Reputation: 323
I'm trying to complete Exercise 3 from Chapter 7 of Applied Predictive Modeling (Max Kuhn), which uses a bagged MARS model. The code I'm using is straight from the solutions found here: Chapter 7 Solutions
However, when I train the bagEarth model:
meatBMARS <- train(x = absorpTrain, y = proteinTrain,
+ method = "bagEarth",
+ trControl = ctrl,
+ tuneLength = 25,
+ B = 20)
I get the error:
Something is wrong; all the RMSE metric values are missing:
RMSE Rsquared
Min. : NA Min. : NA
1st Qu.: NA 1st Qu.: NA
Median : NA Median : NA
Mean :NaN Mean :NaN
3rd Qu.: NA 3rd Qu.: NA
Max. : NA Max. : NA
NA's :25 NA's :25
Error in train.default(x = absorpTrain, y = proteinTrain, method = "bagEarth", :
Stopping
In addition: There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In eval(expr, envir, enclos) :
predictions failed for Fold01.Rep1: degree=1, nprune=32 Error in eval(expr, envir, enclos) :
could not find function "bagEarth.default"
2: In eval(expr, envir, enclos) :
predictions failed for Fold02.Rep1: degree=1, nprune=32 Error in eval(expr, envir, enclos) :
could not find function "bagEarth.default"
3: In eval(expr, envir, enclos) :
predictions failed for Fold03.Rep1: degree=1, nprune=32 Error in eval(expr, envir, enclos) :
could not find function "bagEarth.default"
4: In eval(expr, envir, enclos) :
predictions failed for Fold04.Rep1: degree=1, nprune=32 Error in eval(expr, envir, enclos) :
could not find function "bagEarth.default
...
The data being trained is the tecator data from the caret package, divided into training and test sets:
> data(tecator)
> set.seed(1029)
> inMeatTraining <- createDataPartition(endpoints[, 3], p = 3/4, list= FALSE)
> absorpTrain <- absorp[ inMeatTraining,]
> absorpTest <- absorp[-inMeatTraining,]
> proteinTrain <- endpoints[ inMeatTraining, 3]
> proteinTest <- endpoints[-inMeatTraining,3]
> ctrl <- trainControl(method = "repeatedcv", repeats = 5)
More info on the dataset:
> str(absorpTrain)
num [1:163, 1:100] 2.62 2.83 2.82 2.79 3.01 ...
> str(proteinTrain)
num [1:163] 16.7 13.5 20.7 15.5 13.7 13.7 19.3 17.7 17.7 12.5 ...
I have the earth package installed and loaded, so I'm not sure why this is happening.
Any advice would be much appreciated.
Upvotes: 1
Views: 409