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khabbazian / l1ou

Detection of evolutionary shifts in Ornstein-Uhlenbeck models
GNU General Public License v2.0
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I have made more changes for shift.means and I have added some examples in the documentation. #15

Closed yuqing19118 closed 7 years ago

khabbazian commented 7 years ago

Thank you.

khabbazian commented 7 years ago

I use R CMD check. It runs all the examples. It doesn't catch logical bugs of course.

From: C?cile An? notifications@github.com Sent: Friday, October 28, 2016 5:32:02 PM To: khabbazian/l1ou Cc: Mohammad KHABBAZIAN; State change Subject: Re: [khabbazian/l1ou] I have made more changes for shift.means and I have added some examples in the documentation. (#15)

@cecileane commented on this pull request.

In R/shift_configuration.Rhttps://github.com/khabbazian/l1ou/pull/15:

@@ -27,7 +27,8 @@

' \item{Y}{input trait vector/matrix.}

' \item{tree}{input tree.}

' \item{shift.configuration}{estimated shift positions, i.e. vector of indices of edges where the estimated shifts occur.}

-#' \item{shift.values}{estimates of the shift values.}

This change might also clash with what the plotting function assumes. Mohammad: do you have automatic tests? If you did, it would be great to show Sabrina how to run them, so she could test if any of her changes breaks anything that was working before.

You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/khabbazian/l1ou/pull/15, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AH3bi1-CuZH2SVL-xP1Fwl2hE1KMcGSXks5q4mnSgaJpZM4KjARf.

cecileane commented 7 years ago

I just checked, and the change to shift.optima would have caused errors in several functions inside the package, like convert_shifts2regions and the plotting function. So

There should be such examples. That's one great benefit of exporting functions and providing an example for each function. And R CMD check should be used!

There are ways to include examples for testing, not shown in the manual. There are also ways to show examples that are not run during testing, and other options too (examples are used for 3 types of things).

yuqing19118 commented 7 years ago

Professor Cecile, When I do check('1lou``), there is a warning message like below and also an error related to it. Warning message: The existing 'NAMESPACE' file was not generated by roxygen2, and will not be overwritten.

But when I used roxygen2, it would automatically change the NAMESPACE.

I will try to use R CMD check. Thanks

khabbazian commented 7 years ago

Hi Sabrina,

I attached the Makefile I use for checking and building the package.

It will useful.

Bests,

Mohammad

From: qing yu notifications@github.com Sent: Sunday, October 30, 2016 12:15:15 AM To: khabbazian/l1ou Cc: Mohammad KHABBAZIAN; State change Subject: Re: [khabbazian/l1ou] I have made more changes for shift.means and I have added some examples in the documentation. (#15)

Professor Cecile, When I do check('1lou``), there is a warning message like below and also an error related to it. Warning message: The existing 'NAMESPACE' file was not generated by roxygen2, and will not be overwritten.

But when I used roxygen2, it would automatically change the NAMESPACE.

I will try to use R CMD check. Thanks

You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/khabbazian/l1ou/pull/15#issuecomment-257131120, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AH3biyfz7s6dH3uqzghuv_8UN-U9KZ-Qks5q5BnTgaJpZM4KjARf.