[R] Error with text analysis data

[Neha gupta]

Thank you Tim

My purpose and aim is to train a model (based on the data I provided in my
first email) and predict the output variable (TYPE variable which has three
different values like Severity, bugs, code smell etc) The data as you can
see also have a few text columns which is creating problems for me as I
have never worked before with text data.

I read a tutorial that says stringAsFactor should be false, symbols etc
should be removed, then data should be in tokens, then the text should be
placed in a matrix/table form, and then a model should be built. I am not
sure if these steps are required in my case. Its I think a word2vec problem
though I did not use it before.

Best regards

On Wed, Apr 13, 2022 at 9:53 PM Ebert,Timothy Aaron <tebert using ufl.edu> wrote:

> Is this a different question from the original post? It would be better to
> keep threads separate.
>
> Always pre-process the data. Clean the data of obvious mistakes. This can
> be simple typographical errors or complicated like an author that wrote too
> when they intended two or to. In old English texts spelling was not
> standardized and the same word could have multiple spellings within one
> book or chapter. Removing punctuation is probably a part of this, though a
> program like Grammarly would not work very well if it removed punctuation.
>
>
>
> After that it depends on what you are trying to accomplish. Are you
> interested in the number of times an author used the word “a” or “the” and
> is “The” different from “the?” Are you modeling word use frequency or
> comparing vocabulary between texts.
>
>
>
> Too many choices.
>
>
>
> Tim
>
>
>
> *From:* Neha gupta <neha.bologna90 using gmail.com>
> *Sent:* Wednesday, April 13, 2022 2:49 PM
> *To:* Bill Dunlap <williamwdunlap using gmail.com>
> *Cc:* Ebert,Timothy Aaron <tebert using ufl.edu>; r-help mailing list <
> r-help using r-project.org>
> *Subject:* Re: Error with text analysis data
>
>
>
> *[External Email]*
>
> Someone just told me that you need to pre process the data before model
> construction. For instance, make the text to lower case, remove
> punctuation, symbols etc and tokenize the text (give number to each word).
> Then create word of bags model (not sure about it), and then create a
> model.
>
>
>
> Is it true to perform all these steps?
>
>
>
> Best regards
>
> On Wednesday, April 13, 2022, Bill Dunlap <williamwdunlap using gmail.com>
> wrote:
>
> >  I would always suggest working until the model works, no errors and no
> NA values
>
>
>
> We agree on that.  However, the error gives you no hint about which
> variables are causing the problem.  If it did, then it could only tell
> about the first variable with the problem.  I think you would get to your
> working model faster if you got NA's for the constant columns and then
> could drop them all at once (or otherwise deal with them).
>
>
>
> -Bill
>
>
>
> On Wed, Apr 13, 2022 at 9:40 AM Ebert,Timothy Aaron <tebert using ufl.edu>
> wrote:
>
> I suspect that it is because you are looking at two types of error, both
> telling you that the model was not appropriate. In the “error in contrasts”
> there is nothing to contrast in the model. For a numerical constant the
> program calculates the standard deviation and ends with a division by zero.
> Division by zero is undefined, or NA.
>
>
>
> I would always suggest working until the model works, no errors and no NA
> values. The reason is that I can get NA in several ways and I need to
> understand why. If I just ignore the NA in my model I may be assuming the
> wrong thing.
>
>
>
> Tim
>
>
>
> *From:* Bill Dunlap <williamwdunlap using gmail.com>
> *Sent:* Wednesday, April 13, 2022 12:23 PM
> *To:* Ebert,Timothy Aaron <tebert using ufl.edu>
> *Cc:* Neha gupta <neha.bologna90 using gmail.com>; r-help mailing list <
> r-help using r-project.org>
> *Subject:* Re: [R] Error with text analysis data
>
>
>
> *[External Email]*
>
> Constant columns can be the model when you do some subsetting or are
> exploring a new dataset.  My objection is that constant columns of numbers
> and logicals are fine but those of characters and factors are not.
>
>
>
> -Bill
>
>
>
> On Wed, Apr 13, 2022 at 9:15 AM Ebert,Timothy Aaron <tebert using ufl.edu>
> wrote:
>
> What is the goal of having a constant in the model? To me that seems
> pointless. Also there is no variability in sexCode regardless of whether
> you call it integer or factor. So the model y ~ sexCode is just a strange
> way to look at the variability in y and it would be better to do something
> like summarize(y) or mean(y) if that was the goal.
>
> Tim
>
> -----Original Message-----
> From: R-help <r-help-bounces using r-project.org> On Behalf Of Bill Dunlap
> Sent: Wednesday, April 13, 2022 9:56 AM
> To: Neha gupta <neha.bologna90 using gmail.com>
> Cc: r-help mailing list <r-help using r-project.org>
> Subject: Re: [R] Error with text analysis data
>
> [External Email]
>
> This sounds like what I think is a bug in stats::model.matrix.default(): a
> numeric column with all identical entries is fine but a constant character
> or factor column is not.
>
> > d <- data.frame(y=1:5, sex=rep("Female",5)) d$sexFactor <-
> > factor(d$sex, levels=c("Male","Female")) d$sexCode <-
> > as.integer(d$sexFactor) d
>   y    sex sexFactor sexCode
> 1 1 Female    Female       2
> 2 2 Female    Female       2
> 3 3 Female    Female       2
> 4 4 Female    Female       2
> 5 5 Female    Female       2
> > lm(y~sex, data=d)
> Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
>   contrasts can be applied only to factors with 2 or more levels
> > lm(y~sexFactor, data=d)
> Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
>   contrasts can be applied only to factors with 2 or more levels
> > lm(y~sexCode, data=d)
>
> Call:
> lm(formula = y ~ sexCode, data = d)
>
> Coefficients:
> (Intercept)      sexCode
>           3           NA
>
> Calling traceback() after the error would clarify this.
>
> -Bill
>
>
> On Tue, Apr 12, 2022 at 3:12 PM Neha gupta <neha.bologna90 using gmail.com>
> wrote:
>
> > Hello everyone, I have text data with output variable have three
> subgroups.
> > I am using the following code but getting the error message (see error
> > after the code).
> >
> > d=read.csv("SONAR_RULES.csv", stringsAsFactors = FALSE)
> > d$REMEDIATION_FUNCTION=NULL d$DEF_REMEDIATION_GAP_MULT=NULL
> > d$REMEDIATION_BASE_EFFORT=NULL
> >
> > index <- createDataPartition(d$TYPE, p = .70,list = FALSE) tr <-
> > d[index, ] ts <- d[-index, ]
> >
> > ctrl <- trainControl(method = "cv",number=3, index = index, classProbs
> > = TRUE, summaryFunction = multiClassSummary)
> >
> > ran <- train(TYPE ~ ., data = tr,
> >                     method = "rpart",
> >                     ## Will create 48 parameter combinations
> >                     tuneLength = 3,
> >                     na.action= na.pass,
> >                     metric = "Accuracy",
> >                     preProc = c("center", "scale", "nzv"),
> >                     trControl = ctrl)
> > getTrainPerf(ran)
> >
> > *It gives me error:*
> >
> >
> > *Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
> > contrasts can be applied only to factors with 2 or more levels*
> >
> >
> > *My data is as follow*
> >
> > Rows: 1,819
> > Columns: 14
> > $ PLUGIN_RULE_KEY             <chr> "InsufficientBranchCoverage",
> > "InsufficientLin~
> > $ PLUGIN_CONFIG_KEY           <chr> "", "", "", "", "", "", "", "", "",
> "",
> > "S1120~
> > $ PLUGIN_NAME                 <chr> "common-java", "common-java",
> > "common-java", "~
> > $ DESCRIPTION                 <chr> "An issue is created on a file as
> soon
> > as the ~
> > $ SEVERITY                    <chr> "MAJOR", "MAJOR", "MAJOR", "MAJOR",
> > "MAJOR", "~
> > $ NAME                        <chr> "Branches should have sufficient
> > coverage by t~
> > $ DEF_REMEDIATION_FUNCTION    <chr> "LINEAR", "LINEAR", "LINEAR",
> > "LINEAR_OFFSET",~
> > $ REMEDIATION_GAP_MULT        <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA,
> NA,
> > NA, NA~
> > $ DEF_REMEDIATION_BASE_EFFORT <chr> "", "", "", "10min", "", "",
> > "5min", "5min", "~
> > $ GAP_DESCRIPTION             <chr> "number of uncovered conditions",
> > "number of l~
> > $ SYSTEM_TAGS                 <chr> "bad-practice", "bad-practice",
> > "convention", ~
> > $ IS_TEMPLATE                 <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0,
> > 0, 0, 0~
> > $ DESCRIPTION_FORMAT          <chr> "HTML", "HTML", "HTML", "HTML",
> "HTML",
> > "HTML"~
> > $ TYPE                        <chr> "CODE_SMELL", "CODE_SMELL",
> > "CODE_SMELL", "COD~
> >
> >         [[alternative HTML version deleted]]
> >
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