[R] Error in Rose Method (class balancing)

Sat Jul 25 13:53:29 CEST 2020

OK thanks a lot David, I hope it will work for me.

Best regards
Neha

On Saturday, July 25, 2020, David Winsemius <dwinsemius using comcast.net> wrote:

>
> On 7/24/20 3:08 AM, Neha gupta wrote:
>
> Ohhhh, I am very sorry for that, I have now included
>
> output of dput is: structure(list(unique_id = c("L116", "L117", "L496",
> "L9719",
> "L9720", "L9721", "L9722", "L9723", "L10200", "L10201", "L10202",
> "L10203", "L10204", "L10205", "L10206", "L10705", "L10706", "L10707",
> "L10708", "L10709", "L10710", "L10711", "L10712", "L10713", "L10714",
> "L10715", "L10716", "L10717", "L10718", "L13486"), McCC = c(6,
> 40, 115, 12, 14, 1, 56, 17, 1, 22, 24, 3, 59, 67, 11, 30, 1,
> 16, 1, 18, 4, 4, 1, 44, 1, 18, 40, 54, 1, 23), CLOC = c(0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0), LLOC = c(52, 276, 663, 73, 82, 28, 318,
> 167, 50, 110, 98, 22, 374, 532, 39, 266, 67, 198, 37, 84, 63,
> 68, 4, 372, 58, 97, 290, 318, 8, 90), `Number of previous fixes` = c(1,
> 2, 6, 0, 0, 0, 0, 2, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1,
> 0, 1, 0, 0, 0, 1, 0, 0), `Number of previous modifications` = c(19,
> 58, 195, 50, 22, 11, 43, 47, 25, 14, 24, 10, 53, 97, 13, 58,
> 22, 94, 23, 51, 34, 18, 19, 75, 47, 28, 79, 96, 4, 10), `Number of
> committers` = c(3,
> 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 1, 3, 2, 2,
> 1, 2, 2, 2, 2, 3, 1, 1), `Number of developer commits` = c(1843,
> 1843, 1843, 1300, 1843, 1843, 1843, 1843, 1843, 1843, 1843, 1843,
> 1843, 1843, 1843, 1843, 1843, 1843, 1843, 1843, 1843, 1843, 1843,
> 1843, 1843, 1843, 1843, 1843, 1843, 1843), `Bug class` = structure(c(2L,
> 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("true",
> "false"), class = "factor")), row.names = c(NA, 30L), class = "data.frame")
>
>
> I suggest this pre-processing step:
>
>
> names(d) <- gsub("\\s", "", names(d) )
>
> # then add `library(ROSE)`
>
>
> # and rerun. Some packages are not adept at handling non-standard column
> names.
>
> --
>
> David
>
>
> 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)
>
> On Thu, Jul 23, 2020 at 11:50 PM Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
> wrote:
>
>> All you did was include the dput command in your example. We need the
>> output of dput, not the command itself.
>>
>> On July 23, 2020 2:43:31 PM PDT, Neha gupta <neha.bologna90 using gmail.com>
>> wrote:
>> >David, I understand that the file will not be in your directory but I
>> >have
>> >provided the data using dput? Didn't I? Previously members of this
>> >group
>> >have used dput to provide the detail about their data. Seriously, I
>> >have no
>> >idea how else I can provide a reproducible example.
>> >
>> >
>> >
>> ><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 10:47 PM David Winsemius
>> ><dwinsemius using comcast.net>
>> >wrote:
>> >
>> >>
>> >> 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 using 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$`Bug class`, p = .70,list = FALSE)
>> >>>
>> >>> tr <- d[index, ]
>> >>>
>> >>> ts <- d[-index, ]
>> >>>
>> >>> boot3 <- trainControl(method = "repeatedcv", number=10,
>> >>> repeats=10,classProbs = TRUE,verboseIter = FALSE,
>> >>>
>> >>> summaryFunction = twoClassSummary, sampling = "rose")
>> >>>
>> >>> set.seed(30218)
>> >>>
>> >>> ct <- train(`Bug class` ~ ., data = tr, method = "pls", metric =
>> >"AUC", preProc
>> >>> = c("center", "scale", "nzv"), trControl = boot3)
>> >>>
>> >>> getTrainPerf(ct)
>> >>>
>> >>> On Thu, Jul 23, 2020 at 1:08 AM David Winsemius
>> ><dwinsemius using comcast.net>
>> >>> wrote:
>> >>>
>> >>>>
>> >>>> On 7/22/20 3:43 PM, Neha gupta wrote:
>> >>>> > Hello,
>> >>>> >
>> >>>> >
>> >>>> > I get the following error when I use the ROSE class balancing
>> >method
>> >>>> but
>> >>>> > when I use other methods like SMOTE, up, down, I do not get any
>> >error
>> >>>> > message.
>> >>>> >
>> >>>> >
>> >>>> > Something is wrong; all the ROC metric values are missing:
>> >>>> >
>> >>>> > ROC Sens Spec
>> >>>> >
>> >>>> > Min. : NA Min. : NA Min. : NA
>> >>>> >
>> >>>> > 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA
>> >>>> >
>> >>>> > Median : NA Median : NA Median : NA
>> >>>> >
>> >>>> > Mean :NaN Mean :NaN Mean :NaN
>> >>>> >
>> >>>> > 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA
>> >>>> >
>> >>>> > Max. : NA Max. : NA Max. : NA
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> > library(DMwR)
>> >>>> >
>> >>>> > d=readARFF("bughunter.arff")
>> >>>>
>> >>>> After installing that package and loading pkg:DMwR I get:
>> >>>>
>> >>>>
>> >>>> Error in readARFF("bughunter.arff") : could not find function
>> >"readARFF"
>> >>>>
>> >>>>
>> >>>> Since you also posted in HTML, I suggest you read the Posting
>> >Guide,
>> >>>> restart and R session and post a reproducible example that loads
>> >all
>> >>>> needed packages and data.
>> >>>>
>> >>>> --
>> >>>>
>> >>>> David.
>> >>>>
>> >>>> >
>> >>>> > index <- createDataPartition(d$`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 using 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 using 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.
>>
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>

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