[R] Error in Rose Method (class balancing)

Jeff Newmiller
Thu, 23 Jul 2020 20:10:59 -0000

The R Administration and Installation manual explains this nomenclature. OP _is_
typically using two libraries... the one installed with R and the
"personal" library which contains the packages installed by the user.
You retrieve packages from libraries using library(somepackage)

Of more relevance here is the fact that OP has yet again failed to read the
Posting Guide, and appears to have attempted to send a disallowed attachment
type through the mailing list and it has been removed from the message.
Ordinarily I would recommend trying to use dput() to remove the need for the
file, but in this case it may be best for the OP to send a link to the file
stored on a file sharing website.

In any event, making the example reproducible is the responsibility of the p
person asking the question. I highly recommend reading [1][2] and using [3] to
verify that the plain text example actually runs up to the point where the error
occurs.

[1]
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

[2] http://adv-r.had.co.nz/Reproducibility.html

[3] https://cran.r-project.org/web/packages/reprex/index.html (read the
vignette)


On July 23, 2020 10:42:55 AM PDT, Bert Gunter <bgunter.4567 at gmail.com>
wrote:
>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]]
>
>______________________________________________
>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.

--
Sent from my phone. Please excuse my brevity.