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Bayesian Learning for Neural Networks
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Dataset worcester_100 not found in BLNN package #11

Open amir1m opened 3 years ago

amir1m commented 3 years ago

The vignette Survival_Modeling.Rmd" documentation says "worcester_100" is included in "BLNN" package. However while trying to run the vignette, the required dataset "worcester_100" seems to be missing.

Am I missing something?

data(package = 'BLNN')
Data sets in package ‘BLNN’:

german (GermanCredit)
nbwiecha commented 2 years ago

Similarly, I receive the following error message when trying to install the package with vignettes. I'm not sure if I'm missing something but it seems not to be included.

Error: Failed to install 'BLNN' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: processing vignette 'Survival_Modeling.Rmd' failed with diagnostics: E> object 'worcester_100' not found E> --- failed re-building 'Survival_Modeling.Rmd' E> E> SUMMARY: processing the following files failed: E> 'Classification_Modeling.Rmd' 'Intro_to_BLNN.Rmd' E> 'Survival_Modeling.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

tsharaf commented 2 years ago

Please try installing with the vignette

Best,

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 4:12 PM, nbwiecha @.***> wrote:



Similarly, I receive the following error message when trying to install the package. I'm not sure if I'm missing something but it seems not to be included.

Error: Failed to install 'BLNN' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: processing vignette 'Survival_Modeling.Rmd' failed with diagnostics: E> object 'worcester_100' not found E> --- failed re-building 'Survival_Modeling.Rmd' E> E> SUMMARY: processing the following files failed: E> 'Classification_Modeling.Rmd' 'Intro_to_BLNN.Rmd' E> 'Survival_Modeling.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

— Reply to this email directly, view it on GitHubhttps://github.com/BLNNdevs/BLNN/issues/11#issuecomment-1108993811, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AJMEWEVZ6DM2ES5ZX5AC37TVG34AZANCNFSM4R23IHGQ. You are receiving this because you are subscribed to this thread.Message ID: @.***>

nbwiecha commented 2 years ago

Hi Taysseer,

Thanks very much for your response. However, this error resulted from running the following code:

install_github("BLNNdevs/BLNN", build_vignettes = TRUE)

I was able to install the package using build_vignettes=FALSE. So I suppose I can copy and paste the raw code for the vignettes from the github repository, but I'm not able to install them into the package at the moment, and it seems like the data for the survival vignette may be missing. Sorry if I am missing something obvious.

Thanks, Nate

On Mon, Apr 25, 2022 at 6:04 PM Taysseer Sharaf @.***> wrote:

Please try installing with the vignette

Best,

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 4:12 PM, nbwiecha @.***> wrote:



Similarly, I receive the following error message when trying to install the package. I'm not sure if I'm missing something but it seems not to be included.

Error: Failed to install 'BLNN' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: processing vignette 'Survival_Modeling.Rmd' failed with diagnostics: E> object 'worcester_100' not found E> --- failed re-building 'Survival_Modeling.Rmd' E> E> SUMMARY: processing the following files failed: E> 'Classification_Modeling.Rmd' 'Intro_to_BLNN.Rmd' E> 'Survival_Modeling.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

— Reply to this email directly, view it on GitHub< https://github.com/BLNNdevs/BLNN/issues/11#issuecomment-1108993811>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AJMEWEVZ6DM2ES5ZX5AC37TVG34AZANCNFSM4R23IHGQ>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

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tsharaf commented 2 years ago

You would find the data inside the package. Type In console: BLNN::

Best

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 6:11 PM, nbwiecha @.***> wrote:



Hi Taysseer,

Thanks very much for your response. However, this error resulted from running the following code:

install_github("BLNNdevs/BLNN", build_vignettes = TRUE)

I was able to install the package using build_vignettes=FALSE. So I suppose I can copy and paste the raw code for the vignettes from the github repository, but I'm not able to install them into the package at the moment, and it seems like the data for the survival vignette may be missing. Sorry if I am missing something obvious.

Thanks, Nate

On Mon, Apr 25, 2022 at 6:04 PM Taysseer Sharaf @.***> wrote:

Please try installing with the vignette

Best,

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 4:12 PM, nbwiecha @.***> wrote:



Similarly, I receive the following error message when trying to install the package. I'm not sure if I'm missing something but it seems not to be included.

Error: Failed to install 'BLNN' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: processing vignette 'Survival_Modeling.Rmd' failed with diagnostics: E> object 'worcester_100' not found E> --- failed re-building 'Survival_Modeling.Rmd' E> E> SUMMARY: processing the following files failed: E> 'Classification_Modeling.Rmd' 'Intro_to_BLNN.Rmd' E> 'Survival_Modeling.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

— Reply to this email directly, view it on GitHub< https://github.com/BLNNdevs/BLNN/issues/11#issuecomment-1108993811>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AJMEWEVZ6DM2ES5ZX5AC37TVG34AZANCNFSM4R23IHGQ>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

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nbwiecha commented 2 years ago

Thank you again for your time. Using BLNN::worcester_100 returns an error. worcester_100 appears to be the name of the dataset referenced in the Survival_Modeling.Rmd vignette. The first line of that vignette, where the data is read in, returns an error as the data is not found.

library(BLNN) library(nnet) SrvDat<-data.frame(scale(worcester_100$lenfol), scale(worcester_100$age), worcester_100$gender, scale(worcester_100$bmi))

Error in scale(worcester_100$lenfol) : object 'worcester_100' not found

Looking at the "data" folder on the github repository, the datasets included in the package appear to be GermanCredit.Rdata and PBC_surv.Rda. After loading the PBC_surv.Rda file, it does not appear to be the worcester_100 data used in the survival modeling vignette.

Thank you again, Nate

On Mon, Apr 25, 2022 at 6:22 PM Taysseer Sharaf @.***> wrote:

You would find the data inside the package. Type In console: BLNN::

Best

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 6:11 PM, nbwiecha @.***> wrote:



Hi Taysseer,

Thanks very much for your response. However, this error resulted from running the following code:

install_github("BLNNdevs/BLNN", build_vignettes = TRUE)

I was able to install the package using build_vignettes=FALSE. So I suppose I can copy and paste the raw code for the vignettes from the github repository, but I'm not able to install them into the package at the moment, and it seems like the data for the survival vignette may be missing. Sorry if I am missing something obvious.

Thanks, Nate

On Mon, Apr 25, 2022 at 6:04 PM Taysseer Sharaf @.***> wrote:

Please try installing with the vignette

Best,

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 4:12 PM, nbwiecha @.***> wrote:



Similarly, I receive the following error message when trying to install the package. I'm not sure if I'm missing something but it seems not to be included.

Error: Failed to install 'BLNN' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: processing vignette 'Survival_Modeling.Rmd' failed with diagnostics: E> object 'worcester_100' not found E> --- failed re-building 'Survival_Modeling.Rmd' E> E> SUMMARY: processing the following files failed: E> 'Classification_Modeling.Rmd' 'Intro_to_BLNN.Rmd' E> 'Survival_Modeling.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

— Reply to this email directly, view it on GitHub< https://github.com/BLNNdevs/BLNN/issues/11#issuecomment-1108993811>, or unsubscribe<

https://github.com/notifications/unsubscribe-auth/AJMEWEVZ6DM2ES5ZX5AC37TVG34AZANCNFSM4R23IHGQ>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

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nbwiecha commented 2 years ago

I am able to find the same dataset, although with different variable names, which allows me to follow the vignette, in the package survBootOutliers with the command get.whas.100.dataset(). So I guess it's not a huge issue, but I think the data is not included in BLNN which stops the package from being installed with vignettes. But I should be able to continue with the other source. Best, Nate

On Mon, Apr 25, 2022 at 6:34 PM Nate Wiecha @.***> wrote:

Thank you again for your time. Using BLNN::worcester_100 returns an error. worcester_100 appears to be the name of the dataset referenced in the Survival_Modeling.Rmd vignette. The first line of that vignette, where the data is read in, returns an error as the data is not found.

library(BLNN) library(nnet) SrvDat<-data.frame(scale(worcester_100$lenfol), scale(worcester_100$age), worcester_100$gender, scale(worcester_100$bmi))

Error in scale(worcester_100$lenfol) : object 'worcester_100' not found

Looking at the "data" folder on the github repository, the datasets included in the package appear to be GermanCredit.Rdata and PBC_surv.Rda. After loading the PBC_surv.Rda file, it does not appear to be the worcester_100 data used in the survival modeling vignette.

Thank you again, Nate

On Mon, Apr 25, 2022 at 6:22 PM Taysseer Sharaf @.***> wrote:

You would find the data inside the package. Type In console: BLNN::

Best

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 6:11 PM, nbwiecha @.***> wrote:



Hi Taysseer,

Thanks very much for your response. However, this error resulted from running the following code:

install_github("BLNNdevs/BLNN", build_vignettes = TRUE)

I was able to install the package using build_vignettes=FALSE. So I suppose I can copy and paste the raw code for the vignettes from the github repository, but I'm not able to install them into the package at the moment, and it seems like the data for the survival vignette may be missing. Sorry if I am missing something obvious.

Thanks, Nate

On Mon, Apr 25, 2022 at 6:04 PM Taysseer Sharaf @.***> wrote:

Please try installing with the vignette

Best,

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 4:12 PM, nbwiecha @.***> wrote:



Similarly, I receive the following error message when trying to install the package. I'm not sure if I'm missing something but it seems not to be included.

Error: Failed to install 'BLNN' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: processing vignette 'Survival_Modeling.Rmd' failed with diagnostics: E> object 'worcester_100' not found E> --- failed re-building 'Survival_Modeling.Rmd' E> E> SUMMARY: processing the following files failed: E> 'Classification_Modeling.Rmd' 'Intro_to_BLNN.Rmd' E> 'Survival_Modeling.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

— Reply to this email directly, view it on GitHub< https://github.com/BLNNdevs/BLNN/issues/11#issuecomment-1108993811>, or unsubscribe<

https://github.com/notifications/unsubscribe-auth/AJMEWEVZ6DM2ES5ZX5AC37TVG34AZANCNFSM4R23IHGQ>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

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tsharaf commented 2 years ago

Thanks

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 6:55 PM, nbwiecha @.***> wrote:



I am able to find the same dataset, although with different variable names, which allows me to follow the vignette, in the package survBootOutliers with the command get.whas.100.dataset(). So I guess it's not a huge issue, but I think the data is not included in BLNN which stops the package from being installed with vignettes. But I should be able to continue with the other source. Best, Nate

On Mon, Apr 25, 2022 at 6:34 PM Nate Wiecha @.***> wrote:

Thank you again for your time. Using BLNN::worcester_100 returns an error. worcester_100 appears to be the name of the dataset referenced in the Survival_Modeling.Rmd vignette. The first line of that vignette, where the data is read in, returns an error as the data is not found.

library(BLNN) library(nnet) SrvDat<-data.frame(scale(worcester_100$lenfol), scale(worcester_100$age), worcester_100$gender, scale(worcester_100$bmi))

Error in scale(worcester_100$lenfol) : object 'worcester_100' not found

Looking at the "data" folder on the github repository, the datasets included in the package appear to be GermanCredit.Rdata and PBC_surv.Rda. After loading the PBC_surv.Rda file, it does not appear to be the worcester_100 data used in the survival modeling vignette.

Thank you again, Nate

On Mon, Apr 25, 2022 at 6:22 PM Taysseer Sharaf @.***> wrote:

You would find the data inside the package. Type In console: BLNN::

Best

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 6:11 PM, nbwiecha @.***> wrote:



Hi Taysseer,

Thanks very much for your response. However, this error resulted from running the following code:

install_github("BLNNdevs/BLNN", build_vignettes = TRUE)

I was able to install the package using build_vignettes=FALSE. So I suppose I can copy and paste the raw code for the vignettes from the github repository, but I'm not able to install them into the package at the moment, and it seems like the data for the survival vignette may be missing. Sorry if I am missing something obvious.

Thanks, Nate

On Mon, Apr 25, 2022 at 6:04 PM Taysseer Sharaf @.***> wrote:

Please try installing with the vignette

Best,

Taysseer Sharaf, PhD Senior Data Scientist Guardian Industries

On Apr 25, 2022, at 4:12 PM, nbwiecha @.***> wrote:



Similarly, I receive the following error message when trying to install the package. I'm not sure if I'm missing something but it seems not to be included.

Error: Failed to install 'BLNN' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> Error: processing vignette 'Survival_Modeling.Rmd' failed with diagnostics: E> object 'worcester_100' not found E> --- failed re-building 'Survival_Modeling.Rmd' E> E> SUMMARY: processing the following files failed: E> 'Classification_Modeling.Rmd' 'Intro_to_BLNN.Rmd' E> 'Survival_Modeling.Rmd' E> E> Error: Vignette re-building failed. E> Execution halted

— Reply to this email directly, view it on GitHub< https://github.com/BLNNdevs/BLNN/issues/11#issuecomment-1108993811>, or unsubscribe<

https://github.com/notifications/unsubscribe-auth/AJMEWEVZ6DM2ES5ZX5AC37TVG34AZANCNFSM4R23IHGQ>.

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