auto-check for binary tree

[bobthacker]

the most common manipulation I need to do to get aRbor to read a tree is to make the tree binary.

Can we add a check when we read trees into any easy mode app:

is.binary.tree(phy) - if it returns FALSE, then do phy<-multi2di(phy)

check again

is.binary.tree(phy) - if it returns TRUE, continue; if FALSE, need to print an error that Arbor could not generate a binary tree.

[jeffbaumes]

We could add this to:

• the conversion to ape tree. We should do this only if we always want binary trees in all of Arbor.
• inside each analysis that needs it. This seems a quick-and-dirty approach that will not be too labor-intensive to do.
• as a separate analysis, and have easy mode apps run a small workflow instead of a single step. I like this best.

Any thoughts from others on the path forward here?

[curtislisle]

I agree with the separate analysis idea outside of tree reading. It does let us start to re-use analyses more than having each easy mode app with its own analysis infrastructure. There will be cases where we want to be able to preserve polytomies (more than 2 children) for some phylogenetic analyses, so this is why I don’t want to force all trees to binary.

I also prefer doing polygamy analysis at the “Upper Arbor” (UI & romanesco) level, instead of adding too much easy-mode specific logic into aRbor.

On Mar 2, 2015, at 9:19 AM, Jeffrey Baumes notifications@github.com wrote:

We could add this to:

the conversion to ape tree. We should do this only if we always want binary trees in all of Arbor. inside each analysis that needs it. This seems a quick-and-dirty approach that will not be too labor-intensive to do. as a separate analysis, and have easy mode apps run a small workflow instead of a single step. I like this best. Any thoughts from others on the path forward here?

— Reply to this email directly or view it on GitHub https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76718707.

[lukejharmon]

I agree with Curt - make it a little mini-step. And I think there are some advantages to allowing easy-mode to run whole workflows! Maybe it already can.

Curt good luck with your polygamy analyses! :)

On Mar 2, 2015, at 6:31 AM, Jeffrey Baumes notifications@github.com<mailto:notifications@github.com> wrote:

I agree with the separate analysis idea outside of tree reading. It does let us start to re-use analyses more than having each easy mode app with its own analysis infrastructure. There will be cases where we want to be able to preserve polytomies (more than 2 children) for some phylogenetic analyses, so this is why I don’t want to force all trees to binary.

I also prefer doing polygamy analysis at the “Upper Arbor” (UI & romanesco) level, instead of adding too much easy-mode specific logic into aRbor.

On Mar 2, 2015, at 9:19 AM, Jeffrey Baumes notifications@github.com<mailto:notifications@github.com> wrote:

We could add this to:

the conversion to ape tree. We should do this only if we always want binary trees in all of Arbor. inside each analysis that needs it. This seems a quick-and-dirty approach that will not be too labor-intensive to do. as a separate analysis, and have easy mode apps run a small workflow instead of a single step. I like this best. Any thoughts from others on the path forward here?

— Reply to this email directly or view it on GitHub https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76718707.

— Reply to this email directly or view it on GitHubhttps://github.com/arborworkflows/aRbor/issues/37#issuecomment-76720827.

[bobthacker]

We don't need for force this for all analyses, but I do think for the current easy mode analyses, we do need to force binary and collapse.singletons. Those are the single two biggest errors for all of the students and Biospherians.

On Mon, Mar 2, 2015 at 10:27 AM, Luke Harmon notifications@github.com wrote:

I agree with Curt - make it a little mini-step. And I think there are some advantages to allowing easy-mode to run whole workflows! Maybe it already can.

Curt good luck with your polygamy analyses! :)

On Mar 2, 2015, at 6:31 AM, Jeffrey Baumes <notifications@github.com mailto:notifications@github.com> wrote:

I agree with the separate analysis idea outside of tree reading. It does let us start to re-use analyses more than having each easy mode app with its own analysis infrastructure. There will be cases where we want to be able to preserve polytomies (more than 2 children) for some phylogenetic analyses, so this is why I don’t want to force all trees to binary.

I also prefer doing polygamy analysis at the “Upper Arbor” (UI & romanesco) level, instead of adding too much easy-mode specific logic into aRbor.

On Mar 2, 2015, at 9:19 AM, Jeffrey Baumes <notifications@github.com mailto:notifications@github.com> wrote:

We could add this to:

the conversion to ape tree. We should do this only if we always want binary trees in all of Arbor. inside each analysis that needs it. This seems a quick-and-dirty approach that will not be too labor-intensive to do. as a separate analysis, and have easy mode apps run a small workflow instead of a single step. I like this best. Any thoughts from others on the path forward here?

— Reply to this email directly or view it on GitHub < https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76718707>.

— Reply to this email directly or view it on GitHub< https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76720827>.

— Reply to this email directly or view it on GitHub https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76744112.

Robert W. Thacker, PhD Professor Department of Biology University of Alabama at Birmingham 464 Campbell Hall 1300 University Boulevard Birmingham, AL 35294-1170 voice: 205-934-9685 fax: 205-975-6097 email: thacker@uab.edu http://www.uab.edu/cas/biology/thacker http://www.uab.edu/biology/thacker http://www.portol.org

[curtislisle]

The current easy mode architecture could be easily retargeted to run a two step workflow, which forces the binary tree then runs ancestral states / phylosignal. I vote this is the best thing to do in the short-term. All we do is make a workflow through advanced mode and change the easy mode code to call the workflow instead of directly calling the second step alone.

On Mar 2, 2015, at 11:31 AM, bobthacker notifications@github.com wrote:

We don't need for force this for all analyses, but I do think for the current easy mode analyses, we do need to force binary and collapse.singletons. Those are the single two biggest errors for all of the students and Biospherians.

On Mon, Mar 2, 2015 at 10:27 AM, Luke Harmon notifications@github.com wrote:

I agree with Curt - make it a little mini-step. And I think there are some advantages to allowing easy-mode to run whole workflows! Maybe it already can.

Curt good luck with your polygamy analyses! :)

On Mar 2, 2015, at 6:31 AM, Jeffrey Baumes <notifications@github.com mailto:notifications@github.com> wrote:

I agree with the separate analysis idea outside of tree reading. It does let us start to re-use analyses more than having each easy mode app with its own analysis infrastructure. There will be cases where we want to be able to preserve polytomies (more than 2 children) for some phylogenetic analyses, so this is why I don’t want to force all trees to binary.

I also prefer doing polygamy analysis at the “Upper Arbor” (UI & romanesco) level, instead of adding too much easy-mode specific logic into aRbor.

On Mar 2, 2015, at 9:19 AM, Jeffrey Baumes <notifications@github.com mailto:notifications@github.com> wrote:

We could add this to:

the conversion to ape tree. We should do this only if we always want binary trees in all of Arbor. inside each analysis that needs it. This seems a quick-and-dirty approach that will not be too labor-intensive to do. as a separate analysis, and have easy mode apps run a small workflow instead of a single step. I like this best. Any thoughts from others on the path forward here?

— Reply to this email directly or view it on GitHub < https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76718707>.

— Reply to this email directly or view it on GitHub< https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76720827>.

— Reply to this email directly or view it on GitHub https://github.com/arborworkflows/aRbor/issues/37#issuecomment-76744112.

Robert W. Thacker, PhD Professor Department of Biology University of Alabama at Birmingham 464 Campbell Hall 1300 University Boulevard Birmingham, AL 35294-1170 voice: 205-934-9685 fax: 205-975-6097 email: thacker@uab.edu http://www.uab.edu/cas/biology/thacker http://www.uab.edu/biology/thacker http://www.portol.org — Reply to this email directly or view it on GitHub.

[jeffbaumes]

Indeed @curtislisle, easy mode should be able to handle running a workflow. In OO terms, a workflow "is a" analysis and is referenced the same way, so no additional logic is needed in the easy mode apps.