+AirToC,correlation=corCAR1(form=~DaysPT|
>> Animal),weights=varPower(form=~DaysPT),method="REML")
>> 
>> 
>> I get this message at the point of inputting the line
>> "b<-predict.gam(g.m$gam,p.d,se=TRUE)"
> 
> Note that p.d doesn't contain Animal. Not sure this is the problem, but
> I would have thought you'd need to supply new values of Animal for the
> data you wish to predict for in order to get the CAR(1) errors correct.
> Is it possible that the model is finding another Animal variable in the
> global environment?
> 
> I have predicted from several thousand GAMMs containing correlation
> structures similar to the way you do above so this does work in general.
> If the above change to p.d doesn't work, you'll probably need to speak
> to Simon Wood to take this further.
> 
> Is mgcv up-to-date? I am using 1.5-5 that was released in the last week
> or so.
> 
> For example, this dummy example runs without error for me and is similar
> to your model
> 
> y1 <- arima.sim(list(order = c(1,0,0), ar = 0.5), n = 200, sd = 1)
> y2 <- arima.sim(list(order = c(1,0,0), ar = 0.8), n = 200, sd = 3)
> x1 <- rnorm(200)
> x2 <- rnorm(200)
> ind <- rep(1:2, each = 200)
> d <- data.frame(Y = c(y1,y2), X = c(x1,x2), ind = ind, time = rep(1:200,
> times = 2))
> require(mgcv)
> mod <- gamm(Y ~ s(X), data = d, corr = corCAR1(form = ~ time | ind),
>             weights = varPower(form = ~ time))
> p.d <- data.frame(X = rep(seq(min(d$X), max(d$X), len = 20), 2),
>                   ind = rep(1:2, each = 20),
>                   time = rep(1:20, times = 2))
> pred <- predict(mod$gam, newdata = p.d, se = TRUE)
> 
> Does this work for you? If not, the above would be a reproducible
> example (as asked for in the posting guide) and might help Simon track
> down the problem if you are running an up-to-date mgcv.
> 
> HTH
> 
> G
> 
>> 
>> 
>> Error in model.frame(formula, rownames, variables, varnames, extras,
>> extranames,  : 
>>         variable lengths differ (found for 'DaysPT')
>> In addition: Warning messages:
>> 1: not all required variables have been supplied in  newdata!
>>  in: predict.gam(g.m$gam, p.d, se = TRUE) 
>> 2: 'newdata' had 25 rows but variable(s) found have 248 rows 
>> 
>> 
>> Is it possible to predict a more complicated model like this on the
>> response
>> scale? How can I incorporate a correlation structure and variance
>> structure
>> in a dataframe when using the predict function for GAMMs?
>> 
>> Any help would be greatly appreciated.
>> 
>> William Paterson
>> 
>> 
>> 
>> 
> -- 
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>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
>  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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> 
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
> 
> 

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