Trying to find a way to serve a Quarto dashboard as a CLI tool like https://colinfay.me/create-r-cli-npm/ for an R script… (@colinfay sorry for the tag, but maybe you have additional insights?!)
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Does #Quarto have a shebang? Like #!/usr/bin/env python3 or #!/usr/bin/env Rscript.
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Last week, I asked here on Mastodon whether it was possible to set dependencies per blog post for a #Quarto blog.
Results are in: It’s possible! And so, I of course wrote a blog post about how: https://roald-arboel.com/blog/posts/2024/10/04/renv-blog/.
Big thanks to @joelnitta and @Drmowinckels for pointing me in the right direction! #rstats
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Leading on, does anyone else use distinct renv profiles with Github Actions for individual blog posts? I really like the idea of it, but can't quite figure out the nitty gritty of it! #rstats #Quarto
https://fosstodon.org/@Drmowinckels/113243803577492548
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I am writing a blogpost in #Quarto where I need different package versions than my current environment. How do people deal with that? My current attempt includes creating a new Github repo where the HTML is rendered and then trying to include the raw HTML code. But it is a bit tricky to get it to work properly. Anyone has any experience with this?
[#]rstats
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@ASAB I would like to have a look at the International Society for Neuroethology too, as they operate without journal income, but I cant get to the documents. They should be available at https://apps.irs.gov/app/eos/ under EIN 33-0103940, but although they appear, everything I click is empty. If anyone has more luck, please share. :-)
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In case anyone else would like to have a look at the inside, let's have a look at the Animal Behaviour Society (@ASAB) which publishes "Animal Behaviour" with Elsevier. I'm a member of ASAB myself, I'm not trying to point fingers, still just beginning to understand the business model of an academic society.
The objective of ASAB is the following: "The object of ASAB and its subsidiary undertaking is the advancement of the science of animal behaviour, the furtherance of education therein, and the promotion of study and research in animal behaviour and related subjects and the publication of the results of all such study and research and certification of clinical animal behaviourists." The journal is one way for them to make money to carry out their activities. But how essential is the journal?
As a UK charity, their finances are available online (https://register-of-charities.charitycommission.gov.uk/en/charity-search?p_p_id=uk_gov_ccew_onereg_charitydetails_web_portlet_CharityDetailsPortlet&p_p_lifecycle=2&p_p_state=maximized&p_p_mode=view&p_p_resource_id=%2Faccounts-resource&p_p_cacheability=cacheLevelPage&_uk_gov_ccew_onereg_charitydetails_web_portlet_CharityDetailsPortlet_objectiveId=A13935464&p_p_auth=SbRECIfD&_uk_gov_ccew_onereg_charitydetails_web_portlet_CharityDetailsPortlet_priv_r_p_mvcRenderCommandName=%2Faccounts-and-annual-returns&_uk_gov_ccew_onereg_charitydetails_web_portlet_CharityDetailsPortlet_priv_r_p_organisationNumber=268494). It's clear that the journal accounts for the vast majority of income to the journal (page 22-23), and the most significant cash flow both in and out (page 13, Charitable activities). It's a bit blurry to me, but it seems that it costs Elsevier ~£80.000 to produce and distribute the journal, while raking in ~£300.000 in profit (happy to be corrected if it's not correct!). However, the journal also makes ~£150.000 profit on the journal overall (page 23), so financially a good deal.
Overall, in 2022, ASAB had a ~£500.000 deficit which was primarily due to investments underperforming. This, in turn, raises a completely different point I hadn't thought of, namely that I've got no clue what the society invests in. The investment portfolio - really roughly, not at all specified - is available on page 27. All I can tell is that some of the investment funds have "sustainable portfolios", most do not, and from the accounts alone, I've no clue whether that's how the money is invested. Oh, how I would love a page on their website listing how they invest the members' money - especially as a society that knows the impacts some industries have on our planet.
I'm left with a question if nothing more: What are the ethical obligations of academic societies? How far should they go to further their own cause at the expense of the wider scientific community and, in the case of investments, the wellbeing of our planet?
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And there are of course alternative venues; I know there are some governmental (or EU) based repositories, but I think society journals play an important role in academic publishing (and from conversations, I believe many researchers place value on society-governed journals). I like that there’s choice, but when the choice is between @PLOS , Royal Society, @Co_Biologists and eLife (I’m broadly a biologist, happy to receive more recommendations!), that’s not that wide. I’d really love for societies to be able to host their own infrastructure (e.g. provided by EU) on EU servers - imagine the money saved… by the EU.
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When academic societies keep their journals in the big publishing houses, what do they get in return? Cheap or free infrastructure? Or do they even still pay even for that?
I’m trying to wrap my head around what it would take for societies to transition their journals elsewhere (or have their own infrastructure). Can anyone pitch in with experience?
[#]ScholarlyPublishing
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I am currently writing an R package for analysis of trackball data (think animals walking on styrofoam balls). I would like it to work with the data formats that people get out from their experiments, but I only have data from experiments within my own lab. Would anyone who does trackball experiments, and has a data file be kind enough to share it with me? Am particularly interested in those working with rodents (which I don’t) or use FicTrac as those are two common use cases that I currently don’t think I’m covering. Please share with your neuroscience friends!
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Let’s dream a little: We’ll write a new open-source GUI for running behavioural experiments. You get full control over cameras and microcontrollers of your choice. Now, you get to call the shots, what would you want it to be capable of?
From: @roaldarboel
https://neuromatch.social/@roaldarboel/112954847605601519
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I'm not forgetting @autopilot (@jonny) of course, but am thinking more of a platform agnostic toolchain.
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Early in my PhD I started writing an application, Bux, which did this (quite well too I think), and the idea was to also connect easily to microcontrollers through Belay (https://github.com/BrianPugh/belay) to synchronise cameras and hardware (maybe even some standardised implementations e.g. BeeHive https://github.com/BeeHive-org/BeeHive).
Would that still be useful to anyone? Not saying my implementation necessarily (I definitely do not want to maintain it alone*, my life's too short for more solo-projects), but could we get behind a piece of software that makes this easy?
(I know Bonsai sits in that space, but to me, it's too complicated for most simple use cases).
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On the software-side, I currently use Bonsai, so I can also export timestamps. Otherwise, OBS? I also think SkellyCam (@freemocap) might be a solution. Any I've missed?
VidGear (https://abhitronix.github.io/vidgear/latest/) supports both webcams and picamera2, so could form a good backend, but I'm not aware of GUI applications using it.
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On the hardware-side, I've not been in a sufficiently well-funded lab to play around with industrial cameras, but is that the way to go? And do they play nice with open software? I like that the new RPi 5 has two camera slots, enabling 3D tracking with a single Pi. I like GoPro's for their versatility, but despite their open API, I've not found good support anywhere.
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Also, I know things just get more muddy if I want to synchronise other data sources, but still interested...
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How do other #neuroscience and #ethology record (pseudo)synchronised videos?
Is there a super easy solution? I'm thinking "connect to my 3 webcams/RPi cams/GoPro/industrial cameras and record"-easy.
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