Displaying 6 results from an estimated 6 matches for "repeatedcv".
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2013 Nov 15
1
Inconsistent results between caret+kernlab versions
...e:
require(repmis) # For downloading from https
df <- source_data('https://dl.dropboxusercontent.com/u/47973221/data.csv', sep=',')
require(caret)
svm.m1 <- train(df[,-1],df[,1],method='svmRadial',metric='Kappa',tunelength=5,trControl=trainControl(method='repeatedcv', number=10, repeats=10, classProbs=TRUE))
svm.m1
sessionInfo()
### Results - R2.15.2
> svm.m1
1241 samples
7 predictors
10 classes: ?O27479?, ?O31403?, ?O32057?, ?O32059?, ?O32060?, ?O32078?, ?O32089?, ?O32663?, ?O32668?, ?O32676?
No pre-processing
Resampling: Cross-Validation (10...
2023 May 09
1
RandomForest tuning the parameters
...gt; predict(modelFit, newdata, type = "prob")
> >
> > customRF$sort <- function(x) x[order(x[,1]),]
> >
> > customRF$levels <- function(x) x$classes
> >
> >
> > # Set grid search parameters
> > control <- trainControl(method="repeatedcv", number=10, repeats=3,
> search='grid')
> >
> > # Outline the grid of parameters
> > tunegrid <- expand.grid(.maxnodes=c(10,20,30,50), .ntree=c(100, 200,
> 300))
> > set.seed(seed)
> >
> > # Train the model
> > rf_gridsearch <- tra...
2012 Nov 29
1
Help with this error "kernlab class probability calculations failed; returning NAs"
...0
## SAMPLING AND FORMULA
dataset <- trainset
index <- 1:nrow(dataset)
testindex <- sample(index, trunc(length(index)*30/100))
trainset <- dataset[-testindex,]
testset <- dataset[testindex,-1]
## TUNE caret / kernlab
set.seed(1)
MyTrainControl=trainControl(
method = "repeatedcv",
number=10,
repeats=5,
returnResamp = "all",
classProbs = TRUE
)
## MODEL
rbfSVM <- train(outcome~., data = trainset,
method="svmRadial",
preProc = c("scale"),
tuneLength = 10,...
2012 May 30
1
caret() train based on cross validation - split dataset to keep sites together?
...?????? 13.8??????????28.9
18994??? 1980-04-05????????? 8.4???????????16.4
18994??? 1980-04-06????????? 8.3???????????12.6
90342??? 1980-07-13????????? 18.9??????????22.3
90342??? 1980-07-14????????? 19.3??????????28.4
EXAMPLE SCRIPT FOR MODEL FITTING
fitControl <- trainControl(method = "repeatedcv", number=10, repeats=3)
tuning <- read.table("temptunegrid.txt",head=T,sep=",")
tuning
# # Model with 100 iterations
registerDoMC(4)
tempmod100its <- train(watmntemp~tempa + tempb + tempc + tempd + tempe +
netarea + netbuffor + strmslope +
netsoilprm + netslope...
2023 May 08
1
RandomForest tuning the parameters
...omRF$prob <- function(modelFit, newdata, preProc = NULL, submodels = NULL)
? predict(modelFit, newdata, type = "prob")
customRF$sort <- function(x) x[order(x[,1]),]
customRF$levels <- function(x) x$classes
?
# Set grid search parameters
control <- trainControl(method="repeatedcv", number=10, repeats=3, search='grid')
?
# Outline the grid of parameters
tunegrid <- expand.grid(.maxnodes=c(10,20,30,50), .ntree=c(100, 200, 300))
set.seed(seed)
?
# Train the model
rf_gridsearch <- train(x=X_train_, y=y_train_, method=customRF, metric=metric, tuneGrid=tunegrid...
2023 Jul 09
0
caret package
...caret package to analyze a microarray dataset with feature
selection using sbf(). My dataset is 3500 samples with 2200 genes, the
outcome Y variable is a factor of 12 levels. I used the following script to
run the feature selection:
library(caret)
ctrl <- sbfControl(functions=rfSBF, method='repeatedcv', repeats=5)
### x is a matrix of 3500x2200, y is a factor of 12 levels
obj <- sbf(x, y, sbfControl=ctrl)
But it has been more than 15 hours, the code is still running!
My computer has the following specifications:
Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz 2.00 GHz, 8 cores
16.0 GB...