train, trainControl function not working.

[level]

That code clip did a lot of downloading, here's the reprex()

install.packages("devtools", repos = "http://cran.r-project.org")
#> Installing package into 'C:/Users/userOne/Documents/R/win-library/3.5'
#> (as 'lib' is unspecified)
#> package 'devtools' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#>  C:\Users\userOne\AppData\Local\Temp\RtmpYV53Gm\downloaded_packages
devtools::install_github("r-lib/pkg")
#> Skipping install of 'pkg' from a github remote, the SHA1 (582d0d5f) has not changed since last install.
#>   Use `force = TRUE` to force installation

if (require(pkg)) {
  pkg::pkg_install("caret")
}
#> Loading required package: pkg
#> i Checking for package metadata updates
#> v Using cached package metadata
#> v 1 + 60 pkgs | kept 60, updated 0, new 0 | downloaded 0 (0 B) [3.7s]

^{Created on 2019-02-02 by the reprex package (v0.2.1)}

[level]

@Taras mentioned that I should have multiple versions of R and rStudio. From what I know I have only one. Should I try to add more, or is there a good way that this should be done?

[Max]

What happens with library(caret) now?

[level]

Sorry for the late response, I was updating the file and accidentally deleted it. I pieced it back together from my prior post. From what I can see library(caret) is now working. However, I'm getting an error about my data that I don't understand. I checked the excel and the "Age" column is there.

Reprex():

model <- train(Fentanyl~
                 Age+Sex+Race+
                 Oxycodone+Hydrocodone+Buprenorphine+
                 Morphine+Codeine+Norbuprenorphine+
                 Naloxone,
               ToTrain,
               method = "glm", family = "poisson",
               trControl = ctrl,
               tuneLength = 10)#end train
#> Error in train(Fentanyl ~ Age + Sex + Race + Oxycodone + Hydrocodone + : could not find function "train"

install.packages("devtools", repos = "http://cran.r-project.org")
#> Installing package into 'C:/Users/userOne/Documents/R/win-library/3.5'
#> (as 'lib' is unspecified)
#> package 'devtools' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#>  C:\Users\userOne\AppData\Local\Temp\Rtmp6HFdgS\downloaded_packages
devtools::install_github("r-lib/pkg")
#> Skipping install of 'pkg' from a github remote, the SHA1 (582d0d5f) has not changed since last install.
#>   Use `force = TRUE` to force installation

if (require(pkg)) {
  pkg::pkg_install("caret")
}
#> Loading required package: pkg
#> i Checking for package metadata updates
#> v Using cached package metadata
#> v 1 + 60 pkgs | kept 60, updated 0, new 0 | downloaded 0 (0 B) [3.8s]

library(caret)
#> Loading required package: lattice
#> Loading required package: ggplot2

predicted <- predict(model, ToTrain["Fentanyl"], type = "prob")
#> Error in predict(model, ToTrain["Fentanyl"], type = "prob"): object 'model' not found

#actual <- ToTrain["Fentanyl"]

^{Created on 2019-02-03 by the reprex package (v0.2.1)}

[level]

I think I might be doing something fundamentally wrong. When I run a script in rStudio I put the cursor at the top and hit run on each line. Sometimes I have issues when running on an install.packages(somePackage) line. I will get a prompt asking if I want to restart rStudio, I'll hit yes, but it seem to get stuck in a loop asking me to restart over and over again. So what I do now is, under the packages tab in the user library, I just check each package I want and then run the library(somePackage) command.

Is all of this okay, or should I be doing it a different way?

Thanks

[taras]

@level

should I be doing it a different way?

yes, absolutely.

@level

I have issues when running on an install.packages(somePackage) line

You shouldn't be running install.package more than 1 time per package ever. Just like you don't install a piece of software every time you need to run it, you don't install packages every time you run the script.
I suggest you remove every mentioning of any flavor of install.package from your script.

---

Now to your script.

@level

From what I can see library(caret) is now working. However, I'm getting an error about my data that I don't understand. I checked the excel and the "Age" column is there.

As a rule of thumb, a good habit is to load packages at the top of your script.
What we have here is:

• You attempt to create a model object using the train function from caret package
• Since you attempt to do this before you actually load the caret package, you get an error (obviously), and the object model is not created.
• You then load the caret package.
• When you try to create a predicted object, it fails. Why? Well, because you call your model object, but remember that it doesn't exist because it failed earlier.

---

Your code should probably look something like this instead (my best guess based on reading your code, I haven't actually run it):

library(caret)
model <- train(Fentanyl~
                 Age+Sex+Race+
                 Oxycodone+Hydrocodone+Buprenorphine+
                 Morphine+Codeine+Norbuprenorphine+
                 Naloxone,
               ToTrain,
               method = "glm", family = "poisson",
               trControl = ctrl,
               tuneLength = 10)
predicted <- predict(model, ToTrain["Fentanyl"], type = "prob")

---

Here are a few suggestions beyond this particular problem that I hope might help you in the future.

• You may benefit from looking into programming fundamentals and understanding the process.
• A book about R fundamentals may also help you conquer the language better. I suggest starting with "R For Data Science"
• Error messages are sometimes helpful and may guide you in troubleshooting.

[level]

Thanks for the suggestions.

[taras]

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