[R] [mgcv][gam] Odd error: Error in PredictMat(object$smooth[[k]], data) : , `by' variable must be same dimension as smooth arguments
Andrew Crane-Droesch
andrewcd at gmail.com
Thu Mar 21 22:14:31 CET 2013
Dear List,
I'm getting an error in mgcv, and I can't figure out where it comes
from. The setup is the following: I've got a fitted GAM object called
"MI", and a vector of "prediction data" (with default values for
predictors). I feed this into predict.gam(object, newdata = whatever)
via the following function:
makepred = function(varstochange,val){
for (i in 1:length(varstochange)){
if (varstochange[i] == "pot.trial"){j=1}
if (varstochange[i] == "year"){j=2}
if (varstochange[i] == "crop.legume"){j=3}
if (varstochange[i] == "crop.fruit"){j=4}
if (varstochange[i] == "feedstock"){j=5}
if (varstochange[i] == "BCAR.imp"){j=8}
if (varstochange[i] == "INAR.imp"){j=9}
if (varstochange[i] == "bcph.imp"){j=10}
if (varstochange[i] == "phi.imp"){j=11}
if (varstochange[i] == "htt.imp"){j=12}
if (varstochange[i] == "bc.prc.C.imp"){j=13}
if (varstochange[i] == "CEC.imp"){j=14}
if (varstochange[i] == "soc.imp"){j=15}
if (varstochange[i] == "sand.imp"){j=16}
if (varstochange[i] == "clay.imp"){j=17}
if (varstochange[i] == "abslat.imp"){j=18}
preddat[j] = val[i]
}
predict.gam(MI,newdata=preddat,se.fit=TRUE)
}
I then make predictions that look like this:
a = makepred(c("phi.imp","bcph.imp","year"),c(4.5,7.25,1))
b = makepred(c("phi.imp","bcph.imp","year"),c(5.5,7.25,1))
c = makepred(c("phi.imp","bcph.imp","year"),c(6.5,7.25,1))
d = makepred(c("phi.imp","bcph.imp","year"),c(7.5,7.25,1))
makepHplot(a,b,c,d,title="1st harvest, BC pH = 7.25")
where "makepHplot" is a different function that I made.
This worked for quite some time. Then I added some data to the model
and changed the specification slightly. Now I'm getting this error message:
1> a = makepred(c("bcph.imp","year"),c(7.5,1))
Error in PredictMat(object$smooth[[k]], data) :
`by' variable must be same dimension as smooth arguments
I never got this message with the old fitted model (and still don't).
What is happening? I can't figure out what about the new fitted model
is causing this problem. Typing "PredictMat" isn't helping me, nor is
google. The problem isn't that all of the variables aren't in the
prediction data.
Would appreciate any help here.
Thanks,
Andrew
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