[R] Help Required for R Markdown function.
Jeff Newmiller
jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Tue Mar 2 02:55:18 CET 2021
It is standard for install.packages to download packages into a temporary directory before actually installing them. That message has been there for many many years every time you install a contributed package.
You have not provided a complete copy of the errors that were generated... I am certain something else happened that was in the output you failed to show us.
While I think RStudio is a fine tool, it does sometimes make non-trivial changes to standard outputs... I recommend that you try things in RGui or R from the command line (in this case the install.packages call) and describe them as such when asking for help here to reduce possible confusion as to where the problem is coming from. If it works in RGui but not in RStudio then you probably need to get help in their community forum.
Also, don't hijack conversation threads... start your own to ask a question, and reply to it as needed. Even changing the subject line doesn't disconnect your question from the original thread in the archive (or most email programs).
On February 28, 2021 2:04:52 PM PST, Avi Gross via R-help <r-help using r-project.org> wrote:
>I am sure you can get more done with a caret than a stick. I need a
>stick for another problem, though.
>
>A serious question. I somehow upset my R/RSTUDIO setup while trying to
>see why a markdown only allowed me to save an HTML version, not PDF and
>DOC as it used to. It now fails on any such document with a code that
>indicates it is not set to find a CRAN mirror:
>
>It seems to be upset by a simple call to get the tidyverse loaded and
>may succeed in one sense but not continue:
>
>" Installing package into
>�C:/Users/avid2016/Documents/R/win-library/4.0�
>(as �lib� is unspecified)
>trying URL
>'https://cran.rstudio.com/bin/windows/contrib/4.0/tidyverse_1.3.0.zip'
>Content type 'application/zip' length 439972 bytes (429 KB)
>downloaded 429 KB
>
>package ‘tidyverse’ successfully unpacked and MD5 sums checked
>..."
>
>The R Markdown lower console window says:
>
>"Error in contrib.url(repos, "source") : trying to use CRAN without
>setting a mirror calls <Anonymous> ...
>withVisible -> eval -> eval install.packages -> contrib.url Exection
>halted"
>
>I have done some work that failed. I am running on windows with the
>latest versions of both R and RSTUDIO after removing all old versions
>and re-installing both. I have seen hints I need to set some
>definitions in a .Rprofile or so and tried but it continues to fail. So
>I now can knit nothing!
>
>Anyone have a pointer on problems like this? My next attempt would be
>to reinstall the programs on another hard disk entirely in case the
>problem is in my folder structure of ~/R and below but I dod not want
>to toss years of work because of one errant configuration file or the
>lack thereof.
>
>Thanks in advance for any advice. It may be something trivial such as
>kit not knowing where to place a library so it puts it into a temp
>area?
>
>Avi
>
>-----Original Message-----
>From: R-help <r-help-bounces using r-project.org> On Behalf Of John Kane
>Sent: Saturday, February 27, 2021 3:07 PM
>To: Kishor raut <rautkishor01 using gmail.com>
>Cc: R. Help Mailing List <r-help using r-project.org>
>Subject: Re: [R] Help Required for R Markdown function.
>
>The "confusionMatrix" function appears to be from the 'caret' package.
>Have you loaded 'caret' with the library(caret) command?
>
>On Sat, 27 Feb 2021 at 14:20, Kishor raut <rautkishor01 using gmail.com>
>wrote:
>
>> Respected Sir,
>>
>> I Mr Kishor Tried to get help online but wont found the solution so
>> writting an email.
>>
>> Step1: While writting in rmarkdown all codes get executted very well
>> till the fuction Confusionmatrix were written on it.
>>
>> Step2: As confusionmatrix command inserted following error is on
>> screen board
>>
>>
>> processing file: RMarkdown.Rmd
>> |.....
> |
>> 7%
>> ordinary text without R code
>>
>> |.........
> |
>> 13%
>> label: unnamed-chunk-1
>> |..............
> |
>> 20%
>> ordinary text without R code
>>
>> |...................
> |
>> 27%
>> label: unnamed-chunk-2
>> |.......................
> |
>> 33%
>> ordinary text without R code
>>
>> |............................
> |
>> 40%
>> label: unnamed-chunk-3
>> |.................................
> |
>> 47%
>> ordinary text without R code
>>
>> |.....................................
> |
>> 53%
>> label: unnamed-chunk-4
>> |..........................................
> |
>> 60%
>> ordinary text without R code
>>
>> |...............................................
> |
>> 67%
>> label: unnamed-chunk-5
>> |...................................................
> |
>> 73%
>> ordinary text without R code
>>
>> |........................................................
> |
>> 80%
>> label: unnamed-chunk-6
>> |.............................................................
> |
>> 87%
>> ordinary text without R code
>>
>> |.................................................................
> |
>> 93%
>> label: unnamed-chunk-7
>> Quitting from lines 98-104 (RMarkdown.Rmd) Error in
>> confusionMatrix(p1, train$CTestresult) :
>> could not find function "confusionMatrix"
>> Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible
>->
>> eval
>> -> eval
>>
>> Execution halted
>>
>> Step4: As codes were written these
>>
>>
>> Using function “sample” the data takes into sample of the specified
>> size from the stored data ```{r}
>> set.seed(1234)
>> ind<-sample(2,nrow(FEVER1),replace=TRUE, pro = c(0.7,0.3))
>> train<-FEVER1[ind==1,] test<-FEVER1[ind==2,] ```
>>
>> Application of Random Forest
>>
>> ```{r}
>> library(randomForest)
>> set.seed(123)
>> rfmodel<-randomForest(CTestresult~.,data = train,prox=TRUE) #
>Random
>> Forest Model
>> plot(rfmodel,main="RandomForest Model")
>> print(rfmodel,train) # Printing Outcome of 'model
>for
>> Training Data
>>
>> ```
>>
>> Prediction using Randome Forest Model
>> ```{r}
>> # Prediction of RandomForest Intial Model for Test and Train Data
>>
>> ptrain1<-predict(rfmodel,train) # Predicting model
>Prediction
>> On Training Data
>> # First Six Outcomes with prediction
>> head(ptrain1) # Printing First Six
>Prediction
>> using Random Forest Model
>> head(train$CTestresult) # Printing First Six
>(6)
>> Actual outcomes
>>
>> ```
>>
>>
>> Tuning Model:
>> Tuning of Machine learning model is important step for building good
>> model for best outcome of research.
>>
>> ```{r}
>> # Tunning RandomForest Model using Algorithm
>>
>> t<-tuneRF(train[,-11],train$CTestresult, mtryStart = 2,ntreeTry =
>100,
>> stepFactor =2,improve = 0.051,trace = TRUE, plot = TRUE, doBest=TRUE)
>>
>>
>> ```
>>
>> Building New Model:
>>
>> New model was build on the basis of tunned model parameters and
>controls.
>>
>> ```{r}
>> # New Model After Tuning Random Forest Model
>>
>> rf1<-randomForest(CTestresult~.,data = train,ntree = 100, mtry = 8,
>> importance = TRUE,proximity = TRUE)
>>
>> print(rf1)
>> ```
>>
>> Prediction and Confusion MAtrix:
>>
>> outcome of model will mesuare with the help of predictive outcomes
>> with the help of confusion matrix.
>>
>> ```{r}
>> # Prediction using Random Forest and Confusion Matrix for Train Data
>> p1<-predict(rf1,train)
>> cmatrix<-confusionMatrix(p1,train$CTestresult)
>> cmatrix
>>
>>
>> ```
>>
>>
>> I will great thank full if you will help me for to remove the error.
>>
>>
>>
>>
>> --
>> *Kind Regards*
>>
>> Kishor Raut
>> *Cell No.-07387706552*
>>
>> [[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.
>>
>
>
>--
>John Kane
>Kingston ON Canada
>
> [[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.
>
>______________________________________________
>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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