Help Required for R Markdown function.

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 at r-project.org> On Behalf Of John Kane
Sent: Saturday, February 27, 2021 3:07 PM
To: Kishor raut <rautkishor01 at gmail.com>
Cc: R. Help Mailing List <r-help at 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 at 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

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  |

 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]]

--
John Kane
Kingston ON Canada

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