Naupaka Zimmerman
@phytobio.me
Associate Prof at U of San Francisco. Microbial Ecology, Bioinformatics, Open Science, R, emacs. he/him 🌱 🍄 🔬 🧬 📈 👨💻
Reposted by Naupaka Zimmerman
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.
genzplyr is dplyr, but bussin fr fr no cap.
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.
github.com
November 6, 2025 at 11:25 PM
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.
genzplyr is dplyr, but bussin fr fr no cap.
Reposted by Naupaka Zimmerman
When all your PCRs fail, except for the negative control 😱
October 30, 2025 at 7:43 PM
When all your PCRs fail, except for the negative control 😱
Yeah this caused quite a bit of consternation yesterday
The AWS outage took down an online learning platform that half of all college students in the US rely on every day. from @mollytaft.com
The AWS Outage Was a Nightmare for College Students
The outage impacted online learning platform Canvas, which is used by half of college students across the US, leaving many unable to access course materials or contact professors.
www.wired.com
October 21, 2025 at 3:40 PM
Yeah this caused quite a bit of consternation yesterday
Reposted by Naupaka Zimmerman
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
Anyhoo, here’s every apple
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...
assisted.site
July 4, 2025 at 10:25 PM
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
Anyhoo, here’s every apple
Reposted by Naupaka Zimmerman
"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.
Buddy, I can see mountains reflected in the eyes of a trailside pika.
August 28, 2025 at 4:18 PM
"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.
Buddy, I can see mountains reflected in the eyes of a trailside pika.
Reposted by Naupaka Zimmerman
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/
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/
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
jasonjwilliamsny.github.io
September 25, 2025 at 10:09 PM
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/
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/
Reposted by Naupaka Zimmerman
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
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
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 11:20 AM
Reposted by Naupaka Zimmerman
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
Small Things Considered
Big Things Achieved
August 15, 2025 at 3:12 PM
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
Small Things Considered
Big Things Achieved
Reposted by Naupaka Zimmerman
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...
Read the full story on Forbes: www.forbes.com/sites/johndr...
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.
www.forbes.com
August 8, 2025 at 2:41 PM
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...
Read the full story on Forbes: www.forbes.com/sites/johndr...
Reposted by Naupaka Zimmerman
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.
August 10, 2025 at 9:19 PM
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.
Reposted by Naupaka Zimmerman
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...
However...
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...
carpentries.org
June 19, 2025 at 4:35 PM
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...
However...
Reposted by Naupaka Zimmerman
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!)
Junior/Assistant Specialist - Koskella Lab - Department of Integrative Biology
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
April 20, 2025 at 10:34 PM
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!)
Reposted by Naupaka Zimmerman
🚨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...
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...
April 19, 2025 at 12:11 AM
🚨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...
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...
Reposted by Naupaka Zimmerman
Started a Theoretical Ecology starter pack. For from complete. Respond if you want to be added or removed.
go.bsky.app/PwpvZLb
go.bsky.app/PwpvZLb
December 27, 2024 at 12:30 AM
Started a Theoretical Ecology starter pack. For from complete. Respond if you want to be added or removed.
go.bsky.app/PwpvZLb
go.bsky.app/PwpvZLb
Reposted by Naupaka Zimmerman
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
Inclusion is essential to science, and science is only worthwhile if it lifts everyone up together.
ropensci.org/blog/2025/02... #OpenSource #OpenScience
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.
ropensci.org
February 5, 2025 at 3:40 PM
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
Inclusion is essential to science, and science is only worthwhile if it lifts everyone up together.
ropensci.org/blog/2025/02... #OpenSource #OpenScience
Reposted by Naupaka Zimmerman
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...
BRC-BIO - new.nsf.gov/funding/oppo...
BIO-LEAPS - new.nsf.gov/funding/oppo...
PRFB - new.nsf.gov/funding/oppo...
Building Research Capacity of New Faculty in Biology (BRC-BIO)
new.nsf.gov
January 23, 2025 at 8:54 PM
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...
BRC-BIO - new.nsf.gov/funding/oppo...
BIO-LEAPS - new.nsf.gov/funding/oppo...
PRFB - new.nsf.gov/funding/oppo...
{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/ropensci/rix
GitHub - ropensci/rix: Reproducible Data Science environments for R with Nix
Reproducible Data Science environments for R with Nix - ropensci/rix
github.com
January 23, 2025 at 5:14 PM
{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/ropensci/rix
Reposted by Naupaka Zimmerman
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
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
January 7, 2025 at 8:27 PM
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
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
Reposted by Naupaka Zimmerman
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...
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...
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.
www.cell.com
January 10, 2025 at 4:28 PM
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...
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...
Reposted by Naupaka Zimmerman
🎨 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
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
November 23, 2024 at 3:50 PM
🎨 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
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
Reposted by Naupaka Zimmerman
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...
November 21, 2024 at 8:54 AM
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...
Reposted by Naupaka Zimmerman
Hi #rstats Twitter. Since many of you were on other platforms for a while, wanted to share that we have been busy building Tidier.jl for #JuliaLang.
The goal? All of tidyverse, written in 100% Julia.
Check it out: tidierorg.github.io/Tidier.jl/dev/
JuliaCon 2023 intro: youtu.be/ZVvP7rAIvkE?...
The goal? All of tidyverse, written in 100% Julia.
Check it out: tidierorg.github.io/Tidier.jl/dev/
JuliaCon 2023 intro: youtu.be/ZVvP7rAIvkE?...
Tidier.jl
A VitePress Site
tidierorg.github.io
November 15, 2024 at 5:00 AM
Hi #rstats Twitter. Since many of you were on other platforms for a while, wanted to share that we have been busy building Tidier.jl for #JuliaLang.
The goal? All of tidyverse, written in 100% Julia.
Check it out: tidierorg.github.io/Tidier.jl/dev/
JuliaCon 2023 intro: youtu.be/ZVvP7rAIvkE?...
The goal? All of tidyverse, written in 100% Julia.
Check it out: tidierorg.github.io/Tidier.jl/dev/
JuliaCon 2023 intro: youtu.be/ZVvP7rAIvkE?...
Reposted by Naupaka Zimmerman
My postdoctoral colleague 🙌 Stephanie Wilson of SERC led this great #rstats package paper — fluxfinder: An R Package for Reproducible Calculation and Initial Processing of Greenhouse Gas Fluxes From Static Chamber Measurements agupubs.onlinelibrary.wiley.com/doi/10.1029/...
fluxfinder: An R Package for Reproducible Calculation and Initial Processing of Greenhouse Gas Fluxes From Static Chamber Measurements
fluxfinder is a highly adaptable R package designed to calculate greenhouse gas fluxes The package allows users to parse gas analyzer data files, match data and metadata, compute fluxes, and gene...
agupubs.onlinelibrary.wiley.com
November 24, 2024 at 11:03 PM
My postdoctoral colleague 🙌 Stephanie Wilson of SERC led this great #rstats package paper — fluxfinder: An R Package for Reproducible Calculation and Initial Processing of Greenhouse Gas Fluxes From Static Chamber Measurements agupubs.onlinelibrary.wiley.com/doi/10.1029/...
'The {messy} R package takes a clean dataset, and randomly adds these features of real datasets in - giving students the opportunity to practice their data cleaning and wrangling skills without educators having to change all of their examples.' nrennie.rbind.io/blog/introdu...
Introducing the {messy} package | Nicola Rennie
The {messy} R package takes a clean dataset, and randomly adds mess to create data more similar to that which you'd find in the real world. This is an easy way for educators to create data sets that g...
nrennie.rbind.io
January 20, 2025 at 4:48 AM
'The {messy} R package takes a clean dataset, and randomly adds these features of real datasets in - giving students the opportunity to practice their data cleaning and wrangling skills without educators having to change all of their examples.' nrennie.rbind.io/blog/introdu...