CODEWITHSUNDEEP
r
notrick
notrick

Reputation: 227

Call to plot doesn't actually produce plot

See the loop below--it calls plot k(k-1)/2 times, but no plots are ever actually produced.. Yet if I change the code to call the plots manually (e.g. plot(my_tree,c(1,2),..), plots ARE produced.)

my_tree is a GBM object. See the full code below 

#there is nothing wrong with this code, but yet it does not work
for (i in my_tree$var.names) {
        for (j in my_tree$var.names) {
                if (i < j) plot(my_tree, c(i, j), n.trees=best.iter)
        }
}

==== full program below

pdf("demo.pdf")

N <- 100000
alldata <- data.frame();
train <- factor( ifelse(runif(N)<0.5, 'T', 'V'))
X1 <- rnorm(N);
X2 <- rnorm(N);
X3 <- runif(N);
X4 <- rpois(N, lambda=4);
linear.pred <- -3 + 0.25*X1 + 0.125*X2 - X3 + X4**abs(X1)
temp <- binomial()
y <- rbinom(N, 1, p=temp$linkinv(linear.pred))

alldata <- data.frame(train,X1,X2,X3,X4,y)
rm(train,X1,X2,X3,X4,y,linear.pred)

train <- alldata[alldata$train=='T',]

library(gbm)
my_tree<-gbm(y ~ X1 + X2 + X3 + X4,
    distribution="bernoulli",
    data=train,
    train.fraction=0.5,
    interaction.depth=8,
    n.trees=300,
    shrinkage=0.1,
    verbose=TRUE)

best.iter <- gbm.perf(my_tree, method="test")
print(best.iter)

summary(my_tree, ntrees=best.iter)

# make one and two ways
for (i in my_tree$var.names) {
        plot(my_tree, i, best.iter)      
}

#there is nothing wrong with this code, but yet it does not work
for (i in my_tree$var.names) {
        for (j in my_tree$var.names) {
                if (i < j) plot(my_tree, c(i, j), n.trees=best.iter)
        }
}

Upvotes: 1

Views: 1838

Answers (1)

Greg Snow
Greg Snow

Reputation: 49640

If you look at the help page for plot.gbm it mentions that lattice plots are used, so this could very well be a case of FAQ 7.22. Try "printing" the plots.

Upvotes: 2

Related Questions