Hello David, thanks for your reply. I have added the information.
library(caret)
library(farff)
library(DMwR)
d=readARFF("bughunter.arff")
dput( head( d, 30 ) )
index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE)
tr <- d[index, ]
ts <- d[-index, ]
boot3 <- trainControl(method = "repeatedcv", number=10,
repeats=10,classProbs = TRUE,verboseIter = FALSE,
summaryFunction = twoClassSummary, sampling = "rose")
set.seed(30218)
ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric =
"AUC", preProc
= c("center", "scale", "nzv"), trControl = boot3)
getTrainPerf(ct)
On Thu, Jul 23, 2020 at 1:08 AM David Winsemius <dwinsemius at
comcast.net>
wrote:
>
> On 7/22/20 3:43 PM, Neha gupta wrote:
> > Hello,
> >
> >
> > I get the following error when I use the ROSE class balancing method
but
> > when I use other methods like SMOTE, up, down, I do not get any error
> > message.
> >
> >
> > Something is wrong; all the ROC metric values are missing:
> >
> > ROC Sens Spec
> >
> > Min. : NA Min. : NA Min. : NA
> >
> > 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA
> >
> > Median : NA Median : NA Median : NA
> >
> > Mean :NaN Mean :NaN Mean :NaN
> >
> > 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA
> >
> > Max. : NA Max. : NA Max. : NA
> >
> >
> >
> > library(DMwR)
> >
> > d=readARFF("bughunter.arff")
>
> After installing that package and loading pkg:DMwR I get:
>
>
> Error in readARFF("bughunter.arff") : could not find function
"readARFF"
>
>
> Since you also posted in HTML, I suggest you read the Posting Guide,
> restart and R session and post a reproducible example that loads all
> needed packages and data.
>
> --
>
> David.
>
> >
> > index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE)
> >
> > tr <- d[index, ]
> >
> > ts <- d[-index, ]
> >
> > boot3 <- trainControl(method = "repeatedcv", number=10,
> > repeats=10,classProbs = TRUE,verboseIter = FALSE,
> >
> > summaryFunction = twoClassSummary, sampling = "rose")
> >
> > set.seed(30218)
> >
> > ct <- train(`Bug class` ~ ., data = tr,
> >
> > method = "pls",
> >
> > metric = "AUC",
> >
> > preProc = c("center", "scale", "nzv"),
> >
> > trControl = boot3)
> >
> > getTrainPerf(ct)
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
On 7/23/20 7:01 AM, Neha gupta wrote:> > library(caret) > library(farff) > library(DMwR) > > d=readARFF("bughunter.arff")Error in readARFF("bughunter.arff") : ? Assertion on 'path' failed: File does not exist: 'bughunter.arff'. I say again:> I suggest you read the Posting Guide, > restart and R session and post a reproducible example that loads all > needed packages and data.-- David.> dput( head( d, 30 ) ) > > index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE) > > tr <- d[index, ] > > ts <- d[-index, ] > > boot3 <- trainControl(method = "repeatedcv", number=10, > repeats=10,classProbs = TRUE,verboseIter = FALSE, > > summaryFunction = twoClassSummary, sampling = "rose") > > set.seed(30218) > > ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric = > "AUC", preProc = c("center", "scale", "nzv"), trControl = boot3) > > getTrainPerf(ct) >[[alternative HTML version deleted]]
Hello David, file not found should be the path problem I guess. I just
forgot the pROC library, which I included here. These are all the libraries
I am using.
library(caret)
library(farff)
library(DMwR)
library(pROC)
library(pls)
setwd("C:/Users/PC/Documents")
d=readARFF("bughunter.arff")
dput( head( d, 30 ) )
index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE)
tr <- d[index, ]
ts <- d[-index, ]
boot3 <- trainControl(method = "repeatedcv", number=10,
repeats=10,classProbs = TRUE,verboseIter = FALSE,
summaryFunction = twoClassSummary, sampling = "rose")
set.seed(30218)
ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric =
"AUC", preProc
= c("center", "scale", "nzv"), trControl = boot3)
getTrainPerf(ct)
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On Thu, Jul 23, 2020 at 4:01 PM Neha gupta <neha.bologna90 at gmail.com>
wrote:
>
> Hello David, thanks for your reply. I have added the information.
>
> library(caret)
> library(farff)
> library(DMwR)
>
> d=readARFF("bughunter.arff")
> dput( head( d, 30 ) )
>
> index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE)
>
> tr <- d[index, ]
>
> ts <- d[-index, ]
>
> boot3 <- trainControl(method = "repeatedcv", number=10,
> repeats=10,classProbs = TRUE,verboseIter = FALSE,
>
> summaryFunction = twoClassSummary, sampling = "rose")
>
> set.seed(30218)
>
> ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric
= "AUC", preProc
> = c("center", "scale", "nzv"), trControl =
boot3)
>
> getTrainPerf(ct)
>
> On Thu, Jul 23, 2020 at 1:08 AM David Winsemius <dwinsemius at
comcast.net>
> wrote:
>
>>
>> On 7/22/20 3:43 PM, Neha gupta wrote:
>> > Hello,
>> >
>> >
>> > I get the following error when I use the ROSE class balancing
method but
>> > when I use other methods like SMOTE, up, down, I do not get any
error
>> > message.
>> >
>> >
>> > Something is wrong; all the ROC metric values are missing:
>> >
>> > ROC Sens Spec
>> >
>> > Min. : NA Min. : NA Min. : NA
>> >
>> > 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA
>> >
>> > Median : NA Median : NA Median : NA
>> >
>> > Mean :NaN Mean :NaN Mean :NaN
>> >
>> > 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA
>> >
>> > Max. : NA Max. : NA Max. : NA
>> >
>> >
>> >
>> > library(DMwR)
>> >
>> > d=readARFF("bughunter.arff")
>>
>> After installing that package and loading pkg:DMwR I get:
>>
>>
>> Error in readARFF("bughunter.arff") : could not find function
"readARFF"
>>
>>
>> Since you also posted in HTML, I suggest you read the Posting Guide,
>> restart and R session and post a reproducible example that loads all
>> needed packages and data.
>>
>> --
>>
>> David.
>>
>> >
>> > index <- createDataPartition(d$`Bug class`, p = .70,list =
FALSE)
>> >
>> > tr <- d[index, ]
>> >
>> > ts <- d[-index, ]
>> >
>> > boot3 <- trainControl(method = "repeatedcv",
number=10,
>> > repeats=10,classProbs = TRUE,verboseIter = FALSE,
>> >
>> > summaryFunction = twoClassSummary, sampling = "rose")
>> >
>> > set.seed(30218)
>> >
>> > ct <- train(`Bug class` ~ ., data = tr,
>> >
>> > method = "pls",
>> >
>> > metric = "AUC",
>> >
>> > preProc = c("center", "scale",
"nzv"),
>> >
>> > trControl = boot3)
>> >
>> > getTrainPerf(ct)
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>
[[alternative HTML version deleted]]
Actually, you are using no libraries. You are using R *packages* . Don't ask me why the call is library() and not package() -- I'm just another worker bee. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Thu, Jul 23, 2020 at 9:35 AM Neha gupta <neha.bologna90 at gmail.com> wrote:> Hello David, file not found should be the path problem I guess. I just > forgot the pROC library, which I included here. These are all the libraries > I am using. > > library(caret) > library(farff) > library(DMwR) > library(pROC) > library(pls) > > setwd("C:/Users/PC/Documents") > d=readARFF("bughunter.arff") > dput( head( d, 30 ) ) > > index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE) > > tr <- d[index, ] > > ts <- d[-index, ] > > boot3 <- trainControl(method = "repeatedcv", number=10, > repeats=10,classProbs = TRUE,verboseIter = FALSE, > > summaryFunction = twoClassSummary, sampling = "rose") > > set.seed(30218) > > ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric = "AUC", > preProc > = c("center", "scale", "nzv"), trControl = boot3) > > getTrainPerf(ct) > > > < > https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon > > > Virus-free. > www.avast.com > < > https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On Thu, Jul 23, 2020 at 4:01 PM Neha gupta <neha.bologna90 at gmail.com> > wrote: > > > > > Hello David, thanks for your reply. I have added the information. > > > > library(caret) > > library(farff) > > library(DMwR) > > > > d=readARFF("bughunter.arff") > > dput( head( d, 30 ) ) > > > > index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE) > > > > tr <- d[index, ] > > > > ts <- d[-index, ] > > > > boot3 <- trainControl(method = "repeatedcv", number=10, > > repeats=10,classProbs = TRUE,verboseIter = FALSE, > > > > summaryFunction = twoClassSummary, sampling = "rose") > > > > set.seed(30218) > > > > ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric = "AUC", > preProc > > = c("center", "scale", "nzv"), trControl = boot3) > > > > getTrainPerf(ct) > > > > On Thu, Jul 23, 2020 at 1:08 AM David Winsemius <dwinsemius at comcast.net> > > wrote: > > > >> > >> On 7/22/20 3:43 PM, Neha gupta wrote: > >> > Hello, > >> > > >> > > >> > I get the following error when I use the ROSE class balancing method > but > >> > when I use other methods like SMOTE, up, down, I do not get any error > >> > message. > >> > > >> > > >> > Something is wrong; all the ROC metric values are missing: > >> > > >> > ROC Sens Spec > >> > > >> > Min. : NA Min. : NA Min. : NA > >> > > >> > 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA > >> > > >> > Median : NA Median : NA Median : NA > >> > > >> > Mean :NaN Mean :NaN Mean :NaN > >> > > >> > 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA > >> > > >> > Max. : NA Max. : NA Max. : NA > >> > > >> > > >> > > >> > library(DMwR) > >> > > >> > d=readARFF("bughunter.arff") > >> > >> After installing that package and loading pkg:DMwR I get: > >> > >> > >> Error in readARFF("bughunter.arff") : could not find function "readARFF" > >> > >> > >> Since you also posted in HTML, I suggest you read the Posting Guide, > >> restart and R session and post a reproducible example that loads all > >> needed packages and data. > >> > >> -- > >> > >> David. > >> > >> > > >> > index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE) > >> > > >> > tr <- d[index, ] > >> > > >> > ts <- d[-index, ] > >> > > >> > boot3 <- trainControl(method = "repeatedcv", number=10, > >> > repeats=10,classProbs = TRUE,verboseIter = FALSE, > >> > > >> > summaryFunction = twoClassSummary, sampling = "rose") > >> > > >> > set.seed(30218) > >> > > >> > ct <- train(`Bug class` ~ ., data = tr, > >> > > >> > method = "pls", > >> > > >> > metric = "AUC", > >> > > >> > preProc = c("center", "scale", "nzv"), > >> > > >> > trControl = boot3) > >> > > >> > getTrainPerf(ct) > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > ______________________________________________ > >> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> > https://stat.ethz.ch/mailman/listinfo/r-help > >> > PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >> > and provide commented, minimal, self-contained, reproducible code. > >> > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
On 7/23/20 9:34 AM, Neha gupta wrote:> > Hello David, file not found should be the path problem I guess. I just > forgot the pROC library, which I included here. These are all the > libraries I am using. > > library(caret) > library(farff) > library(DMwR) > library(pROC) > library(pls) > > setwd("C:/Users/PC/Documents") > d=readARFF("bughunter.arff")I suppose *you* might have such a file in that directory, but do you assume that *we* will???? A reproducible example will allow others to run your code. Seems fairly clear that we are not there yet. -- David.> dput( head( d, 30 ) ) > > index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE) > > tr <- d[index, ] > > ts <- d[-index, ] > > boot3 <- trainControl(method = "repeatedcv", number=10, > repeats=10,classProbs = TRUE,verboseIter = FALSE, > > summaryFunction = twoClassSummary, sampling = "rose") > > set.seed(30218) > > ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric = > "AUC", preProc = c("center", "scale", "nzv"), trControl = boot3) > > getTrainPerf(ct) > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon> > Virus-free. www.avast.com > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link> > > > > On Thu, Jul 23, 2020 at 4:01 PM Neha gupta <neha.bologna90 at gmail.com > <mailto:neha.bologna90 at gmail.com>> wrote: > > > Hello David, thanks for your?reply. I have added the information. > > library(caret) > library(farff) > library(DMwR) > > d=readARFF("bughunter.arff") > dput( head( d, 30 ) ) > > index <- createDataPartition(d$`Bug class`, p = .70,list = FALSE) > > tr <- d[index, ] > > ts <- d[-index, ] > > boot3 <- trainControl(method = "repeatedcv", number=10, > repeats=10,classProbs = TRUE,verboseIter = FALSE, > > summaryFunction = twoClassSummary, sampling = "rose") > > set.seed(30218) > > ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric > "AUC", preProc = c("center", "scale", "nzv"), trControl = boot3) > > getTrainPerf(ct) > > > On Thu, Jul 23, 2020 at 1:08 AM David Winsemius > <dwinsemius at comcast.net <mailto:dwinsemius at comcast.net>> wrote: > > > On 7/22/20 3:43 PM, Neha gupta wrote: > > Hello, > > > > > > I get the following error when I use the ROSE class > balancing method but > > when I use other methods like SMOTE, up, down, I do not get > any error > > message. > > > > > > Something is wrong; all the ROC metric values are missing: > > > > ROC Sens Spec > > > > Min. : NA Min. : NA Min. : NA > > > > 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA > > > > Median : NA Median : NA Median : NA > > > > Mean :NaN Mean :NaN Mean :NaN > > > > 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA > > > > Max. : NA Max. : NA Max. : NA > > > > > > > > library(DMwR) > > > > d=readARFF("bughunter.arff") > > After installing that package and loading pkg:DMwR I get: > > > Error in readARFF("bughunter.arff") : could not find function > "readARFF" > > > Since you also posted in HTML, I suggest you read the Posting > Guide, > restart and R session and post a reproducible example that > loads all > needed packages and data. > > -- > > David. > > > > > index <- createDataPartition(d$`Bug class`, p = .70,list > FALSE) > > > > tr <- d[index, ] > > > > ts <- d[-index, ] > > > > boot3 <- trainControl(method = "repeatedcv", number=10, > > repeats=10,classProbs = TRUE,verboseIter = FALSE, > > > > summaryFunction = twoClassSummary, sampling = "rose") > > > > set.seed(30218) > > > > ct <- train(`Bug class` ~ ., data = tr, > > > > method = "pls", > > > > metric = "AUC", > > > > preProc = c("center", "scale", "nzv"), > > > > trControl = boot3) > > > > getTrainPerf(ct) > > > >? ? ? ?[[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org <mailto:R-help at r-project.org> mailing > list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible > code. >[[alternative HTML version deleted]]