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stephenslab / susieR

R package for "sum of single effects" regression.
https://stephenslab.github.io/susieR
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add examples for susie_trendfilter #68

Closed stephens999 closed 5 years ago

stephens999 commented 5 years ago

@KaiqianZhang can you add some simple examples to the documentation?

KaiqianZhang commented 5 years ago

sure!

On Mon, Oct 29, 2018 at 10:36 AM stephens999 notifications@github.com wrote:

@KaiqianZhang https://github.com/KaiqianZhang can you add some simple examples to the documentation?

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gaow commented 5 years ago

I think this is done?

https://github.com/stephenslab/susieR/blob/dc42e47ea5dd26c28a7be94ee2dc1dab8976eeae/R/susie_trendfilter.R#L7

I actually have updated the vignette to use the new interface, while reviewing the trendfiltering code. But @stephens999 are you referring to additional examples?

stephens999 commented 5 years ago

no this was it. maybe we could add something like plot(y) lines(true_mean,col=1) lines(predict(fit),col=2) or similar to the first example to illustrate that one uses predict to obtain the fitted values?

On Tue, Oct 30, 2018 at 7:32 PM gaow notifications@github.com wrote:

I think this is done?

https://github.com/stephenslab/susieR/blob/dc42e47ea5dd26c28a7be94ee2dc1dab8976eeae/R/susie_trendfilter.R#L7

I actually have updated the vignette https://github.com/stephenslab/susieR/blob/master/vignettes/trend_filtering.Rmd to use the new interface, while reviewing the trendfiltering code. But @stephens999 https://github.com/stephens999 are you referring to additional examples?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stephenslab/susieR/issues/68#issuecomment-434519547, or mute the thread https://github.com/notifications/unsubscribe-auth/ABt4xb_mUj2JcNzxBrHYah8OBO7WtVLCks5uqO-hgaJpZM4X_cVx .

KaiqianZhang commented 5 years ago

Do you mean add these plot() to documentation?

On Wed, Oct 31, 2018, 12:21 stephens999 <notifications@github.com wrote:

no this was it. maybe we could add something like plot(y) lines(true_mean,col=1) lines(predict(fit),col=2) or similar to the first example to illustrate that one uses predict to obtain the fitted values?

On Tue, Oct 30, 2018 at 7:32 PM gaow notifications@github.com wrote:

I think this is done?

https://github.com/stephenslab/susieR/blob/dc42e47ea5dd26c28a7be94ee2dc1dab8976eeae/R/susie_trendfilter.R#L7

I actually have updated the vignette < https://github.com/stephenslab/susieR/blob/master/vignettes/trend_filtering.Rmd

to use the new interface, while reviewing the trendfiltering code. But @stephens999 https://github.com/stephens999 are you referring to additional examples?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/stephenslab/susieR/issues/68#issuecomment-434519547 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ABt4xb_mUj2JcNzxBrHYah8OBO7WtVLCks5uqO-hgaJpZM4X_cVx

.

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stephens999 commented 5 years ago

i mean to the example in @examples

On Wed, Oct 31, 2018 at 12:45 PM KaiqianZhang notifications@github.com wrote:

Do you mean add these plot() to documentation?

On Wed, Oct 31, 2018, 12:21 stephens999 <notifications@github.com wrote:

no this was it. maybe we could add something like plot(y) lines(true_mean,col=1) lines(predict(fit),col=2) or similar to the first example to illustrate that one uses predict to obtain the fitted values?

On Tue, Oct 30, 2018 at 7:32 PM gaow notifications@github.com wrote:

I think this is done?

https://github.com/stephenslab/susieR/blob/dc42e47ea5dd26c28a7be94ee2dc1dab8976eeae/R/susie_trendfilter.R#L7

I actually have updated the vignette <

https://github.com/stephenslab/susieR/blob/master/vignettes/trend_filtering.Rmd

to use the new interface, while reviewing the trendfiltering code. But @stephens999 https://github.com/stephens999 are you referring to additional examples?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/stephenslab/susieR/issues/68#issuecomment-434519547 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/ABt4xb_mUj2JcNzxBrHYah8OBO7WtVLCks5uqO-hgaJpZM4X_cVx

.

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.

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KaiqianZhang commented 5 years ago

Sure! I just added it in the trendfiltering branch. You can see it from the pull request.

On Wed, Oct 31, 2018, 13:08 stephens999 <notifications@github.com wrote:

i mean to the example in @examples

On Wed, Oct 31, 2018 at 12:45 PM KaiqianZhang notifications@github.com wrote:

Do you mean add these plot() to documentation?

On Wed, Oct 31, 2018, 12:21 stephens999 <notifications@github.com wrote:

no this was it. maybe we could add something like plot(y) lines(true_mean,col=1) lines(predict(fit),col=2) or similar to the first example to illustrate that one uses predict to obtain the fitted values?

On Tue, Oct 30, 2018 at 7:32 PM gaow notifications@github.com wrote:

I think this is done?

https://github.com/stephenslab/susieR/blob/dc42e47ea5dd26c28a7be94ee2dc1dab8976eeae/R/susie_trendfilter.R#L7

I actually have updated the vignette <

https://github.com/stephenslab/susieR/blob/master/vignettes/trend_filtering.Rmd

to use the new interface, while reviewing the trendfiltering code. But @stephens999 https://github.com/stephens999 are you referring to additional examples?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/stephenslab/susieR/issues/68#issuecomment-434519547 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/ABt4xb_mUj2JcNzxBrHYah8OBO7WtVLCks5uqO-hgaJpZM4X_cVx

.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/stephenslab/susieR/issues/68#issuecomment-434770891 , or mute the thread <

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.

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