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Naupaka Zimmerman

@phytobio.me
2.3K followers 8.9K following 22 posts

Assistant Prof at University of Kansas. Microbial Ecology, Bioinformatics, Environmental Data Science, Open Science, R, emacs. he/him 🌱 🍄 🔬 🧬 📈 👨‍💻

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Reposted by Naupaka Zimmerman
Jeremy Van Cleve @vancleve.theoretical.bio · 29/09/2026
My group is recruiting a Ph.D student for Fall 2027! We're a friendly group of mathematically-minded and computationally-inspired biologists studying topics including social evolution, host-pathogen interactions, genetics, and demography. See vancleve.theoretical.bio for more info!
vancleve.theoretical.bio
van cleve research group
Van Cleve Research Group – theoretical evolution & ecology at the University of Kentucky
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Reposted by Naupaka Zimmerman
Sophien Kamoun @kamounlab.bsky.social · 27/09/2026
I just published: How do we recognize world-class science? Not by the journal it appeared in What I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs. kamounlab.medium.com/how-do-we-re...
kamounlab.medium.com
How do we recognize world-class science? Not by the journal it appeared in
What I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs.
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Reposted by Naupaka Zimmerman
SORTEE @sortee.bsky.social · 17/09/2026
Interested in helping make science a better place? Nominations for 2027 #SORTEE volunteer positions are open now! With 10 committees to choose from and so many ways to get involved, we welcome everyone to volunteer with us! Nominations close 31st Oct. sortee.org/join/ #openscience
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Reposted by Naupaka Zimmerman
EUMETSAT @eumetsat.int · 15/09/2026
We have LIFTOFF! 🚀 #Copernicus Sentinel-3C is on its way to orbit having successfully lifted off aboard a Vega C rocket alongside ESA's FLEX mission from Europe’s Spaceport in Kourou! Next milestone: Spacecraft separation in ~1 hour. stay tuned 🛰️
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Naupaka Zimmerman @phytobio.me · 15/09/2026
Happy to see this. Will make it much easier to use in classes #rstats posit.co/blog/positro...
posit.co
Positron is now available on Posit Cloud in preview
Since we la
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Reposted by Naupaka Zimmerman
Lydia Jennings, PhD @1nativesoilnerd.bsky.social · 03/09/2026
Proud of this feature in @nativenewsonline.bsky.social about our recently (as of yesterday!) released Guidelines for the Publishing of Indigenous Data. Check it out!
nativenewsonline.net
Indigenous Scholars Establish Guidelines for Governance of Indigenous Data in Scholarly Publishing
Overview: Indigenous scholars led by Lydia Jennings have developed new guidelines to help ensure Indigenous peoples’ rights, knowledge and data sovereignty are respected in scientific research and sch...
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Reposted by Naupaka Zimmerman
Crystal Lewis @cghlewis.bsky.social · 02/09/2026
Why have I been using \\ all these years to escape regex patterns, rather than just wrapping text in fixed()? 😜 #rstats
library(tidyverse)

# A tibble: 5 × 2
  name  pizza_toppings     
  <chr> <chr>              
1 Bear  pepperoni, cheese  
2 Rosie cheese             
3 Frank pepperoni, onion   
4 Rudy  sausage (ground)   
5 Baloo pineapple, with ham

# I want to replace the words in the "select all" variable, with numeric values from a key

codes <- c("pepperoni" = "1", "cheese" = "2", "onion" = "3", "sausage (ground)" = "4", "pineapple, with ham" = "5")

# Can't just replace because of () issue

# A tibble: 5 × 2
  name  pizza_toppings  
  <chr> <chr>           
1 Bear  1, 2            
2 Rosie 2               
3 Frank 1, 3            
4 Rudy  sausage (ground)
5 Baloo 5    

# (01) Using \\ to escape () in sausage (ground)

codes_escape <- c("pepperoni" = "1", "cheese" = "2", "onion" = "3", "sausage \\(ground\\)" = "4", "pineapple, with ham" = "5")

df |> 
	mutate(pizza_toppings = str_replace_all(pizza_toppings, codes_escape))

# (02) Using fixed()

codes <- c("pepperoni" = "1", "cheese" = "2", "onion" = "3", "sausage (ground)" = "4", "pineapple, with ham" = "5")

df |> 
	mutate(pizza_toppings = str_replace_all(pizza_toppings, fixed(codes)))

# A tibble: 5 × 2
  name  pizza_toppings
  <chr> <chr>         
1 Bear  1, 2          
2 Rosie 2             
3 Frank 1, 3          
4 Rudy  4             
5 Baloo 5
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Reposted by Naupaka Zimmerman
Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · 28/07/2026
The prestigious Miller Research Postdoctoral Fellowship is open! University of California, Berkeley This is a postdoc fellowship with substantial support and independence to be hosted at a lab at Berkeley, reach out with interests! miller.berkeley.edu/nominate-app...
miller.berkeley.edu
Miller Research Fellowship | Miller Institute for Basic Research in Science
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Reposted by Naupaka Zimmerman
Jacquelyn Gill @jacquelyngill.bsky.social · 28/07/2026
My alma mater (College of the Atlantic) is hiring faculty in Field Ecology, Agroecology, and Chemistry. If you're looking for a very cool small liberal arts college on the coast of Maine with a strong environmental focus, check it out (happy to answer questions!): www.coa.edu/human-resour...
coa.edu
Career Opportunities | College of the Atlantic
Career opportunities at the College of the Atlantic in Bar Harbor Maine.
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Naupaka Zimmerman @phytobio.me · 16/07/2026
Great list! US and many other countries too
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Reposted by Naupaka Zimmerman
Tiffany Timbers @tiffanytimbers.bsky.social · 11/06/2026
Thrilled to share that @minecr.bsky.social and my paper on Ten simple rules for teaching data science is now available from @plos.org Computational Biology! journals.plos.org/ploscompbiol...
journals.plos.org
Ten simple rules for teaching data science
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Reposted by Naupaka Zimmerman
Shelly Gaynor @shellygaynor.bsky.social · 10/06/2026
Just got an alert that views for the Biology PhD Stipends database spiked over the past weekend! Lets keep this database up-to-date, if your program increased their EEB PhD stipend, submit an update: mlgaynor.com/BiologyPhDSt...
mlgaynor.com
Biology PhD Stipends
Biology Ph.D. stipend database with live summaries from the shared Google Sheet.
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Reposted by Naupaka Zimmerman
Dr. Carly Kenkel @drcarl.bsky.social · 03/06/2026
The list of Ecology/Evolution/Marine Bio Labs recruiting grad students for Fall 2027 is live! PIs enter your position info here: forms.gle/MAGd4ohyPeoY... students (and PIs not recruiting) share the composite list: docs.google.com/spreadsheets... Please share widely! 🧪
forms.gle
Ecology/Evolution/Marine Biology labs recruiting for Fall 2027
Please complete this form if you are a PI recruiting graduate students for a Fall 2027 start. If you are NOT recruiting, feel free to share the response sheet with prospective students looking for lab...
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Reposted by Naupaka Zimmerman
Dr. Danny Haelewaters 🏳️‍🌈🍄🪰🦇🔬🧬 @dhaelewa.bsky.social · 01/06/2026
Please take the time to review and sign this petition in support of the U.S. National Fungus Collections, which are being threatened in the face of the USDA reorganization efforts. c.org/KQWY7fNhGw 🍄
c.org
Sign the Petition
Preserve and support the U​.​S. National Fungus Collections
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Reposted by Naupaka Zimmerman
Botany One @botany.one · 02/06/2026
Asst Professor - Plant or Fungal Genomics // University of Wyoming jobs.chronicle.com/job/37995586... The Department of Botany and the School of Computing invites applications for a tenure-track position in Plant or Fungal Genomics at the rank of Assistant Professor. #BotanyJobs
jobs.chronicle.com
Asst Professor - Plant or Fungal Genomics - Wyoming, United States job with University of Wyoming | 37995586
Asst Professor - Plant or Fungal Genomics Join Our Campus Community! Thank you for your interest in joining the University of Wyoming. Our...
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Reposted by Naupaka Zimmerman
Posit @posit.co · 18/05/2026
Looking to connect with Posit folks on Bluesky? 🌐 We've updated our Posit Starter Pack! If you haven't looked at it lately (or are seeing it for the first time), discover and add some incredible data scientists, developers, and team members to your feed. bsky.app/starter-pack...
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Reposted by Naupaka Zimmerman
Adam Steinbrenner @adsteinbrenner.bsky.social · 13/05/2026
We hope BAT will help molecular biologists to think in terms of gene trees. Evolutionary signal within gene families is often the first clue that there is amazing, novel biology to be found. Check out our repo and try out BAT analyses of YFGs (Your Favorite Genes!) github.com/steinbrenner...
github.com
GitHub - steinbrennerlab/blast-align-tree: A pipeline to identify BLAST hits and perform phylogenetic analysis across multiple queries and local genome databases
A pipeline to identify BLAST hits and perform phylogenetic analysis across multiple queries and local genome databases - steinbrennerlab/blast-align-tree
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Reposted by Naupaka Zimmerman
Jae Young Choi @jychoi.bsky.social · 30/04/2026
I'm looking to hire a postdoc. Please share if you can!
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Reposted by Naupaka Zimmerman
David Ho @davidho.bsky.social · 24/04/2026
I’m trying to convince my institution that’s it’s worthwhile to be on Bluesky, so I volunteered to setup an account and posted at @soest.hawaii.edu. Please do me a favor and follow the account, share and like some posts before my meeting to discuss the account tomorrow. @joshuajfriedman.com
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Naupaka Zimmerman @phytobio.me · 22/04/2026
I was an intern at the Forest Service in Hilo when I was in college 20+ years ago. It was that experience that led me to decide to become an ecologist. Ecologists there have been lifelong mentors. Closing this would be incredibly shortsighted and a huge loss to STEM workforce development in Hawai'i.
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Reposted by Naupaka Zimmerman
David Ho @davidho.bsky.social · 22/04/2026
The Forest Service’s proposed closure of research facilities in Hawaiʻi, including the Institute of Pacific Islands Forestry and a biocontrol lab, threatens years of research on biocontrol agents and disease-resistant ʻōhiʻa strains, impacting efforts to protect Hawaiʻi’s forests and watersheds.
civilbeat.org
Forest Service Cuts Would Devastate Years Of Hawaiʻi Research, Experts Warn
The Forest Service is looking to close its Big Island labs — the only ones of their kind, researchers say, that help protect the Pacific's unique tropical forests.
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Reposted by Naupaka Zimmerman
Noam Ross @noamross.net · 02/02/2026
NSF GRFP applicants (and mentors): Was your application Returned Without Review and deemed ineligible despite fitting in the allowed topics? 1) Write NSF 2) Write your Congressperson 3) CC us at grfp@grant-witness.us so we can compile + follow up Details and template at grant-witness.us/grfp-letter
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Reposted by Naupaka Zimmerman
Timothée Poisot @ctrlalttim.com · 03/04/2026
Every term without a fault an undergrad tells me "I spent 2 hours on this problem and you identified it in under a minute", and every term without a fault I answer "it took me over a decade to identify it in under a minute"
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Reposted by Naupaka Zimmerman
Noam Ross @noamross.net · 30/03/2026
For #NSF and #NIH watchers, Grant Witness now has interactive data on numbers of grants and total funding obligations, broken down by institute and directorate, new awards and non-competitive renewals. The stranglehold on new awards is still a disaster. grant-witness.us/funding_curv...
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Reposted by Naupaka Zimmerman
Darren Dahly @statsepi.bsky.social · 18/03/2026
Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice. www.tandfonline.com/doi/full/10....
Data Organization in Spreadsheets
Karl W. Broman
& Kara H. Woo
Pages 2-10 | Received 01 Jun 2017, Accepted author version posted online: 29 Sep 2017, Published online: 24 Apr 2018

    1. Introduction
    2. Be Consistent
    3. Choose Good Names for Things
    4. Write Dates as YYYY-MM-DD
    5. No Empty Cells
    6. Put Just One Thing in a Cell
    7. Make it a Rectangle
    8. Create a Data Dictionary
    9. No Calculations in the Raw Data Files
    10. Do Not Use Font Color or Highlighting as Data
    11. Make Backups
    12. Use Data Validation to Avoid Errors
    13. Save the Data in Plain Text Files

ABSTRACT

Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this article offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses. The basic principles are: be consistent, write dates like YYYY-MM-DD, do not leave any cells empty, put just one thing in a cell, organize the data as a single rectangle (with subjects as rows and variables as columns, and with a single header row), create a data dictionary, do not include calculations in the raw data files, do not use font color or highlighting as data, choose good names for things, make backups, use data validation to avoid data entry errors, and save the data in plain text files.
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Reposted by Naupaka Zimmerman
Jeremy Berg @jeremymberg.bsky.social · 01/03/2026
NSF Update (Awards through 2/27/26) Directorates to follow 1/10
A line graph showing NSF grant awards made through 2/27/26 for fiscal year 2026 compared with grant awards for fiscal years 2021-2025.
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Reposted by Naupaka Zimmerman
Tiffany Timbers @tiffanytimbers.bsky.social · 04/02/2026
"Ten simple rules for teaching data science": arxiv.org/abs/2602.02874 A new preprint by @minecr.bsky.social and myself. We'd love any feedback!
arxiv.org
Ten simple rules for teaching data science
Teaching data science presents unique challenges and opportunities that cannot be fully addressed by simply borrowing pedagogical strategies from its parent disciplines of statistics and computer scie...
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Reposted by Naupaka Zimmerman
johnzobitz.bsky.social @johnzobitz.bsky.social · 01/02/2026
Thanks for the love! This was a bright spot to my day (and unexpected!) @phytobio.me @methodsinecoevol.bsky.social
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Reposted by Naupaka Zimmerman
Hadley Wickham @hadley.nz · 06/11/2025
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
github.com
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
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Reposted by Naupaka Zimmerman
Sam Mugford @samtmugford.bsky.social · 30/10/2025
When all your PCRs fail, except for the negative control 😱
A pumpkin carved to depict an agarose gel electrophoesis with all lanes blank apart from the size ladder on the left and a single band in the lane on the far right
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Naupaka Zimmerman @phytobio.me · 21/10/2025
Yeah this caused quite a bit of consternation yesterday
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Naupaka Zimmerman @phytobio.me · 21/10/2025
Just announced from @anthropic.com This stuff is moving very fast. www.anthropic.com/news/claude-...
anthropic.com
Claude for Life Sciences
Discover how Claude accelerates life sciences research with new scientific connectors, skills, and improved performance for drug discovery and clinical work.
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Reposted by Naupaka Zimmerman
Luke Ontario @coolhand.bsky.social · 04/07/2025
I’m going to start doing “wholesome graphic of the day” posts lol. The maps and infographics have been veering political Anyhoo, here’s every apple
assisted.site
Apple Cultivar Genealogy Chart
This image is a comprehensive chart titled 'Apples: A Genealogy of Culinary Cultivars' that maps out the relationships between various apple cultivars. Each apple type is represented by a circle, with...
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Reposted by Naupaka Zimmerman
Patrick Vallely @pjvphotography.bsky.social · 28/08/2025
"Pat, why do you carry that ridiculous 600mm lens on long hikes?" Buddy, I can see mountains reflected in the eyes of a trailside pika.
A pika sits on a mossy rock.Tighter crop of the same pika, focusing on its head.An even tighter crop, focusing more on the pika's eye.An extremely tight crop of the pika's eye, emphasizing their reflection of an early morning mountain scene.
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Reposted by Naupaka Zimmerman
Jason “Obstacle to Progress” Williams @jasonwilliamsny.bsky.social · 25/09/2025
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment. The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP jasonjwilliamsny.github.io/grfp2025/
jasonjwilliamsny.github.io
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
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Reposted by Naupaka Zimmerman
Thomas Lin Pedersen @thomasp85.com · 11/09/2025
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
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Reposted by Naupaka Zimmerman
ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 15/08/2025
Saddened to learn of the passing of Moselio "Elio" Schaechter—Distinguished Professor at Tufts, SDSU and UCSD—humanist and visionary leader in the fields of microbiology and scientific communication—mentor, friend, and inspiration to me and so many others Small Things Considered Big Things Achieved
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John M. Drake @jdrakephd.bsky.social · 08/08/2025
I spoke with Kari Jordan and Erin Becker of The Carpentries about why they declined a $1.5M NSF grant intended to expand data science training. Their decision highlights the growing intersection of #science, #DEI, and federal policy. Read the full story on Forbes: www.forbes.com/sites/johndr...
forbes.com
Nonprofit Refuses $1.5M Science Grant Due To New Federal DEI Rules
A coding nonprofit turned down a $1.5M NSF grant after new DEI restrictions, highlighting the clash between federal policy and scientific community values.
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Reposted by Naupaka Zimmerman
Jacquelyn Gill @jacquelyngill.bsky.social · 10/08/2025
Do you love alpine plants, ancient DNA, and/or population genetics? My lab will be hiring a postdoc soon to be based at the University of Maine! We’re looking for someone who uses genetic tools and thinks like a community ecologist. Happy to chat at #ESA2025 if you’re interested.
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Reposted by Naupaka Zimmerman
The Carpentries @carpentries.carpentries.org · 19/06/2025
ICYMI: In September 2024, The Carpentries submitted a proposal for 1.5 million USD to the U.S. National Science Foundation (NSF) Pathways to Enable Open-Source Ecosystems (POSE) Program, and were extremely pleased to learn that the proposal was recommended for funding. However...
carpentries.org
Announcing Withdrawal of NSF Pathways to Enable Open-Source Ecosystems Proposal
In September 2024, The Carpentries submitted a proposal to the U.S. National Science Foundation (NSF) Pathways to Enable Open-Source Ecosystems (POSE) Program. This project would position The Carpentr...
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Reposted by Naupaka Zimmerman
Britt Koskella @bkoskella.bsky.social · 20/04/2025
Know any soon to graduate or recently graduated postbac researchers interested in / with experience working with phages? We are hiring a junior specialist/research tech! Apply here: aprecruit.berkeley.edu/JPF04863 (start date more flexible than stated in ad!)
aprecruit.berkeley.edu
Junior/Assistant Specialist - Koskella Lab - Department of Integrative Biology
University of California, Berkeley is hiring. Apply now!
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Noam Ross @noamross.net · 19/04/2025
🚨Report your NSF grant terminations! 🚨 We are starting to collect information on NSF grant terminations to create a shared resource as we have for NIH. The more information we collect, the more we can organize, advocate, and fight back! Please share widely! airtable.com/appGKlSVeXni...
NSF Grant Termination Information Collection Form

Please use this form to submit information identifying specific NSF grants that have been cancelled for any reason after January 20, 2025.


We are tracking these grants to increase transparency, organize affected PIs, and facilitate responses, including via litigation. Please share the form as widely as possible with your networks. 


We are actively building a pipeline to organize these terminations and will soon have a tracker akin to our NIH grant tracker at https://airtable.com/appjhyo9NTvJLocRy/shrNto1NNp9eJlgpA


WE WILL NOT DISCLOSE THE IDENTITY OF ANYONE WHO USES THIS FORM TO PROVIDE INFORMATION. We will keep your identity confidential.


These resources are maintained by Noam Ross of rOpenSci and Scott Delaney of the Harvard T.H. Chan School of Public Health, with input and support from additional volunteers. For any questions, please contact Scott Delaney on Signal (sdelaney.84).


THANK YOU FOR YOUR ASSISTANCE!
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Reposted by Naupaka Zimmerman
Sebastian Schreiber @sebastianschreiber.bsky.social · 27/12/2024
Started a Theoretical Ecology starter pack. For from complete. Respond if you want to be added or removed. go.bsky.app/PwpvZLb
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Reposted by Naupaka Zimmerman
Noam Ross @noamross.net · 05/02/2025
Open Science and Open Source only with Diversity, Equity, Inclusion and Accessibility. Inclusion is essential to science, and science is only worthwhile if it lifts everyone up together. ropensci.org/blog/2025/02... #OpenSource #OpenScience
ropensci.org
Open Science and Open Source only with Diversity, Equity, Inclusion, and Accessibility
Including all of humanity is and always will be at the heart of open science.
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Matt Carling @mdcarling.bsky.social · 23/01/2025
Looks like the following programs in #NSF BIO have been 'archived': BRC-BIO - new.nsf.gov/funding/oppo... BIO-LEAPS - new.nsf.gov/funding/oppo... PRFB - new.nsf.gov/funding/oppo...
new.nsf.gov
Building Research Capacity of New Faculty in Biology (BRC-BIO)
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Naupaka Zimmerman @phytobio.me · 23/01/2025
{rix} is an R package that leverages Nix, a package manager focused on reproducible builds. With Nix, you can create project-specific environments with a custom version of R, its packages, and all system dependencies (e.g., GDAL). github.com/ropensci/rix
github.com
GitHub - ropensci/rix: Reproducible Data Science environments for R with Nix
Reproducible Data Science environments for R with Nix - ropensci/rix
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ESA Early Career Ecologists @esa-earlycareer.bsky.social · 07/01/2025
Happy New Year! 🎉 A new year means a lot of uncertainty. However, one thing remains certain: each month, we will continue to bring you awesome resources and relevant news via our newsletter! 🧵#ECEnewsletter
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PEC Exeter @pec-exeter.bsky.social · 10/01/2025
Where are all the field studies? This ⬇️ important but rather depressing paper describes how conducting, & crucially initiating, field studies is becoming harder & rarer. A short 🧵 (and a call for more fieldwork) www.cell.com/trends/ecolo...
cell.com
Extinction of experience among ecologists
Fieldwork-based research and education in ecology are under multiple threats and are progressively declining. We call for greater attention to this ongoing loss of direct field experience within the ecology community, as it could have widespread consequences for science and education, ultimately hindering efforts to address the ongoing biodiversity crisis.
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Jon Lim, FRCP PhD @drjonlim.bsky.social · 23/11/2024
🎨 In case anyone need… The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏! Check it out 👇 bioart.niaid.nih.gov
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Reposted by Naupaka Zimmerman
January Weiner @january3.github.io · 21/11/2024
Today I learned that combining a density plot with a jitter / dot plot is called a "raincloud" plot. And also discovered the {ggrain} package. Very nice, I remember doing it almost by hand in base R. #rstats www.njudd.com/raincloud-gg...
An example of the raincloud using the iris data set
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