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Ornithology Exchange

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This group is dedicated to sharing knowledge and helping others in using R for Ornithology Research. We are an inclusive community built to help Ornithologists learn, teach, build, and troubleshoot in R across a broad range of experience levels. Please read our code of conduct (under General Topics) before posting.

  1. What's new in this group
  2. Note- 'officer' is replacing 'ReporteRs': http://davidgohel.github.io/ReporteRs/index.html so switch over if you have been using ReporteRs
  3. I've recently came across an R package called 'officer' that makes it really easy to export editable figures/graphs (base or ggplot) to an Office application. This makes it really easy to modify figures for presentations or in my case a poster. Every element will be generated as a text/shape etc so you can change colors, text sizes, move them around etc. Also looks as though you could generate an entire presentation or document if you wanted. Figured I would share the knowledge. Here is a link to the vignette for exporting to powerpoint. I was able to follow it exactly and achieve the desired result but if you have issue feel free to reply. There are also other vignettes for the package on CRAN if you are interested in other applications. https://cran.r-project.org/web/packages/officer/vignettes/powerpoint.html -Alli
  4. Hi All, I'm currently in the process of running ZIP models in rjags to test some hypotheses about duck pair abundance. The zero-inflated models include only an intercept parameter and then 3 different dummy parameters to represent the wetland cover class variables 2, 3, and 4. In theory, one would expect the non-transformed value of the parameter estimates to decrease in value from cover class 1 to 4 sequentially. I'm seeing this trend in the MLE models we ran first actually: (Intercept) WCCone WCCthree WCCtwo -6.4537 6.0062 0.8016 3.5753 Unfortunately, I'm running up against a bit of a snag in rjags. The parameter estimates for the wetland cover classes in the zero-inflated portion of the model all end up being relatively the same (~-7 - -8) and are truncated at -10 (see the not-so-nice looking trace plots in attached word file: a2,a3,a4). I've checked for correlations among the covariates, mistakes in the data, and at this point, I am concerned that this might be a coding problem. I realize this is somewhat of an inane question to ask, however, I'm unfortunately not in an academic lab where I can easily find a fellow JAGS coder, so usually end up having to turn to sources like these if I want a second set of eyes. So, I'm hoping there's someone out there who is willing to look through the attached code and let me know if they see an error that might be causing these weird results. I've literally spent the last 6 months digging through these data and this code so I think my eyes cross every time I look at it. Any help would be great. Thanks, KC Example.docx KCScript.R
  5. Any of you who have talked with me about teaching R for any length of time have heard me talk about how 'life changing' the instructor training I received through Data Carpentry and Software Carpentry as been. A big part of that is because Software Carpentry was founded by Greg Wilson, and he has spent a LOT of time thinking about teaching, and learning from the best pedagogical research on how to teach coding. Greg just released a new book all about teaching technology, and while not all of will apply to teaching R, this is 100% what I recommend folks read if they want to learn how to teach coding based on the best science of how people learn. Greg is also fantastic at building practices into his classrooms that are welcoming to new comers and make sure that some of the barriers that those with great experience sometimes put up without thinking are broken down. The book is available open source online, more info here. http://third-bit.com/2018/07/15/teaching-tech-together.html
  6. Hi All, This is likely to become the largest tab within R Onithology. Here is where you can post on most any topic, but we request you use tags to help other users sort through the posts and find things of interest. Possible tags could include bioacoustics, power analysis, distance sampling, radar, modeling, and many many others. Feel free to start new tags of your own!
  7. quresh.latif

    Base R Graphing Resources

    Sorry, wrong link. This should be the right one: http://vinr.ir/sites/default/files/Winston%20Chang-R%20Graphics%20Cookbook-O%27Reilly%20Media%20%282013%29.pdf
  8. quresh.latif

    Base R Graphing Resources

    The R Graphics Cookbook has both ggplot and base R recipes: http://www.bagualu.net/wordpress/wp-content/uploads/2015/10/R_Cookbook.pdf.
  9. Auriel Fournier

    We need a logo/hex sticker!

    There is a R package to help build hex stickers! https://cran.r-project.org/web/packages/hexSticker/index.html I wonder if we could graph the outline of a bird or something and use that?
  10. Auriel Fournier

    Base R Graphing Resources

    Hi Everyone, I almost exclusively use ggplot for my graphing, but sometimes I have folks ask me questions about how to do something graphing related in base R. Anyone know of good resources I can point them to?
  11. Packages are a useful way to bundle the codes you made and load them quickly. It may seem that this is an advanced user kind of task, but I feel moderate experience users can grasp the concept of creating their own package quite quickly. You dont even need to publish anything on CRAN, just load it locally! To get people started I'd suggest looking at Hillary Parkers quick and relatively easy guide to creating your first package: https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/ After you get started playing around with that, you'll learn that function writing has its own set of quirks, especially as your codes get more complex. At that point I'd send people to start reading Hadley Wickhams Advanced R online book. Just read all through the 'Foundations' section atleast, to get a good grasp on why certain things do and don't work for you: http://adv-r.had.co.nz/ There's a lot to learn and gain from learning about packages, and users can certainly take it as far as they want. Feel free to share any tips or tricks of package building!
  12. Currently this is an open forum to discuss what other points we might need to address and add to our code of conduct. Feel free to discuss any changes.
  13. So with this group launching and even having had our first meeting, we should create a logo. Any one have any great ideas or want to post a design for everyone to see, please share! Examples of current hex stickers and R logos: https://www.redbubble.com/shop/rstudio+stickers
  14. Please read. Youre continued use of this forum is an implicit agreement to adhere to the Code of Conduct. Rnithology is dedicated to providing a harassment-free experience for everyone. We do not tolerate harassment of participants in any form. This code of conduct applies to all Rnithology spaces, including meetups, Twitter, mailing lists, both online and offline. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the Leadership Team. Some Rnithology spaces may have additional rules in place, which will be made clearly available to participants. Participants are responsible for knowing and abiding by these rules. Harassment includes: Offensive comments related to gender, gender identity and expression, sexual orientation, disability, mental illness, neuro(a)typicality, physical appearance, body size, age, race, or religion. Unwelcome comments regarding a person's lifestyle choices and practices, including those related to food, health, parenting, drugs, and employment. Deliberate misgendering or use of 'dead' or rejected names. Gratuitous or off-topic sexual images or behaviour in spaces where they're not appropriate. Threats of violence. Incitement of violence towards any individual, including encouraging a person to commit suicide or to engage in self-harm. Deliberate intimidation. Stalking or following. Harassing photography or recording, including logging online activity for harassment purposes. Sustained disruption of discussion. Unwelcome sexual attention. Continued one-on-one communication after requests to cease. Deliberate "outing" of any aspect of a person's identity without their consent except as necessary to protect vulnerable people from intentional abuse. Publication of non-harassing private communication. Rnithology prioritizes marginalized people's safety over privileged people's comfort. The Leadership Team will not act on complaints regarding: 'Reverse' -isms, including 'reverse racism,' 'reverse sexism,' and 'cisphobia'. Reasonable communication of boundaries, such as "leave me alone," "go away," or "I'm not discussing this with you." Communicating in a 'tone' you don't find congenial. Criticizing racist, sexist, cissexist, or otherwise oppressive behavior or assumptions. Reporting If you are being harassed by a member/guest/participant of/at Rnithology, notice that someone else is being harassed, or have any other concerns, please contact the Leadership Team via EMAIL ADDRESS. Local incidences will be handled together with the local organisers. If the person who is harassing you is on the team, they will recuse themselves from handling your incident. We will respond as promptly as we can. We will take all good-faith reports of harassment by Rnithology members seriously. This includes harassment outside our spaces and harassment that took place at any point in time. In order to protect volunteers from abuse and burnout, we reserve the right to reject any report we believe to have been made in bad faith. Reports intended to silence legitimate criticism may be deleted without response. We will respect confidentiality requests for the purpose of protecting victims of abuse. At our discretion, we may publicly name a person about whom we've received harassment complaints, or privately warn third parties about them, if we believe that doing so will increase the safety of Rnithology members or the general public. We will not name harassment victims without their affirmative consent. Consequences Participants asked to stop any harassing behavior are expected to comply immediately. If a participant engages in harassing behavior, the Leadership Team may take any action they deem appropriate, up to and including expulsion from all Rnithology spaces and identification of the participant as a harasser to other Rrnithology members or the general public.
  15. Auriel Fournier

    Sharing teaching resources

    We are working on putting together a blog post for the ROpenSci blog that will better outline the community we want to create, I'll be sure to post a link here when it goes live [might be a few weeks]. Glad to hear about github classroom, I've not used it myself but it sounds really powerful. Certainly a great skillset to give to students.
  16. Chris Merkord

    Sharing teaching resources

    Sounds great! I want to get involved but don't know how... I didn't see any links to a discussion forum or email list and no issues on that repo. As a side note, I used GitHub Classroom last semester for my R class Quantitative Biology. Students generally liked learning Git and using GitHub, and appreciated the many advantages that method of collaboration had to offer.
  17. Michael Hallworth taught some amazing spatial R lessons at the last AOS meeting. Its all available here, do check it out!
  18. Auriel Fournier

    Sharing teaching resources

    Hello Everyone. I had the great chance to attend the ROpenSci 'unconference' this past week and one product to come out of that was a science education group around R, with the goal of sharing teaching resources. More details here - https://github.com/ropenscilabs/rOpenSciEd
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