Unable to execute machine_learn

[BobParker18]

Hello! We appreciate that you've come here to offer feedback of some sort. If you have a general question about how to use the package, consider asking on Slack for a faster response.

Feature Requests

Letting us know how healthcareai could be more useful for you help us make it better. Don't worry about asking; we may not get to it right away, but we're happy to know what you want. Please include what you'd like the package to do and what you would use the functionality for.

Bug Reports

Did you find a new way to break healthcareai? We're happy you came here to tell us about it. We want to help, but it can be very difficult to diagnose a problem that happened on another machine. To help with that please include the following:

A minimal reproducable example

These help us recreate your problem on our machine. This is a good guide on how to write a reproducable example. The reprex package is extraordinarily helpful for this. If you need to include data to recreate the issue, you can paste the output of dput(your_data) here.

The output of sessionInfo()

models <- machine_learn(pima_diabetes, patient_id, outcome = diabetes)

> Error in machine_learn(pima_diabetes, patient_id, outcome = diabetes): could not find function "machine_learn"

Created on 2018-11-27 by the reprex package (v0.2.1)

[glenrs]

@BobParker18, did you load healthcareai in your reprex example?

[BobParker18]

Yes.

Bob Parker, BIAR Statistician DXC Technology Georgia Medicaid 100 Crescent Center Pkwy Tucker, GA 30084 Tel: +1 678 713-3774

From: Rex Sumsion [mailto:notifications@github.com] Sent: Thursday, November 29, 2018 11:36 AM To: HealthCatalyst/healthcareai-r healthcareai-r@noreply.github.com Cc: Parker, Bobby Ing bobby.ing.parker@dxc.com; Mention mention@noreply.github.com Subject: Re: [HealthCatalyst/healthcareai-r] Unable to execute machine_learn (#1278)

@BobParker18https://github.com/BobParker18, did you load healthcareai in your reprex example?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/HealthCatalyst/healthcareai-r/issues/1278#issuecomment-442901949, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ArJI0u7ZpocucY_dv8u6ShbBu5LjvwTZks5u0AzSgaJpZM4Y2COH.

[BobParker18]

Yes I loaded healthcareai before calling machine_learn() and then reprex(). Reprex() does not generate the same error message as that generated, without calling reprex.

Bob Parker, BIAR Statistician DXC Technology Georgia Medicaid 100 Crescent Center Pkwy Tucker, GA 30084 Tel: +1 678 713-3774

From: Rex Sumsion [mailto:notifications@github.com] Sent: Thursday, November 29, 2018 11:36 AM To: HealthCatalyst/healthcareai-r healthcareai-r@noreply.github.com Cc: Parker, Bobby Ing bobby.ing.parker@dxc.com; Mention mention@noreply.github.com Subject: Re: [HealthCatalyst/healthcareai-r] Unable to execute machine_learn (#1278)

@BobParker18https://github.com/BobParker18, did you load healthcareai in your reprex example?

— Y

[glenrs]

The reprex example above does not include loading healthcareai. Will you please paste the entire reprex example?

library(healthcareai)
#> healthcareai version 2.2.0
#> Please visit https://docs.healthcare.ai for full documentation and vignettes. Join the community at https://healthcare-ai.slack.com
models <- machine_learn(pima_diabetes, patient_id, outcome = diabetes)
#> Training new data prep recipe...
#> Variable(s) ignored in prep_data won't be used to tune models: patient_id
#> 
#> diabetes looks categorical, so training classification algorithms.
#> 
#> After data processing, models are being trained on 12 features with 768 observations.
#> Based on n_folds = 5 and hyperparameter settings, the following number of models will be trained: 50 rf's, 50 xgb's, and 100 glm's
#> Training with cross validation: Random Forest
#> Training with cross validation: eXtreme Gradient Boosting
#> Training with cross validation: glmnet
#> 
#> *** Models successfully trained. The model object contains the training data minus ignored ID columns. ***
#> *** If there was PHI in training data, normal PHI protocols apply to the model object. ***

Created on 2018-11-29 by the reprex package (v0.2.0).

[BobParker18]

Rex:

Maybe I am missing something here. The code I am running is:

library(healthcareai)

models <- machine_learn(pima_diabetes, patient_id, outcome = diabetes)

reprex()

What I sent is what reprex puts out as html.

Bob Parker, BIAR Statistician DXC Technology Georgia Medicaid 100 Crescent Center Pkwy Tucker, GA 30084 Tel: +1 678 713-3774

From: Rex Sumsion [mailto:notifications@github.com] Sent: Thursday, November 29, 2018 11:52 AM To: HealthCatalyst/healthcareai-r healthcareai-r@noreply.github.com Cc: Parker, Bobby Ing bobby.ing.parker@dxc.com; Mention mention@noreply.github.com Subject: Re: [HealthCatalyst/healthcareai-r] Unable to execute machine_learn (#1278)

The reprex example above does not include loading healthcareai. Will you please paste the entire reprex example?

library(healthcareai)

> healthcareai version 2.2.0

> Please visit https://docs.healthcare.ai for full documentation and vignettes. Join the community at https://healthcare-ai.slack.com

models <- machine_learn(pima_diabetes, patient_id, outcome = diabetes)

> Training new data prep recipe...

> Variable(s) ignored in prep_data won't be used to tune models: patient_id

>

> diabetes looks categorical, so training classification algorithms.

>

> After data processing, models are being trained on 12 features with 768 observations.

> Based on n_folds = 5 and hyperparameter settings, the following number of models will be trained: 50 rf's, 50 xgb's, and 100 glm's

> Training with cross validation: Random Forest

> Training with cross validation: eXtreme Gradient Boosting

> Training with cross validation: glmnet

>

> Models successfully trained. The model object contains the training data minus ignored ID columns.

> If there was PHI in training data, normal PHI protocols apply to the model object.

Created on 2018-11-29 by the reprex packagehttp://reprex.tidyverse.org (v0.2.0).

— -.

[glenrs]

@BobParker18 sorry for the slow reply. To use a reprex example you copy the code you would like to run to your clipboard and then run reprex::reprex() in your R console. reprex will reference your code in your clipboard. After it runs the output of reprex will now be attached to your clipboard where you can just paste the response. Is that your question?

Also, I found versions of packages that will help with your error. The following lines of code should help. Let me know if you have further issues.

library(versions)
install.versions("caret", "6.0-79")
remotes::install_github("HealthCatalyst/healthcareai-r@v2.2.0", force = TRUE)
devtools::install_version("recipes", version = "0.1.3")

[BobParker18]

Thanks Rex:

Applying your instructions provides the same output I sent earlier. I suspect some dependency is causing reprex() unable to produce that error message, a package you have installed which I do not have installed.

I will continue to work with it. I would also appreciate you directing me to the version of the healthcareai package and/or the recipe package I need to load.

Bob Parker, BIAR Statistician DXC Technology Georgia Medicaid 100 Crescent Center Pkwy Tucker, GA 30084 Tel: +1 678 713-3774

From: Rex Sumsion [mailto:notifications@github.com] Sent: Tuesday, December 04, 2018 12:32 PM To: HealthCatalyst/healthcareai-r healthcareai-r@noreply.github.com Cc: Parker, Bobby Ing bobby.ing.parker@dxc.com; Mention mention@noreply.github.com Subject: Re: [HealthCatalyst/healthcareai-r] Unable to execute machine_learn (#1278)

@BobParker18https://github.com/BobParker18 sorry for the slow reply. To use a reprex example you copy the code you would like to run to your clipboard and then run reprex::reprex() in your R console. reprex will reference your code in your clipboard. After it runs the output of reprex will now be attached to your clipboard where you can just paste the response. Is that your question?

Also, I found versions of packages that will help with your error.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/HealthCatalyst/healthcareai-r/issues/1278#issuecomment-444186723, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ArJI0udBCHctHM81gtdTljwBeG3__ouxks5u1rGngaJpZM4Y2COH.

DXC Technology Company - Headquarters: 1775 Tysons Boulevard, Tysons, Virginia 22102, USA. DXC Technology Company -- This message is transmitted to you by or on behalf of DXC Technology Company or one of its affiliates. It is intended exclusively for the addressee. The substance of this message, along with any attachments, may contain proprietary, confidential or privileged information or information that is otherwise legally exempt from disclosure. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient of this message, you are not authorized to read, print, retain, copy or disseminate any part of this message. If you have received this message in error, please destroy and delete all copies and notify the sender by return e-mail. Regardless of content, this e-mail shall not operate to bind DXC Technology Company or any of its affiliates to any order or other contract unless pursuant to explicit written agreement or government initiative expressly permitting the use of e-mail for such purpose. --.

[glenrs]

@BobParker18, the issue that you had was a dependency of the latest version of caret on the latest dependency of recipes. If you revert to these versions I have provided you should not have any issues.

We will have our version 2.3.0 release soon where we have updated our package for these dependencies.

[willgilks]

I had also issues with machine_learn() generating 'new data not recognised'. Running the version code for caret and recipes packages fixed this though, so thanks for putting this up.

Windows x64, R 3.5.1

[BobParker18]

Rex:

That has resolved the issue. Thanks.

Bob Parker, BIAR Statistician DXC Technology Georgia Medicaid 100 Crescent Center Pkwy Tucker, GA 30084 Tel: +1 678 713-3774

From: Rex Sumsion [mailto:notifications@github.com] Sent: Tuesday, December 04, 2018 4:20 PM To: HealthCatalyst/healthcareai-r healthcareai-r@noreply.github.com Cc: Parker, Bobby Ing bobby.ing.parker@dxc.com; Mention mention@noreply.github.com Subject: Re: [HealthCatalyst/healthcareai-r] Unable to execute machine_learn (#1278)

@BobParker18https://github.com/BobParker18, the issue that you had was a dependency of the latest version of caret on the latest dependency of recipes. If you revert to these versions I have provided you should not have any issues.

We will have our version 2.3.0 release soon where we have updated our package for these dependencies.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/HealthCatalyst/healthcareai-r/issues/1278#issuecomment-444262444, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ArJI0vNoNeyDeXeariA6vfuMT-ZuTP9Zks5u1ucIgaJpZM4Y2COH.

DXC Technology Company - Headquarters: 1775 Tysons Boulevard, Tysons, Virginia 22102, USA. DXC Technology Company -- This message is transmitted to you by or on behalf of DXC Technology Company or one of its affiliates. It is intended exclusively for the addressee. The substance of this message, along with any attachments, may contain proprietary, confidential or privileged information or information that is otherwise legally exempt from disclosure. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient of this message, you are not authorized to read, print, retain, copy or disseminate any part of this message. If you have received this message in error, please destroy and delete all copies and notify the sender by return e-mail. Regardless of content, this e-mail shall not operate to bind DXC Technology Company or any of its affiliates to any order or other contract unless pursuant to explicit written agreement or government initiative expressly permitting the use of e-mail for such purpose. --.

[glenrs]

@willgilks That is the error you will receive if you have updated caret and recipes. They released "breaking changes" in their latest release. If you revert to the versions above, you will no longer have issues.

We will have our version 2.3.0 release soon where we have updated our package for these dependencies.