Comments (140)
LGTM! Pending editorial input on the license (my personal take on the best compromise solution is above in the discussion related to adding a LICENSE.md
file) and the version being updated to 1.0.0
I think this is ready to go. Nice work @wrightaprilm!
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"This course is a 30-day paleobiological data" - there's a typo here
shinyapps.io limits you to 25 hours / month - if you have more than 50 undergrads using this app for class I forsee a problem that instructors should be aware of before attempting to use the app to teach
Remind users how to install ggtree in the readme (it's a bioconductor package not cran)
need to fix link to instructor's guide in readme
typo in Parsimony Questions (01-treesiftr.pdf) q3
Reorder questions to group LOs
Need to tell students to uncheck "show parsimony score" after q1
q2 is difficult and confusing - I was looking for a monophyletic clade of a genus, which isn't the case and leaves me asking questions about what the data are telling me. I also have a hard time switching back and forth between the two trees and remember what was where.
Now you can add a question about parsimony scores on random trees and students can see reversals / repeat substitutions for a suboptimal tree
Are q1 and q3 essentially the same question? Does this serve a purpose? If the goal is to see a sub that happens in two different parts of the tree ask students about this.
q4 - prompt students to view the tree estimated from 8-10 first
q6 - I'm not sure what to do here. Do you need to prompt students to look at several different datasets that have the same parsimony score? Do you mean characters or alignments?
q7 - Since you don't have branch lengths on the tree I'm not sure how students are supposed to know that changes are occurring on longer or shorter branches.
q9 - Technically the answer to this q is 0 so you might want to clarify that you're only using PI sites.
q10 - point students to a specific set of characters
I expect most users will want to teach with the app so maybe point toward that first and tell people not to worry about the code.
Hide the Rmd output for the libraries in the readme.
In the readme you assign two different things to sample_df
Maybe just show generating one tree in the readme - you jump straight to instructions for generating a batch of trees from a batch of datasets.
To get at @ethanwhite request for more clarity on the use of the module I suggest looking at the literature on tree-thinking, particularly concept inventories. This work would provide motivation for teachers to use a tool to address specific thought processes that students find challenging. You need to point out to potential users that students really struggle to understand certain concepts and this app provides a hands-on way for them to work on these concepts.
Also, do you picture this as a lab / recitation? homework? small class? large class? one question at a time during a lecture? I'm picturing this as a lab/recitation with a TA circulating to provide help, but curious what you're thinking.
Sorry this is a lot for a second round - the first time I was struggling with the interface so didn't look at the questions. I'm ok with the Shiny app now there is more guidance on what I'm looking at.
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I confirm my recommendation to publish. Very nice work @wrightaprilm!
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I also confirm. Go ahead and publish.
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All right, I zapped one of them. There's still a tiny bit of template breaking on the phylogeny.io citation, but I'm happy enough with it. I'd be fine to go ahead, then fix it later.
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Attempting PDF compilation. Reticulating splines etc...
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@ethanwhite, @rachelss β Thank you for agreeing to review this submission for JOSE! We are happy to welcome you to our adventure in scholarly publishing of open-source educational software and learning resources.
JOSE has published seven papers so far
Check our Reviewer Guidelines and let us know if you have any questions.
@juanklopper will be your handling editor: you're in good hands.
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@ethanwhite, @rachelss a big thank you from me too. I look forward to your input with this submission. Let me know if there are any questions. If I can't help then @labarba will most definitely have the answers.
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@juanklopper - @wrightaprilm and I are co-authors on a Data Carpentry lesson (http://doi.org/10.5281/zenodo.570050). There are a large number of authors and I don't believe that this interferes with my objectivity, but it was in the last 4 years. I am reporting this to you as requested in the CoI link for your input.
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Thanks for reporting this, @ethanwhite. I agree that this doesn't present conflict.
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OK, great. Thanks @labarba. I will proceed.
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A couple of questions/comments for @wrightaprilm from the "General checks" section:
License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
Following the R packaging standard the LICENSE
file does not include the actual license, only the year and copyright holder. The license is given in the DESCRIPTION
file. One common approach to dealing with the conflicts between R's packaging standard and the more general open source standard of having the full license in the LICENSE
file is to have the full license in LICENSE.md
(which is included in .Rbuildignore
) and keep LICENSE
in the standard R format. This is rOpenSci's general strategy. I'm not sure what JOSS or JOSE's general approach is to this issue.
Version: Does the release version given match the repository release (v1.0.0)?
The repository is lacking a current release. If you're waiting to tag 1.0.0
until other comments have been satisfied that makes sense and I'll wait until it looks like things are wrapping up and then ping this issue again about tagging a release.
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One common approach to dealing with the conflicts between R's packaging standard and the more general open source standard of having the full license in the LICENSE file is to have the full license in LICENSE.md (which is included in .Rbuildignore) and keep LICENSE in the standard R format. This is rOpenSci's general strategy. I'm not sure what JOSS or JOSE's general approach is to this issue.
This uncertainty is why the package is the way it is right now. I put the MIT license in the description, but wasn't sure where else that info needed to be, if anywhere.
The repository is lacking a current release. If you're waiting to tag 1.0.0 until other comments have been satisfied
Bingo!
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There are a couple of typos in paper.md - specifically [application]((https://wrightaprilm.shinyapps.io/treesiftr_app/) has an extra parenthesis in two places; the phrase "30-day paleobiological data " needs to be fixed, "non-paramtric" should be "non-parametric", "and use in " should be "which I use in". You might want to render with pandoc to check everything looks write prior to resubmission.
@juanklopper - I'd suggest that the submission requirements suggest submitters render paper.md with pandoc prior to submission in general as it's easier to proofread that way.
To install treesiftR I need ggtree. To install ggtree I need BiocManager. To install BiocManager I need R >= v3.5 . Alternatively I was able to install ggtree on my older version of R with older version of bioconductor with BiocInstaller::biocLite("ggtree"). I should probably keep everything up to date, and I realize listing dependencies is sufficient, but I bet I'm not the only one who doesn't update so including these extra instructions would help out.
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@rachelss β Our dear bot whedon
generates the PDF for us right here in this issue. Scroll up and you will see:
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@wrightaprilm I could use a bit more explanation in the Instructor's Guide and the Shiny app. Or maybe I missed a piece of documentation? I went straight to Guide and app.
After navigating to the app I am instructed to subset a phylogenetic matrix. Where did the matrix come from? Maybe you could explain the data a bit first. That would help understand when I'm setting start = 1 what that means. You might put similar text on the app itself for users.
The character matrix on the righthand side of the app is not intuitive. Some words in the app to explain what these blocks are would help. Also, just having the blocks on the right doesn't make it obvious that the root / internal nodes are one color or the other - can you put colors of ancestral states on the tree?
Is the ability to view the likelihood score useful? I can see the tree is less likely with more characters but really you want to compare likelihoods for a single dataset not across datasets, and students can't do that here. But maybe parsimony isn't sufficient to really explain phylogeny estimation - it would depend on the class.
How much can Shinyapps.io handle? How many students could be using the app simultaneously? How many students across the country could be using it in a class (ie if a bunch of classes start using this will the app no longer be available)? Just wondering if there will end up being limitations that will make this difficult to use widely. You might need to provide guidance for users to prevent the app from crashing.
@juanklopper - is this how we're supposed to write these reviews?
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Thanks, @rachelss, for these comments. I'll start working on them.
With re:
I'd suggest that the submission requirements suggest submitters render paper.md with pandoc prior to submission in general as it's easier to proofread that way.
I agree that this would be a useful addition to the author guidelines. I rendered in RStudio, which has its own idiosyncrasies. With a research paper submission, we normally think about grabbing the Latex template and rendering as you go, so that is a suggestion that would feel natural to people. Including a link to the template or preferred pandoc settings is something folks should have no real trouble with.
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@wrightaprilm I'm back from all my duties as external examiner and wanted to know how you are getting along. Big thanks to @rachelss Excellent insight and suggestions.
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I think we're good, thanks! Just waiting on @ethanwhite, in case there are conflicts between the two reviews.
Which is fine, I think we've all had some end-of-semester stuff going on that would make revising hard ;)
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Here's my review. Thanks for your patience and understanding @wrightaprilm. The end of the semester is indeed an... interesting time.
Overall, great work and really useful. I think this will be a great addition to a number of workshops and classrooms. For every checkbox that I haven't checked I've provided a description of what I think can be improved to make this ready to go.
General Checks
- License: The license file follows R's guidelines, but as a result the repository does not include an actual license.
- Version: The versions do not currently match because v1.0.0 does not currently exists. The author plans to release this version once the rest of the review is complete.
Documentation
- Usage: There are examples of how to use the module and questions that can be asked of students along with the answers. These are both very helpful. I think it would be useful in both the README and the Instructions guide to include some documentation designed to explain specifically how someone would adopt the module in a teaching setting. This is covered a bit in the JOSE paper and you get the idea that the learning material is lab exercise focused from the vignettes, but I'd suggest also putting some of those ideas front and center in the README and Instructors Guide so that folks more immediately understand the goals of the package and learing materials.
- I'd also suggest adding a pdf of the Instructors Guide and linking to it directly from the README so that it is easy to find and read for someone first encountering the package online.
- Community guildelines: There is a code of conduct (which is awesome!) but I didn't find information on how to contribute or seek support.
Pedagogy / Instructional design
- Learning Objectives: are a little difficult to determine from the current documentation. I understand that they are about helping students understand tree construction and phylogeny more broadly, but it would be helpful to lay this out a little more explicitly. I think a second short paragraph in the Introduction of the Instructors guide should be sufficient.
JOSE paper
- Use in classroom or other settings: I think just a couple of additional sentences describing how to adopt this material would make a big differences for helping make clear to readers exactly how they could use the material.
- Could someone else teach with this module: I think the module needs just a little more documentation. Once the changes described above are made I think this criteria will be satisfied.
- References: Lewis 2001 is missing the DOI: 10.1080/106351501753462876
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Great, thanks both. Doesn't look like there's too much conflict between these two reviews. So revisions should go like dominoes, eh?
@juanklopper - what do I have for timing here? Am I OK to come back with these notes addressed in January?
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Happy New Year, y'all.
I've responded to most of the points raised by reviewers. I'm still working on @rachelss's excellent suggestions about ancestral states + random trees, and should finish it tomorrow. I made the rest of the suggested edits, but made notes where I found suggestions confusing and/or wasn't sure how to resolve them within journal style.
Edit: Thanks much to all four of you; this has been really helpful!
Rachel's review:
I could use a bit more explanation in the Instructor's Guide and the Shiny app. Or maybe I missed a piece of documentation? I went straight to Guide and app.
After navigating to the app I am instructed to subset a phylogenetic matrix. Where did the matrix come from? Maybe you could explain the data a bit first. That would help understand when I'm setting start = 1 what that means. You might put similar text on the app itself for users.
I added some text to the instructor's guide, and added popify objects to the web interface to provide more information about the options, and a citation for the dataset.
The character matrix on the righthand side of the app is not intuitive. Some words in the app to explain what these blocks are would help. Also, just having the blocks on the right doesn't make it obvious that the root / internal nodes are one color or the other - can you put colors of ancestral states on the tree?
This is a fantastic idea. I'm still working on this, but the short answer should be yes.
Is the ability to view the likelihood score useful? I can see the tree is less likely with more characters but really you want to compare likelihoods for a single dataset not across datasets, and students can't do that here. But maybe parsimony isn't sufficient to really explain phylogeny estimation - it would depend on the class.
Ideally, you're correct. But I'm likely to add to this package later. We have a paper in the works on some alternative models of morphological evolution, and something that I'm likely to expand into in the future is adding more buttons to see how the assumptions made about the data change the likelihood score we compute for the data. The differences are large enough that they can be seen on a single character.
How much can Shinyapps.io handle? How many students could be using the app simultaneously? How many students across the country could be using it in a class (ie if a bunch of classes start using this will the app no longer be available)? Just wondering if there will end up being limitations that will make this difficult to use widely. You might need to provide guidance for users to prevent the app from crashing.
Thank you, added this info!
Ethan's:
License: The license file follows R's guidelines, but as a result the repository does not include an actual license.
Could I have some editor guidance on this one? I followed R conventions (LICENSE file + link in the DESCRIPTION to a license), but if there's something else required, I'm happy to provide it.
I'd also suggest adding a pdf of the Instructors Guide and linking to it directly from the README so that it is easy to find and read for someone first encountering the package online.
Good plan! Done.
Community guildelines: There is a code of conduct (which is awesome!) but I didn't find information on how to contribute or seek support.
Good catch - I put these in the .github folder, which I then forgot to commit and push. I moved the CONDUCT file in here, too, so it pops up when someone opens an issue or PR.
Question on this - rOpenSci allows you to put an email for the organization, if people need to report that a maintainer (i.e. me) is the problem on a code of conduct issue. Does JOSE have a similar email address? I didn't see one, but it's possible I did not look in the right place.
Learning Objectives: are a little difficult to determine from the current documentation. I understand that they are about helping students understand tree construction and phylogeny more broadly, but it would be helpful to lay this out a little more explicitly. I think a second short paragraph in the Introduction of the Instructors guide should be sufficient.
Good idea. I added a list of learning objectives to each subsection of the instructor guide, and which questions addressed each.
Usage: I think it would be useful in both the README and the Instructions guide to include some documentation designed to explain specifically how someone would adopt the module in a teaching setting. This is covered a bit in the JOSE paper and you get the idea that the learning material is lab exercise focused from the vignettes, but I'd suggest also putting some of those ideas front and center in the README and Instructors Guide so that folks more immediately understand the goals of the package and learing materials.
&
Use in classroom or other settings: I think just a couple of additional sentences describing how to adopt this material would make a big differences for helping make clear to readers exactly how they could use the material.
I'm not quite sure how to get at this differently than I have. I added one sentence on this at the end of the second paragraph of the statement of need, and one to the end of the introduction to the instructor's guide.
References: Lewis 2001 is missing the DOI: 10.1080/106351501753462876
Good catch.
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All right, I implemented Rachel's idea to generate random trees to show how traits score differently when phylogenetic relationships are not informative with respect to trait evolution.
With respect to the question of ancestral states: ggtree is developed quite separately from the rest of the phylogenetics R space. I think the appropriate way to handle this feature is to make a pull request against Phangorn to add an additional output type for their ancestral state estimation machinery. Would it be all right if I put this suggestion on a longer-term feature request timetable, as opposed to immediately for review? I'm happy to do it, but with involving additional developers on other projects, there is a lot out of my control on this.
Again, thanks all four of you.
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@whedon generate pdf
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Attempting PDF compilation. Reticulating splines etc...
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@wrightaprilm You have an extra paren that breaks the link in the beginning of the second paragraph.
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I looked. I'm sorry, but I do have more comments, just not right this second. I was trying to figure out exactly how to explain the challenges I would still have in teaching from the given instructions and material.
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@wrightaprilm and everyone involved, please accept my best wishes for a fantastic 2019. @rachelss, we eagerly await your comments.
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No need to apologize - these are all great notes. I'll try to get them turned around tomorrow!
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Sorry, I meant to get these in yesterday. This was really helpful feedback, @rachelss, and it's a cool feature of this review process to get notes from people who are both experts and potentially end users.
"This course is a 30-day paleobiological data" - there's a typo here
Fixed.
shinyapps.io limits you to 25 hours / month - if you have more than 50 undergrads using this app for class I forsee a problem that instructors should be aware of before attempting to use the app to teach
I'm actually on the "Basic" plan, which is 500 active hours a month. I'm not quite sure where to fit that information in.
Remind users how to install ggtree in the readme (it's a bioconductor package not cran)
Added, and noted which packages can be installed via CRAN and which cannot.
need to fix link to instructor's guide in readme
And the logo, apparently!
typo in Parsimony Questions (01-treesiftr.pdf) q3
I had fixed this, and forgotten to re-export. Fixed now.
Reorder questions to group LOs
Done.
Need to tell students to uncheck "show parsimony score" after q1
Done.
q2 is difficult and confusing - I was looking for a monophyletic clade of a genus, which isn't the case and leaves me asking questions about what the data are telling me. I also have a hard time switching back and forth between the two trees and remember what was where.
You are right - I switched this around to be more explicit about which characters to look at.
Now you can add a question about parsimony scores on random trees and students can see reversals / repeat substitutions for a suboptimal tree
Are q1 and q3 essentially the same question? Does this serve a purpose? If the goal is to see a sub that happens in two different parts of the tree ask students about this.
I Q3 over to be a random tree question, and also switched the position or 2 and 3 to match the LOs.
q4 - prompt students to view the tree estimated from 8-10 first
Done.
q6 - I'm not sure what to do here. Do you need to prompt students to look at several different datasets that have the same parsimony score? Do you mean characters or alignments?
Edited to make an explicit comparison between two character sets.
q7 - Since you don't have branch lengths on the tree I'm not sure how students are supposed to know that changes are occurring on longer or shorter branches.
Oh, this is a tricky one. I kind of relied on the visual cue of some branch lengths being longer. Perhaps I should add a scale bar?
q9 - Technically the answer to this q is 0 so you might want to clarify that you're only using PI sites.
Spot the paleontologist!
q10 - point students to a specific set of characters
Good idea, and I made some additional notes in the Instructor's Guide about why we get fully-resolved trees even when little/no data supports such.
I expect most users will want to teach with the app so maybe point toward that first and tell people not to worry about the code.
Great idea - I switched the order in both the README and the paper.
Hide the Rmd output for the libraries in the readme.
Done.
In the readme you assign two different things to sample_df
Good catch.
Maybe just show generating one tree in the readme - you jump straight to instructions for generating a batch of trees from a batch of datasets.
Good idea!
To get at @ethanwhite request for more clarity on the use of the module I suggest looking at the literature on tree-thinking, particularly concept inventories. This work would provide motivation for teachers to use a tool to address specific thought processes that students find challenging. You need to point out to potential users that students really struggle to understand certain concepts and this app provides a hands-on way for them to work on these concepts.
Good point - I added a paragraph to the statement of need in which I review some of the literature on this point and highlight the misconceptions treesiftr is meant to address.
Also, do you picture this as a lab / recitation? homework? small class? large class? one question at a time during a lecture? I'm picturing this as a lab/recitation with a TA circulating to provide help, but curious what you're thinking.
I think it works in a variety of contexts. For the analytical paleobiology workshop, it was only 12 students, so I just circulated. I did this as a homework in my genetics class, after having done a lab on Shiny for population genetics. Therefore, the students weren't naive with respect to how to operate a Shiny app. So my feeling is that if this is their first introduction to R, or to operating a Shiny app, it should probably be in a lab or similar.
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Thank you for your patience with my extensive review. I think it's good to go. I hope to get a chance to use the Shiny app with undergrads - I think it's a really useful tool and having a set of questions ready to go is very helpful. Well done!
fyi - Please rebuild the Instructor's Guide pdf.
also fyi - I'm picturing this done with learnr to combine questions and app with instant feedback, but that's for the future
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@rachelss β You have some unchecked items in the review checklist. Please check these off, when ready, and give me your recommendation to accept and publish, at that point.
@ethanwhite β You're missing the license checkmark. As for the version, after @wrightaprilm ups the version on the submission repository, for archival, we can use @whedon set vx.x.x as version
here, to match.
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@labarba - My license checkmark is missing due to what I think is the still unresolved issue related to the fact that CRAN's approach to licensing does not include having the license text itself in the repository. I've suggested a solution to this and @wrightaprilm was requested editorial guidance. If JOSE is OK with not including the actual license text anywhere in the repository then I'm happy to check the box.
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Thank you, @ethanwhite.
@wrightaprilm : Ethan said:
One common approach to dealing with the conflicts between R's packaging standard and the more general open source standard of having the full license in the
LICENSE
file is to have the full license inLICENSE.md
(which is included in.Rbuildignore
) and keepLICENSE
in the standard R format.
Could you do that?
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I checked off everything but license and version. Once those are resolved I think this should be published.
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-
[ x ] fyi - Please rebuild the Instructor's Guide pdf.
-
[ x ] also fyi - I'm picturing this done with learnr to combine questions and app with instant feedback, but that's for the future
Hadn't seen learnr - so cool!
-
[ x ] You have an extra paren that breaks the link in the beginning of the second paragraph.
-
[ x ] Added LICENSE.md - let me know if this is satisfactory. I'd also be happy to contribute lanugage to the author's guide for JOSE about reconciling CRAN-style licensing and JOSE's requirements, if that would be helpful.
-
[ x ] Version is now 1.0.0
Thanks to all four of you for all your help and comments. I really appreciate it, and I think the content delivery has improved a lot through this process.
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@ethanwhite, @rachelss β The author has addressed remaining items. Could you check off the list and confirm your recommendation to publish?
@juanklopper β When both reviewers recommend publication, next step will be for @wrightaprilm to create an archive in Zenodo and report the DOI here. You can then use @whedon set <doi> as archive
, and add the "accepted" label. I'll then publish!
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@wrightaprilm β Please now make an archive on Zenodo, and report the DOI here. Make sure to edit the metadata as needed to match the paper (title and authors), as Zenodo just grabs that info from the repo.
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Thanks @labarba. Will wait for the DOI.
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Thanks so much for all your help, everyone! I've never made a Zenodo before - is this right? I had to hand-edit some things, as a user who made a PR showed up as an author.
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Thanks @wrightaprilm. I see a DOI of 10.5281/zenodo.2541824 @labarba would you have a look if this is okay before I do the whedon command?
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It looks good to me!
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@whedon set 10.5281/zenodo.2541824 as archive
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OK. 10.5281/zenodo.2541824 is the archive.
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@whedon accept
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Attempting dry run of processing paper acceptance...
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from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
from jose-reviews.
Oops, forgot to push my updated .bib file. And because all my references in the vignettes and website build locally before pushing, this is the first step where that would be caught. I've pushed it now. Sorry all!
from jose-reviews.
@wrightaprilm okay, no problem, let's try this again.
from jose-reviews.
@whedon accept
from jose-reviews.
Attempting dry run of processing paper acceptance...
from jose-reviews.
PDF failed to compile for issue #35 with the following error:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 14 0 14 0 0 39 0 --:--:-- --:--:-- --:--:-- 39
pandoc-citeproc: reference sandvik not found
pandoc-citeproc: reference sandvik not found
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/bibtex.rb:44:in make_citation': undefined method
has_field?' for #<BibTeX::String an = "The American Naturalist"> (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/bibtex.rb:31:in block in generate_citations' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:in
each'
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generate_citations'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:214:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:91:in
compile'
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dispatch'
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from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
from jose-reviews.
@whedon generate pdf
from jose-reviews.
Attempting PDF compilation. Reticulating splines etc...
from jose-reviews.
from jose-reviews.
@whedon accept
from jose-reviews.
Attempting dry run of processing paper acceptance...
from jose-reviews.
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 14 0 14 0 0 19 0 --:--:-- --:--:-- --:--:-- 19
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/bibtex.rb:44:in make_citation': undefined method
has_field?' for #<BibTeX::String an = "The American Naturalist"> (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/bibtex.rb:31:in block in generate_citations' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:in
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generate_citations'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:214:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:91:in
compile'
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run'
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dispatch'
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from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
from jose-reviews.
Hmm ... I think we ran into a funky bug. @arfon β What could be going on? @whedon accept
fails, but @whedon generate pdf
does compile the paper.
from jose-reviews.
I think this is actually my issue. I use this bibtex on multiple multiple-author projects, and we include some string expansions for journals we cite from a bunch. I removed the translation block.
from jose-reviews.
@whedon accept
from jose-reviews.
Attempting dry run of processing paper acceptance...
from jose-reviews.
PDF failed to compile for issue #35 with the following error:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 14 0 14 0 0 46 0 --:--:-- --:--:-- --:--:-- 46
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:225:in ``': Argument list too long - cd tmp/35 && pandoc -V timestamp=20190116200213 -V doi_batch_id=858dbd49d7453083a43e92e3a1843090 -V formatted_doi=10.21105/jose.00035 -V archive_doi="https://doi.org/10.5281/zenodo.2541824" -V review_issue_url=#35 -V paper_url=http://www.theoj.org/openjournals/jose-papers/jose.00035/10.21105.jose.00035.pdf -V joss_resource_url=https://jose.theoj.org/papers/10.21105/jose.00035 -V journal_alias=jose -V journal_abbrev_title=JOSE -V journal_url=https://jose.theoj.org -V journal_name='Journal of Open Source Education' -V journal_issn=2577-3569 -V citations='<citation_list> (Errno::E2BIG)
<unstructured_citation>\textitKretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade, Abella, Juan and Alba, David M. and Robles, Josep M. and Valenciano, Alberto and Rotgers, Cheyenn and Carmona, RaΓΌl and Montoya, Plinio and Morales, Jorge, PLoS One, 2012, e48985, 17</unstructured_citation>
<unstructured_citation>Una nueva especie de \textitAgriarctos (Ailuropodinae, Ursidae, Carnivora) en la localidad de Nombrevilla 2 (Zaragoza, EspaΓ±a), Abella, J and Montoya, P and Morales, J, Estudios GeolΓ³gicos, 2011, 2, 187β191, 67</unstructured_citation>
10.1371/journal.pcbi.1003537
<unstructured_citation>The fossilized birth-death process for coherent calibration of divergence-time estimates, Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja, pnas, 2014, 29, E2957βE2966, 111, National Acad Sciences, 2015.05.31</unstructured_citation>
<unstructured_citation>PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Lartillot, N. and Lepage, T. and Blanquart, S., bi, 2009, 17, 2286, 25, Oxford Univ Press, 2011.07.11</unstructured_citation>
<unstructured_citation>APE: analyses of phylogenetics and evolution in R language, Paradis, E. and Claude, J. and Strimmer, K., bi, 2004, 2, 289β290, 20, Oxford Univ Press, 2012.09.26</unstructured_citation>
10.1093/bioinformatics/btu033
10.1111/j.2041-210X.2011.00169.x
<unstructured_citation>Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors, Wright, April M. and Lloyd, Graeme T. and Hillis, David M., sysbio, 2016, 4, 602-611, 65</unstructured_citation>
<unstructured_citation>Confidence limits on phylogenies: an approach using the bootstrap, Felsenstein, J., evolution, 1985, 4, 783β791, 39, shhn001, 2008.11.25</unstructured_citation>
<unstructured_citation>Numerical taxonomy, Sneath, P.H.A. and Sokal, R.R., Springer, 1973, shhn001, 2009.02.23</unstructured_citation>
<unstructured_citation>APE: analyses of phylogenetics and evolution in R language, Paradis, E. and Claude, J. and Strimmer, K., bi, 2004, 2, 289β290, 20, Oxford Univ Press, 2012.09.26</unstructured_citation>
10.1093/bioinformatics/btu033
10.1111/j.2041-210X.2011.00169.x
<unstructured_citation>\textitKretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade, Abella, Juan and Alba, David M. and Robles, Josep M. and Valenciano, Alberto and Rotgers, Cheyenn and Carmona, RaΓΌl and Montoya, Plinio and Morales, Jorge, PLoS One, 2012, e48985, 17</unstructured_citation>
<unstructured_citation>Una nueva especie de \textitAgriarctos (Ailuropodinae, Ursidae, Carnivora) en la localidad de Nombrevilla 2 (Zaragoza, EspaΓ±a), Abella, J and Montoya, P and Morales, J, Estudios GeolΓ³gicos, 2011, 2, 187β191, 67</unstructured_citation>
10.1073/pnas.1116871109
<unstructured_citation>On Small-Sample Confidence Intervals for Parameters in Discrete Distributions, Agresti, Alan and Min, Yongyi, Biometrics, 2001, 963β971, 57, The traditional definition of a confidence interval requires the coverage probability at any value of the parameter to be at least the nominal confidence level. In constructing such intervals for parameters in discrete distributions, less conservative behavior results from inverting a single two-sided test than inverting two separate one-sided tests of half the nominal level each. We illustrate for a variety of discrete problems, including interval estimation of a binomial parameter, the difference and the ratio of two binomial parameters for independent samples, and the odds ratio., Copyright οΏ½ 2001 International Biometric Society, 0006341X, primary_article, Sep., 2001, shhn001, International Biometric Society, 2008.12.04</unstructured_citation>
<unstructured_citation>Mathematical foundations for signal processing, communications, and networking, Ahmadi, Aitzaz and Serpedini, Erchin and Qaraqell, Khalid Az, 13. Factor Graphs and Message Passing Algorithms, Erchin Serpedini, Thomas Chen and Rajan, Dinesh, CRC Press, 2012, hoehna, 2013.12.03</unstructured_citation>
<unstructured_citation>Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions, Aho, AV and Sagiv, Y. and Szymanski, TG and Ullman, JD, SIAM Journal on Computing, 1981, 405, 10, shhn001, SIAM, 2008.09.17</unstructured_citation>
<unstructured_citation>Posterior bayes factors, Aitkin, Murray, Journal of the Royal Statistical Society. Series B (Methodological), 1991, 111β142, 53, hoehna, JSTOR, 2013.03.26</unstructured_citation>
<unstructured_citation>Information theory and an extension of the maximum likelihood principle, Akaike, Hirotogu, Selected Papers of Hirotugu Akaike, Springer, 1998, 199β213, hoehna, 2013.04.07</unstructured_citation>
<unstructured_citation>A new look at the statistical model identification, Akaike, Hirotugu, Automatic Control, IEEE Transactions on, 1974, 6, 716β723, 19, hoehna, Ieee, 2013.04.23</unstructured_citation>
<unstructured_citation>A critical branching process model for biodiversity, Aldous, D. and Popovic, L., Advances in applied probability, 2005, 4, 1094β1115, 37, hoehna, Applied Probability Trust, 2012.03.16</unstructured_citation>
<unstructured_citation>Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today, Aldous, David J, Statistical Science, 2001, 23β34, hoehna, JSTOR, 2015.08.25</unstructured_citation>
<unstructured_citation>Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates, Alfaro, M.E. and Santini, F. and Brock, C. and Alamillo, H. and Dornburg, A. and Rabosky, D.L. and Carnevale, G. and Harmon, L.J., pnas, 2009, 32, 13410β13414, 106, hoehna, National Acad Sciences, 2012.11.22</unstructured_citation>
<unstructured_citation>The posterior and the prior in Bayesian phylogenetics, Alfaro, Michael E. and Holder, Mark T., arees, 2006, 1, 19-42, 37, http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.37.091305.110021, hoehna, 2009.10.13</unstructured_citation>
<unstructured_citation>Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty, Alfaro, Michael E and Huelsenbeck, John P, sysbio, 2006, 1, 89β96, 55, hoehna, Oxford University Press, 2014.10.18</unstructured_citation>
<unstructured_citation>Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence, Alfaro, Michael E. and Zoller, Stefan and Lutzoni, F., mbe, 2003, 2, 255-266, 20, Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap., http://mbe.oxfordjournals.org/content/20/2/255.full.pdf+html, hoehna, 2011.09.15</unstructured_citation>
<unstructured_citation>Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005β2010: Potential for Molecular Surveillance of New Outbreaks, Alkhamis, Mohammad A and Moore, Brian R and Perez, AndrΓ©s M, Viruses, 2015, 6, 3310β3328, 7, hoehna, Multidisciplinary Digital Publishing Institute, 2015.08.13</unstructured_citation>
<unstructured_citation>Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees, Allen, B.L. and Steel, Mike, Annals of Combinatorics, 2001, 1, 1β15, 5, shhn001, Springer, 2008.12.01</unstructured_citation>
<unstructured_citation>Dynamics of origination and extinction in the marine fossil record, Alroy, John, pnas, 2008, Supplement 1, 11536β11542, 105, hoehna, National Acad Sciences, 2015.05.13</unstructured_citation>
<unstructured_citation>Copeβs rule and the dynamics of body mass evolution in North American fossil mammals, Alroy, John, Science, 1998, 5364, 731β734, 280, hoehna, American Association for the Advancement of Science, 2015.01.20</unstructured_citation>
<unstructured_citation>Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset, AlstrΓΆm, P. and HΓΆhna, S. and Gelang, M. and Ericson, P.G.P. and Olsson, U., bmcevobio, 2011, 1, 352, 11, hoehna, BioMed Central Ltd, 2011.07.12</unstructured_citation>
<unstructured_citation>Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference, Altekar, Gautam and Dwarkadas, Sandhya and Huelsenbeck, John P and Ronquist, Fredrik, bi, 2004, 3, 407β415, 20, hoehna, Oxford Univ Press, 2015.02.25</unstructured_citation>
<unstructured_citation>Adaptive evolution of non-coding DNA in Drosophila, Andolfatto, Peter, Nature, 2005, 7062, 1149β1152, 437, hoehna, Nature Publishing Group, 2013.08.11</unstructured_citation>
<unstructured_citation>New Miocene locality in Turkey with evidence on the origin of \textitRamapithecus and \textitSivapithecus, Andrews, P and Tobien, H, Nature, 1977, 5622, 699, 268</unstructured_citation>
<unstructured_citation>Accuracy and power of Bayes prediction of amino acid sites under positive selection, Anisimova, Maria and Bielawski, Joseph P and Yang, Ziheng, mbe, 2002, 6, 950β958, 19, hoehna, SMBE, 2013.08.10</unstructured_citation>
<unstructured_citation>Investigating protein-coding sequence evolution with probabilistic codon substitution models, Anisimova, Maria and Kosiol, Carolin, mbe, 2009, 2, 255β271, 26, hoehna, SMBE, 2013.08.10</unstructured_citation>
<unstructured_citation>Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites, Anisimova, Maria and Nielsen, Rasmus and Yang, Ziheng, genetics, 2003, 3, 1229β1236, 164, hoehna, Genetics Soc America, 2013.08.10</unstructured_citation>
<unstructured_citation>Mass extinction, gradual cooling, or rapid radiation? Reconstructing the spatiotemporal evolution of the ancient angiosperm genus Hedyosmum (Chloranthaceae) using empirical and simulated approaches, Antonelli, A. and SanmartΔ±Μn, I., sysbio, 2011, 5, 596β615, 60, hoehna, Oxford University Press, 2012.08.01</unstructured_citation>
<unstructured_citation>Dating phylogenies with hybrid local molecular clocks, Aris-Brosou, StΓ©phane, pone, 2007, 9, e879, 2, hoehna, Public Library of Science, 2014.06.05</unstructured_citation>
<unstructured_citation>Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa, Aris-Brosou, StΓ©phane and Yang, Ziheng, mbe, 2003, 12, 1947β1954, 20, hoehna, SMBE, 2013.03.26</unstructured_citation>
<unstructured_citation>Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny, Aris-Brosou, StΓ©phane and Yang, Ziheng, sysbio, 2002, 5, 703β714, 51, hoehna, Oxford University Press, 2014.01.16</unstructured_citation>
<unstructured_citation>Bayesian gene/species tree reconciliation and orthology analysis using MCMC, Arvestad, Lars and Berglund, Ann-Charlotte and Lagergren, Jens and Sennblad, Bengt, bi, 2003, suppl 1, i7βi15, 19, hoehna, Oxford Univ Press, 2015.05.19</unstructured_citation>
<unstructured_citation>BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics, Ayres, Daniel L and Darling, Aaron and Zwickl, Derrick J and Beerli, Peter and Holder, Mark T and Lewis, Paul O and Huelsenbeck, John P and Ronquist, Fredrik and Swofford, David L and Cummings, Michael P and Rambaut, Andrew and Suchard, Marc A, sysbio, 2012, 1, 170-173, 61, hoehna, Oxford University Press, 2014.11.29</unstructured_citation>
<unstructured_citation>Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions, Bader, D.A. and Roshan, U. and Stamatakis, A., ADVANCES IN COMPUTERS, 2006, 128, 68, shhn001, ACADEMIC PRESS, INC, 2008.11.06</unstructured_citation>
<unstructured_citation>Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency, Baele, Guy and Lemey, Philippe, bi, 2013, 16, 1970-1979, 29, hoehna, Oxford University Press, 2015.03.16</unstructured_citation>
<unstructured_citation>Improving the Accuracy of Demographic and Molecular Clock Model Comparison while Accommodating Phylogenetic Uncertainty, Baele, G. and Lemey, P. and Bedford, T. and Rambaut, A. and Suchard, M.A. and Alekseyenko, A.V., mbe, 2012, 9, 2157β2167, 29, hoehna, SMBE, 2013.01.24</unstructured_citation>
<unstructured_citation>Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution, Baele, Guy and Lemey, Philippe and Vansteelandt, Stijn, BMC bioinformatics, 2013, 1, 85, 14, hoehna, BioMed Central Ltd, 2015.03.16</unstructured_citation>
<unstructured_citation>Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics, Baele, G. and Li, W.L.S. and Drummond, A.J. and Suchard, M.A. and Lemey, P., mbe, 2013, 2, 239β243, 30, hoehna, SMBE, 2013.01.24</unstructured_citation>
<unstructured_citation>Chloroplast DNA evidence for a North American origin of the Hawaiian silversword alliance (Asteraceae), Baldwin, Bruce G and Kyhos, Donald W and Dvorak, Jan and Carr, Gerald D, Proceedings of the National Academy of Sciences, 1991, 5, 1840β1843, 88, National Acad Sciences</unstructured_citation>
<unstructured_citation>Age and rate of diversification of the Hawaiian silversword alliance (Compositae), Baldwin, Bruce G and Sanderson, Michael J, Proceedings of the National Academy of Sciences, 1998, 16, 9402β9406, 95, National Acad Sciences</unstructured_citation>
<unstructured_citation>Effects of Oligo-Miocene global climate changes on mammalian species richness in the northwestern quarter of the USA, Barnosky, A.D. and Carrasco, M.A., Evolutionary Ecology Research, 2002, 6, 811β841, 4, hoehna, 2013.01.11</unstructured_citation>
<unstructured_citation>Has the Earthβs sixth mass extinction already arrived?, Barnosky, A.D. and Matzke, N. and Tomiya, S. and Wogan, G.O.U. and Swartz, B. and Quental, T.B. and Marshall, C. and McGuire, J.L. and Lindsey, E.L. and Maguire, K.C. and others, Nature, 2011, 7336, 51β57, 471, hoehna, Nature Publishing Group, 2013.01.11</unstructured_citation>
<unstructured_citation>Late Miocene \textitIndarctos punjabiensis atticus (Carnivora, Ursidae) in Ukraine with survey of \textitIndarctos records from the former USSR, Baryshnikov, Gennady F, Russian J. Theriol, 2002, 2, 83β89, 1</unstructured_citation>
<unstructured_citation>Landscapes on Spaces of Trees, Bastert, Oliver and Rockmore, Dan and Stadler, Peter F. and Tinhofer, Gottfried, Applied Mathematics and Computation, 2002, 439β459, 131, September, 2, 439-459, 131</unstructured_citation>
<unstructured_citation>The MRP method, Baum, B.R. and Ragan, M.A., Kluwer Academic Pub, 2004, Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, shhn001, 17β34, 2008.09.17</unstructured_citation>
10.1126/science.1117727
<unstructured_citation>Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference, and the Desirability of Combining Gene Trees, Baum, Bernard R., Taxon, 1992, 1, 3β10, 41, A procedure of combining trees obtained from data sets of different kinds, similar to Brooksβs technique but for a different purpose, with the aim of combining these data sets, is detailed along with examples used in five unrepeated combinations from a total of 15 published datasets. The procedure does not adjoin raw data sets, but instead combines the binary-coded factors of the trees, each tree from a different data set, together. This allows the combining of data that are only available as pair-wise distances with data obtained directly from characters of the organisms. It economizes the analysis of combined nucleotide sequence data which can be very large, and preserves information for each kind of data in the combination. The procedure allows for missing data as well, and can be regarded as a new consensus method β mathematical properties have yet to be investigated. The desirability of combining gene trees, obtained from molecular data, to enable the inference of species trees is discussed in light of using this procedure., Copyright οΏ½ 1992 International Association for Plant Taxonomy (IAPT), 00400262, primary_article, Feb., 1992, shhn001, International Association for Plant Taxonomy (IAPT), 2008.09.16</unstructured_citation>
<unstructured_citation>The Bayesian revolution in genetics, Beaumont, Mark A and Rannala, Bruce, Nature Reviews Genetics, 2004, 4, 251β261, 5, hoehna, Nature Publishing Group, 2013.08.10</unstructured_citation>
<unstructured_citation>Approximate Bayesian computation in population genetics, Beaumont, M.A. and Zhang, W. and Balding, D.J., genetics, 2002, 4, 2025β2035, 162, hoehna, Genetics Soc America, 2012.09.25</unstructured_citation>
<unstructured_citation>Migrate version 3.0 - a maximum likelihood and Bayesian estimator of gene flow using the coalescent., Beerli, Peter, jul, 2008, shhn001, 2009.01.03, http://popgen.scs.edu/migrate.html, 7</unstructured_citation>
10.1073/pnas.081068098
<unstructured_citation>Maximum-Likelihood Estimation of Migration Rates and Effective Population Numbers in Two Populations Using a Coalescent Approach, Beerli, Peter and Felsenstein, Joseph, genetics, 1999, 2, 763-773, 152, A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics.washington.edu/lamarc.html., http://www.genetics.org/cgi/reprint/152/2/763.pdf, shhn001, 2009.02.16</unstructured_citation>
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<unstructured_citation>THE METHOD OF PROBITS, Bliss, CI, Science, 1934, 2037, 38β39, 79, shhn001, Method for calculating the inverse cumulative distribution function, 2008.05.28</unstructured_citation>
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10.1111/1467-9884.00117
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<unstructured_citation>Minimum spanning trees and single linkage cluster analysis, Gower, John C and Ross, Gavin JS, Applied statistics, 54β64, 1969, JSTOR</unstructured_citation>
<unstructured_citation>RNA PHYLOGENETIC INFERENCE WITH HETEROGENEOUS SUBSTITUTION MODELS, Gowri-Shankar, Vivek, University of Manchester, 2006, shhn001, 2008.03.24</unstructured_citation>
<unstructured_citation>A Reversible Jump Method for Bayesian Phylogenetic Inference with a Nonhomogeneous Substitution Model, Gowri-Shankar, V. and Rattray, M., mbe, 2007, 6, 1286, 24, shhn001, SMBE, First a short introduction about Bayesian MCMC for Phylogenetic Inference. Discussion about rooted and unrooted trees; why they used a rooted one. They used a rooted but not ultrametric tree. So in their description for the NNI and SPR no constraint of the nodeheights are given., 2008.03.24</unstructured_citation>
10.1111/j.1096-0031.2008.00231.x
<unstructured_citation>Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision, Graur, Dan and Martin, William, TRENDS in Genetics, 2004, 2, 80β86, 20, hoehna, Elsevier, 2015.08.07</unstructured_citation>
<unstructured_citation>Trans-dimensional markov chain monte carlo, Green, P.J., Highly structured stochastic systems, 2003, 179β198, 27, Hoehna, Oxford University Press, Reversible Jump MCMC, 2010.03.26</unstructured_citation>
<unstructured_citation>Reversible jump Markov chain Monte Carlo computation and Bayesian model determination, Green, P.J., Biometrika, 1995, 4, 711, 82, hoehna, Biometrika Trust, 2010.10.26</unstructured_citation>
<unstructured_citation>Using more than the oldest fossils: Dating Osmundaceae with three Bayesian clock approaches, Grimm, Guido W and Kapli, Paschalia and Bomfleur, Benjamin and McLoughlin, Stephen and Renner, Susanne S, sysbio, 2015, 3, 396β405, 64, hoehna, Oxford University Press, 2015.09.08</unstructured_citation>
<unstructured_citation>Probability and random processes, Grimmett, Geoffrey and Stirzaker, David, Oxford Univ Press, 1992, 2, hoehna, 2015.05.12</unstructured_citation>
<unstructured_citation>A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences, Groussin, M and Boussau, B and Gouy, M, sysbio, 2013, 4, 523β538, 62, hoehna, Oxford University Press, 2013.07.16</unstructured_citation>
<unstructured_citation>A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Guindon, Stephane and Gascuel, Olivier, sysbio, 2003, 5, 696β704, 52, Copyright Β© 2003 Society of Systematic Biologists, 10635157, primary_article, Oct., 2003, shhn001, Taylor & Francis, Ltd. for the Society of Systematic Biologists, An alternative to MCMC -> Hill Climbing. Gives also a introduction what else can be used and what is good and bad in ML, Hill-Climbing, MCMC..., 2008.04.25</unstructured_citation>
<unstructured_citation>Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses, Guillerme, Thomas and Cooper, Natalie, Biology Letters, 12, 5, 20151003, 2016, The Royal Society</unstructured_citation>
http://dx.doi.org/10.1016/j.jtbi.2015.06.005
<unstructured_citation>Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling, HΓΆhna, Sebastian, pone, 2014, 1, e84184, 9, hoehna, Public Library of Science, 2013.10.13</unstructured_citation>
<unstructured_citation>Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes, HΓΆhna, Sebastian, bi, 2013, 11, 1367β1374, 29, hoehna, Oxford Univ Press, 2013.01.11</unstructured_citation>
<unstructured_citation>New Efficient Algorithms for Bayesian Phylogenetic Inference Using Markov Chain Monte Carlo, HΓΆhna, Sebastian, The Universtiy of Auckland, 2009, The University of Auckland, Department of Computer Science, Private Bag 92019, Auckland, New Zealand., feb, Master Thesis, hoehna, 2009.04.23, 2</unstructured_citation>
<unstructured_citation>Clock-Constrained Tree Proposal Operators in Bayesian Phylogenetic Inference, HΓΆhna, Sebastian and Defoin-Platel, M. and Drummond, A.J., 8th IEEE International Conference on BioInformatics and BioEngineering, 2008. BIBE 2008, 2008, 1β7, hoehna, 2009.04.23</unstructured_citation>
<unstructured_citation>Guided Tree Topology Proposals for Bayesian Phylogenetic Inference, HΓΆhna, Sebastian and Drummond, Alexei J., sysbio, 2012, 1, 1β11, 61, hoehna, Oxford University Press, 2011.07.11</unstructured_citation>
10.1093/sysbio/syu039
<unstructured_citation>Inferring speciation and extinction rates under different species sampling schemes, HΓΆhna, Sebastian and Stadler, Tanja and Ronquist, Fredrik and Britton, Tom, mbe, 2011, 9, 2577β2589, 28, The birth-death process is widely used in phylogenetics to model speciation and extinction. Recent studies have shown that the inferred rates are sensitive to assumptions about the sampling probability of lineages. Here, we examine the effect of the method used to sample lineages. Whereas previous studies have assumed random sampling, we consider two extreme cases of biased sampling: ???diversified sampling???, where tips are selected to maximize diversity, and ???cluster sampling???, where sample diversity is minimized. Diversified sampling appears to be standard practice, e.g., in analyses of higher taxa, while cluster sampling may occur under special circumstances, e.g., in studies of geographically defined floras or faunas. Using both simulations and analyses of empirical data, we show that inferred rates may be heavily biased if the sampling strategy is not modeled correctly. In particular, when a diversified sample is treated as if it were a random or complete sample, the extinction rate is severely underestimated, often close to 0. Such dramatic errors may lead to serious consequences, e.g. if estimated rates are used in assessing the vulnerability of threatened species to extinction. Using Bayesian model testing across 18 empirical data sets, we show that diversified sampling is commonly a better fit to the data than complete, random or cluster sampling. Inappropriate modeling of the sampling method may at least partly explain anomalous results that have previously been attributed to variation over time in birth and death rates., http://mbe.oxfordjournals.org/content/early/2011/04/10/molbev.msr095.full.pdf+html</unstructured_citation>
10.1093/sysbio/syw021
<unstructured_citation>DRAM: efficient adaptive MCMC, Haario, Heikki and Laine, Marko and Mira, Antonietta and Saksman, Eero, Statistics and Computing, 2006, 4, 339β354, 16, hoehna, Springer, 2015.06.16</unstructured_citation>
<unstructured_citation>Adaptive proposal distribution for random walk Metropolis algorithm, Haario, Heikki and Saksman, Eero and Tamminen, Johanna, Computational Statistics, 1999, 3, 375β396, 14, hoehna, Citeseer, 2015.05.19</unstructured_citation>
<unstructured_citation>Time series analysis, Hamilton, J.D., Cambridge Univ Press, 1994, 10, hoehna, 2011.07.19</unstructured_citation>
<unstructured_citation>Monte Carlo methods, Hammersley, J.M. and Handscomb, D.C., Methuen, 1964, shhn001, 2008.09.09</unstructured_citation>
<unstructured_citation>Stabilizing selection and the comparative analysis of adaptation, Hansen, Thomas F, Evolution, 1997, 5, 1341β1351, 51, hoehna, JSTOR, 2015.02.26</unstructured_citation>
<unstructured_citation>GEIGER: investigating evolutionary radiations, Harmon, L.J. and Weir, J.T. and Brock, C.D. and Glor, R.E. and Challenger, W., bi, 2008, 1, 129β131, 24, hoehna, Oxford Univ Press, 2012.09.25</unstructured_citation>
<unstructured_citation>Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters, Harrison, Luke B and Larsson, Hans CE, sysbio, 2015, 2, 307-324, 64, hoehna, Oxford University Press, 2015.02.25</unstructured_citation>
<unstructured_citation>A Formal Basis for the Heuristic Determination of Minimum Cost Paths, Hart, PE and Nilsson, NJ and Raphael, B., Systems Science and Cybernetics, IEEE Transactions on, 1968, 2, 100β107, 4, shhn001, 2009.01.24</unstructured_citation>
<unstructured_citation>Sampling trees from evolutionary models, Hartmann, Klaas and Wong, Dennis and Stadler, Tanja, sysbio, 2010, 4, 465β476, 59, hoehna, Oxford University Press, 2013.09.04</unstructured_citation>
<unstructured_citation>Phylogenies Without Fossils, Harvey, Paul H. and May, Robert M. and Nee, Sean, evolution, 1994, 3, 523β529, 48, Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis., Copyright ? 1994 Society for the Study of Evolution, 00143820, primary_article, Jun., 1994, hoehna, Society for the Study of Evolution, 2009.09.25</unstructured_citation>
<unstructured_citation>The comparative method in evolutionary biology, Harvey, Paul H and Pagel, Mark D, Oxford university press Oxford, 1991, 239, hoehna, 2015.01.20</unstructured_citation>
<unstructured_citation>Dating of the Human-Ape Splitting by a molecular Clock of Mitochondrial DNA, Hasegawa, M. and Kishino, H. and Yano, T., jme, 1985, 2, 160β174, 22, shhn001, Springer, 2008.12.02</unstructured_citation>
<unstructured_citation>The Elements of Statistical Learning, Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome, Springer Series in Statistics, 2009, hoehna, 2012.07.27</unstructured_citation>
<unstructured_citation>Monte Carlo Sampling Methods Using Markov Chains and Their Applications, Hastings, W. K., Biometrika, 1970, 1, 97β109, 57, A generalization of the sampling method introduced by Metropolis et al. (1953) is presented along with an exposition of the relevant theory, techniques of application and methods and difficulties of assessing the error in Monte Carlo estimates. Examples of the methods, including the generation of random orthogonal matrices and potential applications of the methods to numerical problems arising in statistics, are discussed., Copyright Β© 1970 Biometrika Trust, 00063444, primary_article, Apr., 1970, shhn001, Biometrika Trust, 2008.03.24</unstructured_citation>
<unstructured_citation>A hierarchical Bayesian model for calibrating estimates of species divergence times, Heath, Tracy A, sysbio, 2012, 5, 793β809, 61, hoehna, Oxford University Press, 2013.05.08</unstructured_citation>
<unstructured_citation>Bayesian inference of species divergence times, Heath, T. A. and Moore, B. R., Bayesian Phylogenetics: Methods, Algorithms, and Applications, Chapman & Hall/CRC, 2014, Boca Raton, FL, Chen, M.-H. and Kuo, L. and Lewis, P. O., 277β318, Chapman & Hall/CRC Mathematical and Computational Biology</unstructured_citation>
<unstructured_citation>The fossilized birth-death process for coherent calibration of divergence-time estimates, Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja, pnas, 2014, 29, E2957βE2966, 111, hoehna, National Acad Sciences, 2015.05.31</unstructured_citation>
<unstructured_citation>Taxon sampling and the accuracy of phylogenetic analyses, Heath, T.A. and Hedtke, S.M. and Hillis, D.M., Journal of Systematics and Evolution, 2008, 3, 239β257, 46, hoehna, 2012.07.27</unstructured_citation>
<unstructured_citation>A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates, Heath, T.A. and Holder, M.T. and Huelsenbeck, J.P., mbe, 2012, 3, 939β955, 29, hoehna, SMBE, 2012.07.27</unstructured_citation>
<unstructured_citation>Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees, Heath, T.A. and Zwickl, D.J. and Kim, J. and Hillis, D.M., sysbio, 2008, 1, 160β166, 57, hoehna, Oxford University Press, 2012.07.27</unstructured_citation>
<unstructured_citation>Precision of molecular time estimates, Hedges, S Blair and Kumar, Sudhir, TRENDS in Genetics, 2004, 5, 242β247, 20, hoehna, Elsevier, 2015.08.07</unstructured_citation>
<unstructured_citation>Genomic clocks and evolutionary timescales, Hedges, S Blair and Kumar, Sudhir, TRENDS in Genetics, 2003, 4, 200β206, 19, hoehna, Elsevier, 2015.08.07</unstructured_citation>
<unstructured_citation>Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes, Heger, Andreas and Ponting, Chris P, Genome research, 2007, 12, 1837β1849, 17, hoehna, Cold Spring Harbor Lab, 2013.08.12</unstructured_citation>
<unstructured_citation>Simulation run length control in the presence of an initial transient, Heidelberger, P. and Welch, P.D., Operations Research, 1983, 6, 1109β1144, 31, 0030-364X, Hoehna, JSTOR, 2011.02.08</unstructured_citation>
<unstructured_citation>\textitProsansanosmilus peregrinus, ein neuer machairodontider Felidae aus dem MiozΓ€n Deutschlands und Frankreichs, Heizmann, E and Ginsburg, L and Bulot, C, Stuttgarter Beitr. Naturk. B, 1980, 1β27, 58</unstructured_citation>
<unstructured_citation>Bayesian inference of species trees from multilocus data, Heled, J. and Drummond, A.J., mbe, 2010, 3, 570, 27, hoehna, SMBE, 2011.07.12</unstructured_citation>
<unstructured_citation>Bayesian inference of population size history from multiple loci, Heled, Joseph and Drummond, Alexei, bmcevobio, 2008, 1, 289, 8, hoehna, BioMed Central Ltd, 2013.04.17</unstructured_citation>
<unstructured_citation>Calibrated BirthβDeath Phylogenetic Time-Tree Priors for Bayesian Inference, Heled, Joseph and Drummond, Alexei J, sysbio, 2015, 3, 369β383, 64, hoehna, Oxford University Press, 2015.09.07</unstructured_citation>
<unstructured_citation>Calibrated tree priors for relaxed phylogenetics and divergence time estimation, Heled, Joseph and Drummond, Alexei J, Systematic Biology, 2012, 1, 138β149, 61, hoehna, Oxford University Press, 2015.09.07</unstructured_citation>
<unstructured_citation>Using phylogenetic trees to study speciation and extinction, Hey, J., evolution, 1992, 627β640, 46, hoehna, JSTOR, 2012.03.16</unstructured_citation>
<unstructured_citation>Analysis and Visualization of Tree Space, Hillis, D.M. and Heath, T.A. and John, K.S., sysbio, 2005, 3, 471β482, 54, shhn001, Taylor & Francis, 2009.01.22</unstructured_citation>
<unstructured_citation>Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology, Hipsley, Christy A and MΓΌller, Johannes, Frontiers in genetics, 2014, 138, 1β11, 5, hoehna, Frontiers Media SA, 2015.09.08</unstructured_citation>
<unstructured_citation>The changing face of the molecular evolutionary clock, Ho, Simon YW, Trends in ecology & evolution, 2014, 9, 496β503, 29, hoehna, Elsevier, 2015.08.07</unstructured_citation>
<unstructured_citation>Calibrating molecular estimates of substitution rates and divergence times in birds, Ho, Simon YM, Journal of Avian Biology, 2007, 4, 409β414, 38, hoehna, Wiley Online Library, 2015.08.06</unstructured_citation>
<unstructured_citation>Molecular-clock methods for estimating evolutionary rates and timescales, Ho, Simon YW and DuchΓͺne, SebastiΓ‘n, Molecular ecology, 2014, 24, 5947β5965, 23, hoehna, Wiley Online Library, 2015.08.07</unstructured_citation>
<unstructured_citation>Simulating and detecting autocorrelation of molecular evolutionary rates among lineages, Ho, Simon YW and DuchΓͺne, SebastiΓ‘n and DuchΓͺne, David, Molecular ecology resources, 2014, hoehna, Wiley Online Library, 2015.10.22</unstructured_citation>
<unstructured_citation>Biogeographic calibrations for the molecular clock, Ho, Simon YW and Tong, K Jun and Foster, Charles SP and Ritchie, Andrew M and Lo, Nathan and Crisp, Michael D, Biology Letters, 11, 9, 20150194, 2015, The Royal Society</unstructured_citation>
<unstructured_citation>Molecular clocks: when timesare a-changinβ, Ho, Simon YW and Larson, Greger, TRENDS in Genetics, 2006, 2, 79β83, 22, hoehna, Elsevier, 2015.08.07</unstructured_citation>
<unstructured_citation>Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times, Ho, Simon YW and Phillips, Matthew J, Systematic Biology, 2009, syp035, hoehna, Oxford University Press, 2015.08.07</unstructured_citation>
<unstructured_citation>Evidence for time dependency of molecular rate estimates, Ho, Simon YW and Shapiro, Beth and Phillips, Matthew J and Cooper, Alan and Drummond, Alexei J, sysbio, 2007, 3, 515β522, 56, hoehna, Oxford University Press, 2015.02.25</unstructured_citation>
<unstructured_citation>Successive radiations, not stasis, in the South American primate fauna, Hodgson, Jason A and Sterner, Kirstin N and Matthews, Luke J and Burrell, Andrew S and Jani, Rachana A and Raaum, Ryan L and Stewart, Caro-Beth and Disotell, Todd R, pnas, 2009, 14, 5534β5539, 106, hoehna, National Acad Sciences, 2015.07.30</unstructured_citation>
<unstructured_citation>Phylogeny estimation: traditional and Bayesian approaches, Holder, M. and Lewis, P.O., Nature Reviews Genetics, 2003, 4, 275, 4, shhn001, Nature Publishing Group, 2008.12.03</unstructured_citation>
<unstructured_citation>A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics, Holder, Mark T and Sukumaran, Jeet and Lewis, Paul O, sysbio, 2008, 5, 814β821, 57, hoehna, Oxford University Press, 2013.05.06</unstructured_citation>
<unstructured_citation>Indel-associated mutation rate varies with mating system in flowering plants, Hollister, Jesse D and Ross-Ibarra, Jeffrey and Gaut, Brandon S, mbe, 2010, 2, 409β416, 27, hoehna, SMBE, 2013.08.05</unstructured_citation>
<unstructured_citation>Using guide trees to construct multiple-sequence evolutionary HMMs, Holmes, Ian, bi, 2003, suppl 1, i147βi157, 19, hoehna, Oxford Univ Press, 2013.08.01</unstructured_citation>
<unstructured_citation>Evolutionary HMMs: a Bayesian approach to multiple alignment, Holmes, Ian and Bruno, William J, bi, 2001, 9, 803β820, 17, hoehna, Oxford Univ Press, 2013.08.01</unstructured_citation>
<unstructured_citation>Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity, Hoorn, Carina and Wesselingh, FP and Ter Steege, H and Bermudez, MA and Mora, A and Sevink, J and SanmartΔ±Μn, I and Sanchez-Meseguer, A and Anderson, CL and Figueiredo, JP and others, science, 2010, 6006, 927β931, 330, hoehna, American Association for the Advancement of Science, 2013.05.14</unstructured_citation>
<unstructured_citation>RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences, Hudelot, C. and Gowri-Shankar, V. and Jow, H. and Rattray, M. and Higgs, P.G., mpe, 2003, 2, 241β252, 28, shhn001, Elsevier, A Description about PhASE Version 1.1, 2008.03.24</unstructured_citation>
<unstructured_citation>Bayesian Phylogenetic Model Selection using Reversible Jump Markov Chain Monte Carlo, Huelsenbeck, J.P. and Larget, B. and Alfaro, M.E., mbe, 2004, 6, 1123, 21, hoehna, SMBE, 2010.10.21</unstructured_citation>
<unstructured_citation>Potential Applications and Pitfalls of Bayesian Inference of Phylogeny, Huelsenbeck, JP and Larget, B. and Miller, RE and Ronquist, F., sysbio, 2002, 5, 673β688, 51, shhn001, Taylor and Francis Ltd, 2008.03.24</unstructured_citation>
<unstructured_citation>MRBAYES: Bayesian inference of phylogenetic trees, Huelsenbeck, J.P. and Ronquist, F., bi, 2001, 8, 754β755, 17, shhn001, Oxford Univ Press, 2008.04.02</unstructured_citation>
<unstructured_citation>Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology, Huelsenbeck, J.P. and Ronquist, F. and Nielsen, R. and Bollback, J.P., Science, 2001, 5550, 2310 β 2314, 294, shhn001, 2008.04.02</unstructured_citation>
<unstructured_citation>Performance of phylogenetic methods in simulation, Huelsenbeck, J. P., sysbio, 1995, 17β48, 44, hoehna, 2013.08.01</unstructured_citation>
10.1080/10635150802166046
<unstructured_citation>Empirical and hierarchical Bayesian estimation of ancestral states, Huelsenbeck, John P and Bollback, Jonathan P, sysbio, 2001, 3, 351β366, 50, hoehna, Oxford University Press, 2013.05.31</unstructured_citation>
<unstructured_citation>Combining data in phylogenetic analysis, Huelsenbeck, John P and Bull, JJ and Cunningham, Clifford W, tee, 1996, 4, 152β158, 11, hoehna, Elsevier, 2015.02.25</unstructured_citation>
<unstructured_citation>Bayesian estimation of positively selected sites, Huelsenbeck, John P and Dyer, Kelly A, jme, 2004, 6, 661β672, 58, hoehna, Springer, 2013.08.10</unstructured_citation>
<unstructured_citation>Parametric bootstrapping in molecular phylogenetics: applications and performance, Huelsenbeck, JOHN P and Hillis, DAVID M and Jones, ROBERT, Molecular zoology: advances, strategies, and protocols, 1996, 19β45, 3, hoehna, Wiley-Liss, New York, NY, 2013.04.19</unstructured_citation>
10.1073/pnas.0508279103
<unstructured_citation>A compound Poisson process for relaxing the molecular clock, Huelsenbeck, J. P. and Larget, B. and Swofford, D. L., genetics, 2000, 1879β1892, 154, hoehna, 2013.08.01</unstructured_citation>
10.1080/10635150490522629
<unstructured_citation>Detecting correlation between characters in a comparative analysis with uncertain phylogeny, Huelsenbeck, John P and Rannala, Bruce, evolution, 2003, 6, 1237β1247, 57, hoehna, Wiley Online Library, 2015.01.22</unstructured_citation>
<unstructured_citation>Phylogenetic methods come of age: testing hypotheses in an evolutionary context, Huelsenbeck, John P and Rannala, Bruce, Science, 1997, 5310, 227β232, 276, hoehna, American Association for the Advancement of Science, 2013.08.10</unstructured_citation>
<unstructured_citation>Accommodating phylogenetic uncertainty in evolutionary studies, Huelsenbeck, John P and Rannala, Bruce and Masly, John P, Science, 2000, 5475, 2349β2350, 288, hoehna, American Association for the Advancement of Science, 2013.05.31</unstructured_citation>
<unstructured_citation>An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson?s rule, Hug, Sabine and Schwarzfischer, Michael and Hasenauer, Jan and Marr, Carsten and Theis, Fabian J, Statistics and Computing, 2015, 1β15, hoehna, Springer, 2015.03.16</unstructured_citation>
<unstructured_citation>The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times, Inoue, J. and Donoghue, P.C.J. and Yang, Z., sysbio, 2010, 1, 74β89, 59, hoehna, 2010.04.21</unstructured_citation>
<unstructured_citation>Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT, Janzen, Thijs and HΓΆhna, Sebastian and Etienne, Rampal S, Methods in Ecology and Evolution, 2015, 5, 566β575, 6, hoehna, Wiley Online Library, 2015.06.16</unstructured_citation>
<unstructured_citation>The Theory of Probability, Jeffreys, Harold, Oxford University Press, 1961, hoehna, 2015.01.20</unstructured_citation>
<unstructured_citation>Blocking Gibbs sampling in very large probabilistic expert systems, Jensen, C.S. and KjΓ¦rulff, U. and Kong, A., International Journal of Human Computer Studies, 1995, 6, 647β666, 42, Hoehna, Citeseer, 2010.10.12</unstructured_citation>
<unstructured_citation>The global diversity of birds in space and time, Jetz, W. and Thomas, GH and Joy, JB and Hartmann, K. and Mooers, AO, Nature, 2012, 7424, 444β448, 491, hoehna, Nature Publishing Group, 2013.01.11</unstructured_citation>
<unstructured_citation>The first skull of the earliest giant panda, Jin, Changzhu and Ciochon, Russell L and Dong, Wei and Hunt, Robert M and Liu, Jinyi and Jaeger, Marc and Zhu, Qizhi, pnas, 2007, 26, 10932β10937, 104</unstructured_citation>
<unstructured_citation>On the Markov chain central limit theorem, Jones, G.L., Probability surveys, 2004, 299β320, 1, 1549-5787, Hoehna, IMS and ISI/Bernoulli Society, 2011.03.03</unstructured_citation>
<unstructured_citation>Fixed-width output analysis for Markov chain Monte Carlo, Jones, G.L. and Haran, M. and Caffo, B.S. and Neath, R., jasa, 2006, 476, 1537β1547, 101, 0162-1459, Hoehna, ASA, 2010.12.13</unstructured_citation>
<unstructured_citation>The effects of alignment error and alignment filtering on the sitewise detection of positive selection, Jordan, Gregory and Goldman, Nick, mbe, 2012, 4, 1125β1139, 29, hoehna, SMBE, 2013.08.05</unstructured_citation>
<unstructured_citation>Graphical models, Jordan, M.I., Statistical Science, 2004, 1, 140β155, 19, hoehna, JSTOR, 2010.10.20</unstructured_citation>
<unstructured_citation>Interactive web-based visualization of phylogenetic trees using Phylogeny. IO, Jovanovic, Nikola and Mikheyev, Alexander S, 2016, PeerJ Preprints, 4, e2579v1, PeerJ Inc. San Francisco, USA</unstructured_citation>
<unstructured_citation>Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution, Jow, H. and Hudelot, C. and Rattray, M. and Higgs, P. G., mbe, 2002, 9, 1591-1601, 19, We study the phylogeny of the placental mammals using molecular data from all mitochondrial tRNAs and rRNAs of 54 species. We use probabilistic substitution models specific to evolution in base paired regions of RNA. A number of these models have been implemented in a new phylogenetic inference software package for carrying out maximum likelihood and Bayesian phylogenetic inferences. We describe our Bayesian phylogenetic method which uses a Markov chain Monte Carlo algorithm to provide samples from the posterior distribution of tree topologies. Our results show support for four primary mammalian clades, in agreement with recent studies of much larger data sets mainly comprising nuclear DNA. We discuss some issues arising when using Bayesian techniques on RNA sequence data., http://mbe.oxfordjournals.org/cgi/reprint/19/9/1591.pdf, shhn001, Introduction of PhASE. Our only condition is that the Markov chain be ergodic, i.e., that there is a nonzero probability of reaching any point in the state-space starting from any other point in a finite number of steps. Description of their Conitnous Change proposal and the NNI and SPR. the CC is similar to our, but smother and works similar to a NNI when it causes a topology change., 2008.03.24</unstructured_citation>
<unstructured_citation>A divergence dating analysis of turtles using fossil calibrations: an example of best practices, Joyce, Walter G and Parham, James F and Lyson, Tyler R and Warnock, Rachel CM and Donoghue, Philip CJ, Journal of Paleontology, 2013, 4, 612β634, 87, hoehna, The Paleontological Society, 2015.09.08</unstructured_citation>
<unstructured_citation>Evolution of Protein Molecules, Jukes, TH and Cantor, CR, Mammalian Protein Metabolism, 1969, 21β132, 3, shhn001, New York, 2008.12.02</unstructured_citation>
<unstructured_citation>Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birthβdeath SIR model, KΓΌhnert, Denise and Stadler, Tanja and Vaughan, Timothy G and Drummond, Alexei J, Journal of the Royal Society Interface, 2014, 94, 20131106, 11, hoehna, The Royal Society, 2015.10.21</unstructured_citation>
<unstructured_citation>Bayes Factors, Kass, R.E. and Raftery, A.E., jasa, 1995, 773β795, 90, hoehna, JSTOR, 2011.09.14</unstructured_citation>
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10.1093/molbev/msh156
DOI: 10.1016/j.meegid.2004.07.001
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10.1093/molbev/msm274
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10.1093/molbev/msm088
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10.1093/molbev/msj024
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<unstructured_citation>Robustness of Compound Dirichlet Priors for Bayesian Inference of Branch Lengths, Zhang, Chi and Rannala, Bruce and Yang, Ziheng, sysbio, 2012, 5, 779β784, 61, hoehna, Oxford University Press, 2016.08.01</unstructured_citation>
10.1093/sysbio/syv080
<unstructured_citation>Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level, Zhang, Jianzhi and Nielsen, Rasmus and Yang, Ziheng, mbe, 2005, 12, 2472β2479, 22, hoehna, SMBE, 2013.08.10</unstructured_citation>
<unstructured_citation>Molecular disease, evolution, and genetic heterogeneity, Zuckerkandl, E. and Pauling, L., Horizons in Biochemistry, 1962, Kasha, M. and Pullman, B., 189β225, Academic Press, New York</unstructured_citation>
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10.1111/evo.13117
10.1093/bioinformatics/btx155
10.7287/peerj.preprints.2579v1
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10.1111/evo.13117
10.1093/bioinformatics/btx155
10.7287/peerj.preprints.2579v1
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10.1007/s12052-010-0254-9
10.1662/0002-7685(2007)69[71:CSMAET]2.0.CO;2
</citation_list>' -V authors='
<person_name sequence="first" contributor_role="author">
<given_name>April</given_name>
Wright
http://orcid.org/0000-0003-4692-3225
</person_name>
' -V month=01 -V day=16 -V year=2019 -V issue=11 -V volume=2 -V page=35 -V title='treesiftr: An R package and server for viewing phylogenetic trees and data' -f markdown paper.md -o 10.21105.jose.00035.crossref.xml --template /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/resources/crossref.template
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:225:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:91:in
compile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:76:in `compile'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:in `run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in `invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:in `dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in `start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:113:in `<top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `
from jose-reviews.
That was surprising! Not even a little bit what I expected to occur.
I added back in the string expansion block. There were two of them. It's compiling on local via R's Knitr machinery.
from jose-reviews.
@whedon generate pdf
from jose-reviews.
Attempting PDF compilation. Reticulating splines etc...
from jose-reviews.
from jose-reviews.
It compiles that way ... I notice that two references bleed out of the right margin (long DOIs). Can you think of any way to fix that? @arfon, we may still need your help here, sorry!
from jose-reviews.
It's such an odd format for a DOI. I also see a render issue in the references on a hyphenated first name. I'll wait to push my fix until I hear back on this issue.
from jose-reviews.
It compiles that way ... I notice that two references bleed out of the right margin (long DOIs). Can you think of any way to fix that? @arfon, we may still need your help here, sorry!
Lemme see what I can do. I think openjournals/whedon#39 might fix this.
from jose-reviews.
Unfortunately this is a non-trivial fix. I can fix one of the DOI strings but the longer one is going to require some work. @labarba - it's up to you how we proceed from here, i.e. we could wait to see if we can get this fixed or accept now and update the paper later when we have a fix.
from jose-reviews.
@arfon β What if we publish it, wait for the fix, then fix the PDF and update the Crossref deposit? The downside is remembering to do this β I find it ugly to have a published paper with a broken layout.
from jose-reviews.
@wrightaprilm Another option is for you to use the initial only for the second author and also abbreviate the journal title, in the hopes the DOI moves left enough.
Abbreviation from: http://images.webofknowledge.com/images/help/WOS/A_abrvjt.html
AMERICAN BIOLOGY TEACHER
AM BIOL TEACH
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Let me play with it a bit tomorrow. If I clone Whedon, I can compile within template on my local, correct? That way I can goof around without bothering everyone?
Thanks for all your help - what a weird little hiccup!
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Please note this issue I just opened: wrightaprilm/treesiftr#5
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@wrightaprilm β You can use the command @whedon generate pdf
here, yourself, to see how your changes affect the compiled paper.
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OK, great. I see your issue, and I'm fixing it in a larger 'omnibus' of slightly broken bibtex issues. I have the next 53 minutes earmarked to revise an abstract, but I'll try out a few options for correcting the issue in the morning.
Thanks!
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@arfon β What if we publish it, wait for the fix, then fix the PDF and update the Crossref deposit? The downside is remembering to do this β I find it ugly to have a published paper with a broken layout.
Yes, I think we should do this.
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@whedon generate pdf
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Attempting PDF compilation. Reticulating splines etc...
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@whedon generate pdf
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Attempting PDF compilation. Reticulating splines etc...
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@whedon generate pdf
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Attempting PDF compilation. Reticulating splines etc...
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@whedon generate pdf
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Attempting PDF compilation. Reticulating splines etc...
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Feng & Doolittle (1987) has a DOI (not listed): https://doi.org/10.1007/BF02603120
(also, please capitalize the journal name)
Felsenstein (1973) does, too:
https://doi.org/10.1093/sysbio/22.3.240
Felsenstein (1978) is
https://doi.org/10.2307/2412810
Gower & Ross (1969) is http://doi.org/10.2307/2346439
... please go down the reference list and add any more missing DOIs.
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@whedon generate pdf
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Attempting PDF compilation. Reticulating splines etc...
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