Erro confusionMatrix(Y_test, Y_pred, mode="everything")

General
1

Hello!

I am tryng to have de metrics of a test, so I am doing:

Y_pred <- as.numeric(predict.glmnet(cv.ridge$glmnet.fit, newx=X_test, s=cv.ridge$lambda.min)>
.5)
Y_pred <- as.factor(Y_pred)
Y_test <- as.factor(Y_test)
library(caret)
library(ggplot2)
library(lattice)
library(e1071)
confusionMatrix(Y_test, Y_pred, mode="everything")

but I have to problems, it gives error:

  1. library(caret)
    Error: package or namespace load failed for ‘caret’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
    namespace ‘vctrs’ 0.4.2 is already loaded, but >= 0.5.0 is required

  2. confusionMatrix(Y_test, Y_pred, mode="everything")
    Error in confusionMatrix(Y_test, Y_pred, mode = "everything") :
    could not find function "confusionMatrix"

Can anybody helpe me?

Thank you.

dput(dat)

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103106L, 150564L, 101738L, 95329L, 81035L)), row.names = c(NA,
-397L), class = "data.frame")

2 
install.packages("vctrs")
3

I tryed but it appears the same error:

Error: package or namespace load failed for ‘caret’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘vctrs’ 0.4.2 is already loaded, but >= 0.5.0 is required
In addition: Warning message:
package ‘caret’ was built under R version 4.2.2

4

Shut down RStudio and start a new session before trying to install the package.

5

Please share the complete console output you get when you run this command

install.packages("vctrs")
6

I Shutet down RStudio and startet a new session before trying, but now it appears other errors:

install.packages("vctrs")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/carla/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/vctrs_0.5.1.zip'
Content type 'application/zip' length 1360218 bytes (1.3 MB)
downloaded 1.3 MB

package ‘vctrs’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘vctrs’
Warning in install.packages :
problem copying C:\Users\carla\AppData\Local\R\win-library\4.2\00LOCK\vctrs\libs\x64\vctrs.dll to C:\Users\carla\AppData\Local\R\win-library\4.2\vctrs\libs\x64\vctrs.dll: Permission denied
Warning in install.packages :
restored ‘vctrs’

and I tryed to install Rtools , but it says:

Warning in install.packages :
package ‘Rtools’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at

and when I try again to run install.packages("vctrs"), so appears:

image
image1120×434 25 KB

when i say yes, so appears anothere error:

Restarting R session...

Loading required package: Matrix

install.packages("vctrs")
Error in install.packages : Updating loaded packages

I do not know what to do...

7

I suspect you have enabled the option to restore your previous session on startup and that is loading the package you want to update. Try manually deleting the package from C:\Users\carla\AppData\Local\R\win-library\4.2\vctrs before reinstalling.

8

Thank you a lot, I got to run the command install.packages("vctrs"), but I have another error when I run the command confusionMatrix(Y_test, Y_pred, mode="everything"):

confusionMatrix(Y_test, Y_pred, mode="everything")
Error in confusionMatrix.default(Y_test, Y_pred, mode = "everything") :
the data cannot have more levels than the reference

Here are the commands that I am using:

dat<-read.csv("C:/Salaries.csv")
dat$rank<-as.factor(dat$rank)
dat$discipline<-as.factor(dat$discipline)
dat$sex<-as.factor(dat$sex)

datOHE <- model.matrix(sex~.-1, dat)
train<-datOHE[1:317,]
test<-datOHE[318:nrow(datOHE),]

table(dat[1:317,]$sex)
table(dat[318:nrow(dat),]$sex)

X_train <- data.matrix(train)
Y_train <- data.matrix(dat[1:317,]$salary)

X_test <- data.matrix(test)
Y_test <- data.matrix(dat[318:nrow(dat), ]$salary)

set.seed(42)
cv.ridge <- cv.glmnet(X_train, Y_train, family='gaussian', alpha=0, type.measure='mse')
plot(cv.ridge)
Y_pred <- as.numeric(predict.glmnet(cv.ridge$glmnet.fit, newx=X_test, s=cv.ridge$lambda.min)>
.5)
Y_pred <- as.factor(Y_pred)
Y_test <- as.factor(Y_test)
confusionMatrix(Y_test, Y_pred, mode="everything")

9

A confusion matrix is generally useful for factors, your code looks like you are predicting salary as a numeric variable. Take a look at regression (rather than classification) metrics such as the RMSE!

If you are sure that a confusion matrix is what's right for the problem: The first argument to caret::confusionMatrix() is data which is "a factor of predicted classes" so you'll want to pass Y_pred first.

10

the data cannot have more levels than the reference from this line I believe in your Y_pred you have a variable which does not exist in your Y_test.

to prove that you can compare the output of the lines below

unique(df$Y_pred)
unique(df$Y_test)

11

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