predict.lm(...,type="terms") question
Hello,
John is right, there seems to be an error in predict.lm. It can be made
to work but if the model is fitted with lm(...,data) then it messes
things up. Apparently predict.lm disregards the data argument and uses
whatever it finds in the global environment. In the examples below,
after running David's x <- rnorm(15) example (case 1 is a simplified
version of it), case 3 shows the bug, there are 15 predictions for 4 new
values. Then we must backtrack to case 2 and also consider it a bug.
Examples:
# ------------------- 1
# David's example simplified, only one regressor.
# And with set.seed()
set.seed(4409)
x <- rnorm(15)
y <- x + rnorm(15)
fit <- lm(y ~ x)
new <- data.frame(y = seq(-3.5, 3.5, 0.5))
predict(fit, newdata = new, type = "terms")
# no error is thrown.
# ------------------- 2
# Original post, 'area' and 'concn' are now 'y' and 'x'
# Remove 'x' and 'y' from the global environment.
rm(x, y)
dat <- data.frame(
y = c(4875, 8172, 18065, 34555),
x = c(25, 50, 125, 250))
new <- data.frame(y = c(8172, 10220, 11570, 24150))
model <- lm(y ~ x, data = dat)
predict(model, newdata = new, type = "terms")
# Error in eval(expr, envir, enclos) : object 'x' not found
# ------------------- 3
# Original post.
# Do NOT remove 'x' and 'y' from the global environment.
set.seed(4409)
x <- rnorm(15)
y <- x + rnorm(15)
dat <- data.frame(
y = c(4875, 8172, 18065, 34555),
x = c(25, 50, 125, 250))
new <- data.frame(y = c(8172, 10220, 11570, 24150))
model <- lm(y ~ x, data = dat)
predict(model, newdata = new, type = "terms")
# Warning message:
# 'newdata' had 4 rows but variable(s) found have 15 rows
#------------------- 4
# Original post, no data argument to lm.
y <- c(4875, 8172, 18065, 34555)
x <- c(25, 50, 125, 250)
new <- data.frame(y = c(8172, 10220, 11570, 24150))
model <- lm(y ~ x)
predict(model, newdata = new, type = "terms")
# no warning or error is thrown, predictions seem allright
I haven't looked at the code for predict.lm, and really don't know where
the error is.
Bug report?
Rui Barradas
Em 01-09-2012 06:40, David Winsemius escreveu:
On Aug 31, 2012, at 3:48 PM, jjthaden wrote:
On Aug 30, 2012, at 4:35 PM, David Windemius wrote:
David said my newdata data frame 'new' must have a column named 'area'. It did. Nonetheless predict.lm throws an error with type = "terms" and newdata = new. I see nothing in the predict.lm documentation that bars this usage. Is there a bug?
After correcting the error in your definition of the 'area' vector I get no error from predict.lm().
David.
What error did you correct?
This was the code you offered:
#Ludbrook's data set S1 (except renaming
#his 'x' as 'concn' and his 'y' as 'area')
S1 <- data.frame(
area = c(2.4,2.6,6.0,6.5,8.9,),
concn = c(1.1,4,5,8.5,8.5))
There's an extra comma in the "area" vector.
The newdata data frames in my examples have been pretty simple, and have defined the 'area' vector simply, for instance, new <- data.frame(area = c(8172, 10220, 11570, 24150)) new # area # 1 8172 # 2 10220 # 3 11570 # 4 24150 Is something wrong with this?
I don't really know .... this appears to be a different problem than you posed earlier. If you would learn to post with context, we might not be in the position of trying to read your mind.
Were you able to make predict.lm work with newdata = new and type = "terms"?
Yes. I have no trouble doing so.
x <- rnorm(15); x2=rnorm(15) y <- x + x2 +rnorm(15) fit <- lm(y ~ x+x2) new <- data.frame(x2 = seq(-3.5, 3.5, 0.5) ) predict(fit, newdata=new,type="terms", terms="x2")
x2 1 -4.9230035 2 -4.1850588 3 -3.4471141 4 -2.7091694 5 -1.9712248 6 -1.2332801 7 -0.4953354 8 0.2426093 9 0.9805539 10 1.7184986 11 2.4564433 12 3.1943880 13 3.9323326 14 4.6702773 15 5.4082220 attr(,"constant") [1] 0.4501911
-John
Sent from the (NOT) R help mailing list (and NOT) archive at Nabble.com.
Hmmm ... Nabble ... definitely part of the problem.