I used the caret and glmnet pacakges to run a lasso logistic regression using repeated cross validation to select the optimized minimum lambda.
glmnet.obj <- train(outcome ~ .,
data = df.train,
method = "glmnet",
metric = "ROC",
family = "binomial",
trControl = trainControl(
method = "repeatedcv",
repeats = 10,
number = 10,
summaryFunction = twoClassSummary,
classProbs = TRUE,
savePredictions = "all",
selectionFunction = "best"))
After that, I get the best lambda and alpha:
best_lambda<- get_best_result(glmnet.obj)$lambda
best_alpha<- get_best_result(glmnet.obj)$alpha
Then I obtain the predicted probabilities for the test set:
pred_prob<- predict(glmnet.obj,s=best_lambda, alpha=best_alpha, type="prob", newx = x.test)
and then to get the predicted classes, which I intend to use in ConfusionMatrix:
pred_class<-predict(glmnet.obj,s=best_lambda, alpha=best_alpha, type="raw",newx=x.test)
But when I just run pred_class it returns NULL.
What could I be missing here?
You need to use newdata = as opposed to newx= because when you do predict(glmnet.obj), it is calling predict.train on the caret object.
You did not provide one function, but I suppose it is rom this source:
get_best_result = function(caret_fit) {
best = which(rownames(caret_fit$results) == rownames(caret_fit$bestTune))
best_result = caret_fit$results[best, ]
rownames(best_result) = NULL
best_result
}
Using an example data
set.seed(111)
df = data.frame(outcome = factor(sample(c("y","n"),100,replace=TRUE)),
matrix(rnorm(1000),ncol=10))
colnames(df.train)[-1] = paste0("col",1:10)
df.train = df[1:70,]
x.test = df[71:100,]
And we run your model, then you can predict using the function:
pred_class<-predict(glmnet.obj,type="raw",newdata=x.test)
confusionMatrix(table(pred_class,x.test$outcome))
Confusion Matrix and Statistics
pred_class n y
n 1 5
y 11 13
The arguments for lambda = and newx= comes from glmnet, you can potentially use it on glmnet.obj$finalModel , but you need to convert the data into a matrix, for example:
predict(glmnet.obj$finalModel,s=best_lambda, alpha=best_alpha,
type="class",newx=as.matrix(x.test[,-1]))
When I run a quantile regression forest model with caret::train, I get the following error: Error in { : task 1 failed - "non-numeric argument to binary operator".
When I set ntree to a higher number (in my reproducible example this would be ntree = 150), my code runs without errors.
This code
library(caret)
library(quantregForest)
data(segmentationData)
dat <- segmentationData[segmentationData$Case == "Train",]
dat <- dat[1:50,]
# predictors
preds <- dat[,c(5:ncol(dat))]
# convert all to numeric
preds <- data.frame(sapply(preds, function(x) as.numeric(as.character(x))))
# response variable
response <- dat[,4]
# set up error measures
sumfct <- function(data, lev = NULL, model = NULL){
RMSE <- sqrt(mean((data$pred - data$obs)^2, na.omit = TRUE))
c(RMSE = RMSE)
}
# specify folds
set.seed(42, kind = "Mersenne-Twister", normal.kind = "Inversion")
folds_train <- caret::createMultiFolds(y = dat$Cell,
k = 10,
times = 5)
# specify trainControl for tuning mtry with the created multifolds
finalcontrol <- caret::trainControl(search = "grid", method = "repeatedcv", number = 10, repeats = 5,
index = folds_train, savePredictions = TRUE, summaryFunction = sumfct)
# build grid for tuning mtry
tunegrid <- expand.grid(mtry = c(2, 10, sqrt(ncol(preds)), ncol(preds)/3))
# train model
set.seed(42, kind = "Mersenne-Twister", normal.kind = "Inversion")
model <- caret::train(x = preds,
y = response,
method ="qrf",
ntree = 30, # with ntree = 150 it works
metric = "RMSE",
tuneGrid = tunegrid,
trControl = finalcontrol,
importance = TRUE,
keep.inbag = TRUE
)
produces the error. The model with my real data has ntree = 10000 and still the task is failing.
How can I fix this?
Where in the source code of caret can I find the conditions for the error message Error in { : task 1 failed - "non-numeric argument to binary operator"? From which part of the source code does the error message come from?
UPDATE:
I adapted my code with my real data according to the answer of StupidWolf, so it looks like this:
# train model
set.seed(42, kind = "Mersenne-Twister", normal.kind = "Inversion")
model <- caret::train(x = preds,
y = response,
method ="qrf",
ntree = 30, # with ntree = 150 it works
metric = "RMSE",
sampsize = ceiling(length(response)*0.4)
tuneGrid = tunegrid,
trControl = finalcontrol,
importance = TRUE,
keep.inbag = FALSE
)
With my real data I still get the above error message, so that I had to adapt the sampsize to 0.1*length(response) in the worst case in order to compute the model successfully. So only setting keep.inbag = FALSEstill produced errors. I have up to 1500 predictors while the number of samples (rows) are only 50 to 60. I still don't understand, what exactly causes the error message. I tried the model without the sampsize argument, but always set keep.inbag = FALSE. The error was still occuring. only setting the sampsize very low ensured success.
How can I run the model successfully without setting sampsize? I actually wanted the bootstrap approach for the out of bag data sets and not the artificial sampsize of 40 % or 10% of my data set for training the forest.
You get the error because you used the option keep.inbag = TRUE, in the quantregforest code, line 95:
minoob <- min( apply(!is.na(valuesPredict),1,sum))
if(minoob<10) stop("need to increase number of trees for sufficiently many out-of-bag observations")
So it requires that all of your observations have at least 10 instances of OOB (out of bag), to keep the out of bag predictions. So if your real data is huge, the ntrees required for keeping the out of bag is going to be huge.
If you are using caret for training the data, keeping the OOB and having savePredictions = TRUE seems redundant. On the whole, OOB predictions might not be so useful since you will be using the test fold to predict anyway.
Another option, given the size of your data, is to tweak the sampsize. In randomForest only a number of sampsize observations are sampled with replacement subset to fit a tree. If you set a lower size for this, you ensure there's enough OOB. For example in the example given, we can see:
model <- caret::train(x = preds,
y = response,
method ="qrf",
ntree = 30, sampsize=17,
metric = "RMSE",
tuneGrid = tunegrid,
trControl = finalcontrol,
importance = TRUE,
keep.inbag = TRUE)
model
Quantile Random Forest
50 samples
57 predictors
No pre-processing
Resampling: Cross-Validated (10 fold, repeated 5 times)
Summary of sample sizes: 44, 43, 44, 46, 45, 46, ...
Resampling results across tuning parameters:
mtry RMSE
2.000000 42.53061
7.549834 42.72116
10.000000 43.11533
19.000000 42.80340
RMSE was used to select the optimal model using the smallest value.
The final value used for the model was mtry = 2.
I would like to cross-validate a neural network using the package neuralnet and caret.
The data df can be copied from this post.
When running the neuralnet() function, there is an argument called hidden where you can set the hidden layers and neurons in each. Let's say I want 2 hidden layers with 3 and 2 neurons respectively. It would be written as hidden = c(3, 2).
However, as I want to cross-validate it, I decided to use the fantastic caret package. But when using the function train(), I do not know how to set the number of layers and neurons.
Does anyone know where can I add these numbers?
This is the code I ran:
nn <- caret::train(DC1 ~ ., data=df,
method = "neuralnet",
#tuneGrid = tune.grid.neuralnet,
metric = "RMSE",
trControl = trainControl (
method = "cv", number = 10,
verboseIter = TRUE
))
By the way, I am getting some warnings with the previous code:
predictions failed for Fold01: layer1=3, layer2=0, layer3=0 Error in cbind(1, pred) %*% weights[[num_hidden_layers + 1]] :
requires numeric/complex matrix/vector arguments
Ideas on how to solve it?
When using neural net model in caret in order to specify the number of hidden units in each of the three supported layers you can use the parameters layer1, layer2 and layer3. I found out by checking the source.
library(caret)
grid <- expand.grid(layer1 = c(32, 16),
layer2 = c(32, 16),
layer3 = 8)
Use case with BostonHousing data:
library(mlbench)
data(BostonHousing)
lets just select numerical columns for the example to make it simple:
BostonHousing[,sapply(BostonHousing, is.numeric)] -> df
nn <- train(medv ~ .,
data = df,
method = "neuralnet",
tuneGrid = grid,
metric = "RMSE",
preProc = c("center", "scale", "nzv"), #good idea to do this with neural nets - your error is due to non scaled data
trControl = trainControl(
method = "cv",
number = 5,
verboseIter = TRUE)
)
The part
preProc = c("center", "scale", "nzv")
is essential for the algorithm to converge, neural nets don't like unscaled features
Its super slow though.
nn
#output
Neural Network
506 samples
12 predictor
Pre-processing: centered (12), scaled (12)
Resampling: Cross-Validated (5 fold)
Summary of sample sizes: 405, 404, 404, 405, 406
Resampling results across tuning parameters:
layer1 layer2 RMSE Rsquared MAE
16 16 NaN NaN NaN
16 32 4.177368 0.8113711 2.978918
32 16 3.978955 0.8275479 2.822114
32 32 3.923646 0.8266605 2.783526
Tuning parameter 'layer3' was held constant at a value of 8
RMSE was used to select the optimal model using the smallest value.
The final values used for the model were layer1 = 32, layer2 = 32 and layer3 = 8.
This question is a continuation of the same thread here. Below is a minimal working example taken from this book:
Wehrens R. Chemometrics with R multivariate data analysis in the
natural sciences and life sciences. 1st edition. Heidelberg; New York:
Springer. 2011. (page 250).
The example was taken from this book and its package ChemometricsWithR. It highlighted some pitfalls when modeling using cross-validation techniques.
The Aim:
A cross-validated methodology using the same set of repeated CV to perform a known strategy of PLS followed typically by LDA or cousins like logistic regression, SVM, C5.0, CART, with the spirit of caret package. So PLS would be needed every time before calling the waiting classifier in order to classify PLS score space instead of the observations themselves. The nearest approach in the caret package is doing PCA as a pre-processing step before modeling with any classifier. Below is a PLS-LDA procedure with only one cross-validation to test performance of the classifier, there was no 10-fold CV or any repetition. The code below was taken from the mentioned book but with some corrections otherwise throws error:
library(ChemometricsWithR)
data(prostate)
prostate.clmat <- classvec2classmat(prostate.type) # convert Y to a dummy var
odd <- seq(1, length(prostate.type), by = 2) # training
even <- seq(2, length(prostate.type), by = 2) # holdout test
prostate.pls <- plsr(prostate.clmat ~ prostate, ncomp = 16, validation = "CV", subset=odd)
Xtst <- scale(prostate[even,], center = colMeans(prostate[odd,]), scale = apply(prostate[odd,],2,sd))
tst.scores <- Xtst %*% prostate.pls$projection # scores for the waiting trained LDA to test
prostate.ldapls <- lda(scores(prostate.pls)[,1:16],prostate.type[odd]) # LDA for scores
table(predict(prostate.ldapls, new = tst.scores[,1:16])$class, prostate.type[even])
predictionTest <- predict(prostate.ldapls, new = tst.scores[,1:16])$class)
library(caret)
confusionMatrix(data = predictionTest, reference= prostate.type[even]) # from caret
Output:
Confusion Matrix and Statistics
Reference
Prediction bph control pca
bph 4 1 9
control 1 35 7
pca 34 4 68
Overall Statistics
Accuracy : 0.6564
95% CI : (0.5781, 0.7289)
No Information Rate : 0.5153
P-Value [Acc > NIR] : 0.0001874
Kappa : 0.4072
Mcnemar's Test P-Value : 0.0015385
Statistics by Class:
Class: bph Class: control Class: pca
Sensitivity 0.10256 0.8750 0.8095
Specificity 0.91935 0.9350 0.5190
Pos Pred Value 0.28571 0.8140 0.6415
Neg Pred Value 0.76510 0.9583 0.7193
Prevalence 0.23926 0.2454 0.5153
Detection Rate 0.02454 0.2147 0.4172
Detection Prevalence 0.08589 0.2638 0.6503
Balanced Accuracy 0.51096 0.9050 0.6643
However, the confusion matrix didn't match that in the book, anyway the code in the book did break, but this one here worked with me!
Notes:
Although this was only one CV, but the intention is to agree on this methodology first, sd and mean of the train set were applied on the test set, PLUS transformed into PLS scores based a specific number of PC ncomp. I want this to occur every round of the CV in the caret. If the methodology as code is correct here, then it can serve, may be, as a good start for a minimal work example while modifying the code of the caret package.
Side Notes:
It can be very messy with scaling and centering, I think some of the PLS functions in R do scaling internally, with or without centering, I am not sure, so building a custom model in caret should be handled with care to avoid both lack or multiple scalings or centerings (I am on my guards with these things).
Perils of multiple centering/scaling
The code below is just to show how multliple centering/scaling can change the data, only centering is shown here but the same problem with scaling applies too.
set.seed(1)
x <- rnorm(200, 2, 1)
xCentered1 <- scale(x, center=TRUE, scale=FALSE)
xCentered2 <- scale(xCentered1, center=TRUE, scale=FALSE)
xCentered3 <- scale(xCentered2, center=TRUE, scale=FALSE)
sapply (list(xNotCentered= x, xCentered1 = xCentered1, xCentered2 = xCentered2, xCentered3 = xCentered3), mean)
Output:
xNotCentered xCentered1 xCentered2 xCentered3
2.035540e+00 1.897798e-16 -5.603699e-18 -5.332377e-18
Please drop a comment if I am missing something somewhere in this course. Thanks.
If you want to fit these types of models with caret, you would need to use the latest version on CRAN. The last update was created so that people can use non-standard models as they see fit.
My approach below is to jointly fit the PLS and other model (I used random forest in the example below) and tune them at the same time. So for each fold, a 2D grid of ncomp and mtry is used.
The "trick" is to attached the PLS loadings to the random forest object so that they can be used during prediction time. Here is the code that defines the model (classification only):
modelInfo <- list(label = "PLS-RF",
library = c("pls", "randomForest"),
type = "Classification",
parameters = data.frame(parameter = c('ncomp', 'mtry'),
class = c("numeric", 'numeric'),
label = c('#Components',
'#Randomly Selected Predictors')),
grid = function(x, y, len = NULL) {
grid <- expand.grid(ncomp = seq(1, min(ncol(x) - 1, len), by = 1),
mtry = 1:len)
grid <- subset(grid, mtry <= ncomp)
},
loop = NULL,
fit = function(x, y, wts, param, lev, last, classProbs, ...) {
## First fit the pls model, generate the training set scores,
## then attach what is needed to the random forest object to
## be used later
pre <- plsda(x, y, ncomp = param$ncomp)
scores <- pls:::predict.mvr(pre, x, type = "scores")
mod <- randomForest(scores, y, mtry = param$mtry, ...)
mod$projection <- pre$projection
mod
},
predict = function(modelFit, newdata, submodels = NULL) {
scores <- as.matrix(newdata) %*% modelFit$projection
predict(modelFit, scores)
},
prob = NULL,
varImp = NULL,
predictors = function(x, ...) rownames(x$projection),
levels = function(x) x$obsLevels,
sort = function(x) x[order(x[,1]),])
and here is the call to train:
library(ChemometricsWithR)
data(prostate)
set.seed(1)
inTrain <- createDataPartition(prostate.type, p = .90)
trainX <-prostate[inTrain[[1]], ]
trainY <- prostate.type[inTrain[[1]]]
testX <-prostate[-inTrain[[1]], ]
testY <- prostate.type[-inTrain[[1]]]
## These will take a while for these data
set.seed(2)
plsrf <- train(trainX, trainY, method = modelInfo,
preProc = c("center", "scale"),
tuneLength = 10,
trControl = trainControl(method = "repeatedcv",
repeats = 5))
## How does random forest do on its own?
set.seed(2)
rfOnly <- train(trainX, trainY, method = "rf",
tuneLength = 10,
trControl = trainControl(method = "repeatedcv",
repeats = 5))
Just for kicks, I got:
> getTrainPerf(plsrf)
TrainAccuracy TrainKappa method
1 0.7940423 0.65879 custom
> getTrainPerf(rfOnly)
TrainAccuracy TrainKappa method
1 0.7794082 0.6205322 rf
and
> postResample(predict(plsrf, testX), testY)
Accuracy Kappa
0.7741935 0.6226087
> postResample(predict(rfOnly, testX), testY)
Accuracy Kappa
0.9032258 0.8353982
Max
Based on Max's valuable comments, I felt the need to have IRIS referee, which is famous for classification, and more importantly the Species outcome has more than two classes, which would be a good data set to test the PLS-LDA custom model in caret:
data(iris)
names(iris)
head(iris)
dim(iris) # 150x5
set.seed(1)
inTrain <- createDataPartition(y = iris$Species,
## the outcome data are needed
p = .75,
## The percentage of data in the
## training set
list = FALSE)
## The format of the results
## The output is a set of integers for the rows of Iris
## that belong in the training set.
training <- iris[ inTrain,] # 114
testing <- iris[-inTrain,] # 36
ctrl <- trainControl(method = "repeatedcv",
repeats = 5,
classProbs = TRUE)
set.seed(2)
plsFitIris <- train(Species ~ .,
data = training,
method = "pls",
tuneLength = 4,
trControl = ctrl,
preProc = c("center", "scale"))
plsFitIris
plot(plsFitIris)
set.seed(2)
plsldaFitIris <- train(Species ~ .,
data = training,
method = modelInfo,
tuneLength = 4,
trControl = ctrl,
preProc = c("center", "scale"))
plsldaFitIris
plot(plsldaFitIris)
Now comparing the two models:
getTrainPerf(plsFitIris)
TrainAccuracy TrainKappa method
1 0.8574242 0.7852462 pls
getTrainPerf(plsldaFitIris)
TrainAccuracy TrainKappa method
1 0.975303 0.9628179 custom
postResample(predict(plsFitIris, testing), testing$Species)
Accuracy Kappa
0.750 0.625
postResample(predict(plsldaFitIris, testing), testing$Species)
Accuracy Kappa
0.9444444 0.9166667
So, finally there was the EXPECTED difference, and improvement in the metrics. So this would support Max's notion, that two-class problems because of Bayes' probabilistic approach of plsda function both lead to the same results.
You need to wrap the CV around both PLS and LDA.
Yes, both plsr and lda center the data their own way
I had a closer look at caret::preProcess (): as it is defined now, you will not be able to use PLS as preprocessing method because it is supervised but caret::preProcess () uses unsupervised methods only (there is no way to hand over the dependent variable). This would probably make patching rather difficult.
So inside the caret framework, you'll need to go for a custom model.
If the scenario were to custom a model of PLS-LDA type, according to the code kindly provided by Max (maintainer of CARET), something is not corect in this code, but I didn't figure it out, because I used the Sonar data set the same in caret vignette and tried to reproduce the result one time using method="pls" and another time using the below custom model for PLS-LDA, the results were exactly identical even to the last digit, which was nonsensical. For benchmarking, one need a known data set (I think a cross-validated PLS-LDA for iris data set would fit here as it is famous for this type of analysis and there should be somewhere a cross-validated treatment of it), everything should be the same (the set.seed(xxx) and the no of K-CV repitition) except the code in question so as to rightly compare and to judge the code below:
modelInfo <- list(label = "PLS-LDA",
library = c("pls", "MASS"),
type = "Classification",
parameters = data.frame(parameter = c("ncomp"),
class = c("numeric"),
label = c("#Components")),
grid = function(x, y, len = NULL) {
grid <- expand.grid(ncomp = seq(1, min(ncol(x) - 1, len), by = 1))
},
loop = NULL,
fit = function(x, y, wts, param, lev, last, classProbs, ...) {
## First fit the pls model, generate the training set scores,
## then attach what is needed to the lda object to
## be used later
pre <- plsda(x, y, ncomp = param$ncomp)
scores <- pls:::predict.mvr(pre, x, type = "scores")
mod <- lda(scores, y, ...)
mod$projection <- pre$projection
mod
},
predict = function(modelFit, newdata, submodels = NULL) {
scores <- as.matrix(newdata) %*% modelFit$projection
predict(modelFit, scores)$class
},
prob = function(modelFit, newdata, submodels = NULL) {
scores <- as.matrix(newdata) %*% modelFit$projection
predict(modelFit, scores)$posterior
},
varImp = NULL,
predictors = function(x, ...) rownames(x$projection),
levels = function(x) x$obsLevels,
sort = function(x) x[order(x[,1]),])
Based on Zach's request, the code below is for method="pls" in caret, exactly the same concrete example in caret vigenette on CRAN:
library(mlbench) # data set from here
data(Sonar)
dim(Sonar) # 208x60
set.seed(107)
inTrain <- createDataPartition(y = Sonar$Class,
## the outcome data are needed
p = .75,
## The percentage of data in the
## training set
list = FALSE)
## The format of the results
## The output is a set of integers for the rows of Sonar
## that belong in the training set.
training <- Sonar[ inTrain,] #157
testing <- Sonar[-inTrain,] # 51
ctrl <- trainControl(method = "repeatedcv",
repeats = 3,
classProbs = TRUE,
summaryFunction = twoClassSummary)
set.seed(108)
plsFitSon <- train(Class ~ .,
data = training,
method = "pls",
tuneLength = 15,
trControl = ctrl,
metric = "ROC",
preProc = c("center", "scale"))
plsFitSon
plot(plsFitSon) # might be slightly difference than what in the vignette due to radnomness
Now, the code below is a pilot run to classify Sonar data using the custom model PLS-LDA which is under question, it is expected to come up with any numbers apart from identical with those using PLS only:
set.seed(108)
plsldaFitSon <- train(Class ~ .,
data = training,
method = modelInfo,
tuneLength = 15,
trControl = ctrl,
metric = "ROC",
preProc = c("center", "scale"))
Now comparing the results between the two models:
getTrainPerf(plsFitSon)
TrainROC TrainSens TrainSpec method
1 0.8741154 0.7638889 0.8452381 pls
getTrainPerf(plsldaFitSon)
TrainROC TrainSens TrainSpec method
1 0.8741154 0.7638889 0.8452381 custom
postResample(predict(plsFitSon, testing), testing$Class)
Accuracy Kappa
0.745098 0.491954
postResample(predict(plsldaFitSon, testing), testing$Class)
Accuracy Kappa
0.745098 0.491954
So, the results are exactly the same which cannot be. As if the lda model were not added?