Error message: unused argument (X = train)

Question

Error message: unused argument (X = train)

hanson1005 opened this issue 6 years ago · 12 comments

Hi. While using your package, I got an error message below:

train <- as.data.frame(train)
Q_lib <- c("SL.randomForest", "SL.glmnet", "SL.svm")
g_lib <- c("SL.randomForest", "SL.glmnet", "SL.svm")
vim <- varimpact(Y = label, X = train, Q.library = Q_lib, g.library = g_lib)
Error in varimpact(Y = label, X = train, Q.library = Q_lib, g.library = g_lib) :
unused argument (X = train)

Y is a numeric vector with the length of 1000. X has 1132 variables with 1000 observations. 1132 variables are words from raw document. Entries in each variable are numeric.

I used the same data (X) and the dependent variable (Y) when fitting a Super Learner model:

SLmodel <- SuperLearner(Y = label, X = train, newX=m113_114,
SL.library=c("SL.randomForest", "SL.glmnet", "SL.svm"),
method = "method.NNLS", verbose=TRUE)

It worked fine!
Could you tell me how to fix this issue? What's the problem with my "train" data?
Thank you!

Answer 1 · 2018-08-15T20:12:35.000Z

Hello,

Please specify the training data using the "data = " function argument rather than "X = ". You can see that in the examples here: https://github.com/ck37/varimpact#examples

Thanks,
Chris

Answer 2 · 2018-08-15T20:18:45.000Z

Hi, Chris.
Oh right. Sorry for the mistake. I just realized it and was going to fix the question.
So, I did that. Since my y variable is continuous variable, I specified the family as "gaussian" and got following error message:

vim <- varimpact(Y = label, data = train, Q.library = Q_lib, g.library = g_lib, family="gaussian")
Error in arules::discretize(Xt, method = "frequency", categories = bins_numeric, :
Some breaks are not unique, use fewer breaks for the data.

Could you please help me with solving this problem? Thank you.

Answer 3 · 2018-08-15T20:22:24.000Z

Yeah an update to the arules package is causing that and I'm trying to fix. Does installing this beta version of varimpact resolve that?

devtools::install_github("ck37/varimpact@revamp")

Otherwise I might need another week or two to get it working.

Answer 4 · 2018-08-15T20:36:34.000Z

Hi. I did the following and still get the same error: devtools::install_github("ck37/varimpact@revamp") library(varimpact) => I have to call the package as its original name, right? Also, is it ok to keep the g and q library the same..? I am not familiar with tmle, so wasn't sure about it. I need to compute the variable importance for a specific super learner model I have already fit. By the way, I really like the purpose of your package! Please let me know when you solve this problem. Thanks. Cheers, Julia

…

On Wed, Aug 15, 2018 at 4:22 PM, Chris Kennedy ***@***.***> wrote: Yeah an update to the arules package is causing that and I'm trying to fix. Does installing this beta version of varimpact resolve that? ***@***.***") Otherwise I might need another week or two to get it working. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASRWrvgwOskLsd0cZaGLBZHmF8z8iwu3ks5uRIMAgaJpZM4V-u0F> .

-- Ju Yeon Julia Park Ph.D. in Politics New York University

Answer 5 · 2018-08-15T20:36:55.000Z

Still not working...

Answer 6 · 2018-08-15T20:50:28.000Z

Are you getting the same error or a different error?

More importantly though, I should clarify that this package is not intended to provide variable importance for a particular SuperLearner, it's addressing a different question.

This package might be more relevant to what you're looking to do though: https://github.com/bdwilliamson/vimp

Answer 7 · 2018-08-15T20:51:55.000Z

I got the same error message. Thank you for the suggestion! Best, Julia

On Wed, Aug 15, 2018 at 4:50 PM Chris Kennedy ***@***.***> wrote: Are you getting the same error or a different error? More importantly though, I should clarify that this package is not intended to provide variable importance for a particular SuperLearner, it's addressing a different question. This package might be more relevant to what you're looking to do though: https://github.com/bdwilliamson/vimp — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASRWrvaGC2MePltgVw68hA-RWbls9fzXks5uRImUgaJpZM4V-u0F> .

-- Ju Yeon Julia Park Ph.D. in Politics New York University

Answer 8 · 2018-08-15T20:54:10.000Z

Ok you might try restarting your R session (Session -> Restart R in RStudio) and trying one more time - a lot of times when R reinstalls a loaded package it doesn't use the new version unless it is restarted.

Answer 9 · 2018-08-19T19:13:08.000Z

You may also find this package helpful: https://koalaverse.github.io/vip/articles/vip.html#permutation-method

Answer 10 · 2018-09-07T19:09:34.000Z

Closing this for now - feel free to re-open if more discussion is helpful.

Answer 11 · 2018-09-07T19:10:46.000Z

Ok. Thank you . I didn’t know that it has to be closed. Best, Julia

On Fri, Sep 7, 2018 at 2:09 PM Chris Kennedy ***@***.***> wrote: Closed #10 <#10>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASRWrhyPkOYdabSeM_kUiqTayLhgPmJvks5uYsR0gaJpZM4V-u0F> .

-- Ju Yeon Julia Park Ph.D. in Politics New York University

Answer 12 · 2018-09-07T19:18:45.000Z

Oh it doesn't have to be closed, but usually github repository maintainers will close troubleshooting issues if they've been inactive for a while, as a way to stay organized.