Use of global variables

[FrankD]

We currently use global variables ("<<-" assignment) to avoid having to recompute variables that are used at multiple points in the code. This is bad practice, and CRAN does not accept packages that change the global environment of the user. We need to rewrite the code to remove the use of global variables.

[FrankD]

PS: Once this issue is resolved we can in principle submit to CRAN, although I would also like to write a short vignette to show how to use the package.

[FrankD]

I have updated the code to remove the global variables, and replace them with variables that are passed around as part of auxVars. The package now passes all CRAN checks, and in principle we could submit it. However, as mentioned above, I would like to write a short vignette to show people how to use it; this should not take too long.

[BennMacdonald]

That is brilliant, Frank! Glad we are getting close to submitting. I am happy to wait off for the vignette. What kind of thing did you have in mind to include?

[BennMacdonald]

Hi Frank,

I am going to start writing the vignette today. What kind of thing did you have in mind for it? Something including:

· A synopsis of what the function agm.R does

· What adaptive gradient matching is

· The difference between tempering of mismatch parameter and inferring

· A worked example of the function

Anything else you were thinking of?

Regards, Dr Benn Macdonald

Biometrika Fellow University of Glasgow School of Mathematics and Statistics Room 225 G12 8SQ

From: FrankD [mailto:notifications@github.com] Sent: 21 June 2017 15:35 To: BennMacdonald/AGM_RPackage Cc: Subscribed Subject: Re: [BennMacdonald/AGM_RPackage] Use of global variables (#11)

I have updated the code to remove the global variables, and replace them with variables that are passed around as part of auxVars. The package now passes all CRAN checks, and in principle we could submit it. However, as mentioned above, I would like to write a short vignette to show people how to use it; this should not take too long.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/BennMacdonald/AGM_RPackage/issues/11#issuecomment-310098274, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AZQZ2Zjp298Z5EY0sVIxUKQR6TVOOwIgks5sGSoWgaJpZM4N7G__.

[FrankD]

Hi Benn,

If you look at the latest commits, you'll see I've already started on the vignette, but please go ahead and develop it further since I won't have much more time this week to work on it.

In particular, it would be good if you could write something describing the tempering scheme, and an example of how to use it.

Let me know if you encounter any issues!

Regards,

Frank

On 27 June 2017 at 10:49, BennMacdonald notifications@github.com wrote:

Hi Frank,

I am going to start writing the vignette today. What kind of thing did you have in mind for it? Something including:

· A synopsis of what the function agm.R does

· What adaptive gradient matching is

· The difference between tempering of mismatch parameter and inferring

· A worked example of the function

Anything else you were thinking of?

Regards, Dr Benn Macdonald

Biometrika Fellow University of Glasgow School of Mathematics and Statistics Room 225 G12 8SQ

From: FrankD [mailto:notifications@github.com] Sent: 21 June 2017 15:35 To: BennMacdonald/AGM_RPackage Cc: Subscribed Subject: Re: [BennMacdonald/AGM_RPackage] Use of global variables (#11)

I have updated the code to remove the global variables, and replace them with variables that are passed around as part of auxVars. The package now passes all CRAN checks, and in principle we could submit it. However, as mentioned above, I would like to write a short vignette to show people how to use it; this should not take too long.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ BennMacdonald/AGM_RPackage/issues/11#issuecomment-310098274, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ AZQZ2Zjp298Z5EY0sVIxUKQR6TVOOwIgks5sGSoWgaJpZM4N7G__.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/BennMacdonald/AGM_RPackage/issues/11#issuecomment-311309749, or mute the thread https://github.com/notifications/unsubscribe-auth/AAAstmywODiX_gU67aIxoqSelxkc6BRmks5sINAogaJpZM4N7G__ .

[BennMacdonald]

Thanks, Frank. I will do just that.

Regards, Dr Benn Macdonald

Biometrika Fellow University of Glasgow School of Mathematics and Statistics Room 225 G12 8SQ

From: FrankD [mailto:notifications@github.com] Sent: 27 June 2017 11:03 To: BennMacdonald/AGM_RPackage Cc: Benn Macdonald; Comment Subject: Re: [BennMacdonald/AGM_RPackage] Use of global variables (#11)

Hi Benn,

If you look at the latest commits, you'll see I've already started on the vignette, but please go ahead and develop it further since I won't have much more time this week to work on it.

In particular, it would be good if you could write something describing the tempering scheme, and an example of how to use it.

Let me know if you encounter any issues!

Regards,

Frank

On 27 June 2017 at 10:49, BennMacdonald notifications@github.com wrote:

Hi Frank,

I am going to start writing the vignette today. What kind of thing did you have in mind for it? Something including:

· A synopsis of what the function agm.R does

· What adaptive gradient matching is

· The difference between tempering of mismatch parameter and inferring

· A worked example of the function

Anything else you were thinking of?

Regards, Dr Benn Macdonald

Biometrika Fellow University of Glasgow School of Mathematics and Statistics Room 225 G12 8SQ

From: FrankD [mailto:notifications@github.com] Sent: 21 June 2017 15:35 To: BennMacdonald/AGM_RPackage Cc: Subscribed Subject: Re: [BennMacdonald/AGM_RPackage] Use of global variables (#11)

I have updated the code to remove the global variables, and replace them with variables that are passed around as part of auxVars. The package now passes all CRAN checks, and in principle we could submit it. However, as mentioned above, I would like to write a short vignette to show people how to use it; this should not take too long.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ BennMacdonald/AGM_RPackage/issues/11#issuecomment-310098274, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ AZQZ2Zjp298Z5EY0sVIxUKQR6TVOOwIgks5sGSoWgaJpZM4N7G__.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/BennMacdonald/AGM_RPackage/issues/11#issuecomment-311309749, or mute the thread https://github.com/notifications/unsubscribe-auth/AAAstmywODiX_gU67aIxoqSelxkc6BRmks5sINAogaJpZM4N7G__ .

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[BennMacdonald]

Just to be clear (poor wording) – “I will do just that” meant that I will do as you suggest below. I do not mean “that is the only thing I will do”

Regards, Dr Benn Macdonald

Biometrika Fellow University of Glasgow School of Mathematics and Statistics Room 225 G12 8SQ

From: FrankD [mailto:notifications@github.com] Sent: 27 June 2017 11:03 To: BennMacdonald/AGM_RPackage Cc: Benn Macdonald; Comment Subject: Re: [BennMacdonald/AGM_RPackage] Use of global variables (#11)

Hi Benn,

If you look at the latest commits, you'll see I've already started on the vignette, but please go ahead and develop it further since I won't have much more time this week to work on it.

In particular, it would be good if you could write something describing the tempering scheme, and an example of how to use it.

Let me know if you encounter any issues!

Regards,

Frank

On 27 June 2017 at 10:49, BennMacdonald notifications@github.com wrote:

Hi Frank,

I am going to start writing the vignette today. What kind of thing did you have in mind for it? Something including:

· A synopsis of what the function agm.R does

· What adaptive gradient matching is

· The difference between tempering of mismatch parameter and inferring

· A worked example of the function

Anything else you were thinking of?

Regards, Dr Benn Macdonald

Biometrika Fellow University of Glasgow School of Mathematics and Statistics Room 225 G12 8SQ

From: FrankD [mailto:notifications@github.com] Sent: 21 June 2017 15:35 To: BennMacdonald/AGM_RPackage Cc: Subscribed Subject: Re: [BennMacdonald/AGM_RPackage] Use of global variables (#11)

I have updated the code to remove the global variables, and replace them with variables that are passed around as part of auxVars. The package now passes all CRAN checks, and in principle we could submit it. However, as mentioned above, I would like to write a short vignette to show people how to use it; this should not take too long.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ BennMacdonald/AGM_RPackage/issues/11#issuecomment-310098274, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ AZQZ2Zjp298Z5EY0sVIxUKQR6TVOOwIgks5sGSoWgaJpZM4N7G__.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/BennMacdonald/AGM_RPackage/issues/11#issuecomment-311309749, or mute the thread https://github.com/notifications/unsubscribe-auth/AAAstmywODiX_gU67aIxoqSelxkc6BRmks5sINAogaJpZM4N7G__ .

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/BennMacdonald/AGM_RPackage/issues/11#issuecomment-311312999, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AZQZ2d3BoMIrvel_ffL0ClCXWVV8zSjgks5sINNYgaJpZM4N7G__.