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Francisco Rodriguez-Sanchez

@frodsan.bsky.social

3.3K followers 150 following 180 posts

Computational Ecologist. Researcher @unisevilla.bsky.social. ecology, biogeography, statistics, rstats, GIS, science. https://frodriguezsanchez.net

frodriguezsanchez.net

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · Feb 19

1/ New paper @pnas.org on the structure of mutualistic #networks between individuals plants and frugivore species.

Last chapter of @elequintero.bsky.social's PhD thesis

doi.org/10.1073/pnas... #ecopubs

Downscaling mutualistic networks from species to individuals reveals consistent interaction niches and roles within plant populations

Species-level networks emerge as the combination of interactions spanning multiple individuals, and their study has received considerable attention over the past 30 y. However, less is known about the structure of interaction configurations within species, even though individuals are the actual interacting units in nature. We compiled 46 empirical, individual-based, interaction networks on plant-animal seed dispersal mutualisms, comprising 1,037 plant individuals across 29 species from various regions. We compared the structure of individual-based networks to that of species-based networks and, by extending the niche concept to interaction assemblages, we explored individual plant specialization. Using a Bayesian framework to account for uncertainty derived from sampling, we examined how plant individuals “explore” the interaction niche of their populations. Both individual-based and species-based networks exhibited high variability in network properties, lacking remarkable structural and topological differences between them. Within populations, frugivores’ interaction allocation among plant individuals was highly heterogeneous, with one to three frugivore species dominating interactions. Regardless of species or bioregion, plant individuals displayed a variety of interaction profiles across populations, with a consistently-small percentage of individuals playing a central role and exhibiting high diversity in their interaction assemblage. Plant populations showed variable mid to low levels of niche specialization; and individuals’ interaction niche “breadth” accounted for 70% of the population interaction diversity, on average. Our results highlight how downscaling from species to individual-based networks helps understanding the structuring of interactions within ecological communities.

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Reposted by Francisco Rodriguez-Sanchez

iBartomeus @ibartomeus.bsky.social · 2d

We are offering a 2-year postdoctoral position to join the @valor-project.eu Horizon EU project: Values and dependence of society on pollinators bartomeuslab.com/joining-the-...

Joining the lab

2-year Postdoctoral position on VALOR EU-project: We are offering a 2-year postdoctoral position to join the Horizon EU project: Values and dependence of society on pollinators (VALOR; The candidat…

bartomeuslab.com

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 2d

Yes!! Thanks

Francisco Rodriguez-Sanchez @frodsan.bsky.social · 2d

www.authorea.com/users/571220...

A Critical Analysis of the World’s Top 2% Most Influential Scientists: Examining the Limitations and Biases of Highly Cited Researchers Lists

AbstractThis paper analytically analyzes the use and limitations of ranking systems for highly cited researchers compiled by Stanford University’s ranking of the world’s top 2% most influential scient...

www.authorea.com

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 6d

Finally using {pins} #rstats package to share heavy files that can't be shared among collaborators through GitHub, and it works like a breeze! Supports data versioning, cache, etc. Thanks @posit.co

Here using Google Drive to share files, but can use many different servers, see pins.rstudio.com

library("pins")

# specify folder in Google Drive to store objects
board <- board_gdrive("https://drive.google.com/drive/folders/FOLDER_ID")

# upload file
board |> pin_write(big_dataset, "big_dataset.csv", type = "csv")

# retrieve file (e.g. in another computer)
board |> pin_read("big_dataset.csv")

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Reposted by Francisco Rodriguez-Sanchez

Clayton Hale (he/him) @chale9.bsky.social · 8d

Help! 🚨 Looking for resources on structural equation models—favorite methods papers, example studies, or guides for building an SEM pipeline. Thinking of using one for a dissertation chapter & not sure where to start. Suggestions? Please share!

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Reposted by Francisco Rodriguez-Sanchez

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 7d

Was asked about collinearity again, so here's Vahove's 2019 post on why it isn't a problem that needs a solution. Design the model(s) to answer a formal question and free your mind janhove.github.io/posts/2019-0...

tl;dr

Collinearity is a form of lack of information that is appropriately reflected in the output of your statistical model.
When collinearity is associated with interpretational difficulties, these difficulties aren’t caused by the collinearity itself. Rather, they reveal that the model was poorly specified (in that it answers a question different to the one of interest), that the analyst overly focuses on significance rather than estimates and the uncertainty about them or that the analyst took a mental shortcut in interpreting the model that could’ve also led them astray in the absence of collinearity.
If you do decide to “deal with” collinearity, make sure you can still answer the question of interest.

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 8d

Enhorabuena!! 👏🏼👏🏼

Reposted by Francisco Rodriguez-Sanchez

IPCC @ipcc.bsky.social · 9d

Registration for experts interested in serving as Expert Reviewers and providing scientific comments on the First Order Draft of the Special Report on Climate Change and Cities is now open!

Read more 🔗
www.ipcc.ch/2025/09/17/p...

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Reposted by Francisco Rodriguez-Sanchez

Carl T. Bergstrom @carlbergstrom.com · 16d

Yet again, machine learning — even gussied up via the transformer architecture — encodes and reinforces societal biases.

This study reveals that LLM-based peer review relies heavily on author institution in its decisions.

arxiv.org/abs/2509.15122

Prestige over merit: An adapted audit of LLM bias in peer review

Large language models (LLMs) are playing an increasingly integral, though largely informal, role in scholarly peer review. Yet it remains unclear whether LLMs reproduce the biases observed in human de...

arxiv.org

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Reposted by Francisco Rodriguez-Sanchez

Reassembly Research Unit @reassemblynet.bsky.social · 18d

Three exciting #PostDoc 🧑‍🔬👩‍🔬🧕 positions on #Ecological #Synthesis at TU Darmstadt @tuda.bsky.social for Reassembly #rainforest 🇪🇨 🌱🌴🦜 & #Biodiversity Exploratories 🌲🐄🚜🪲🐝🥀@bexplo.bsky.social
Please spread widely ✉️♥️▶️ & apply quickly 🙃
www.reassembly.de/the-team/job...

Ecological synthesis including forest ecosystems, grassland, land use, climate change, time series, stability, ecosystem functioning, biodiversity, species interaction networks

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 17d

Reverse suggests dependencies from {marginaleffects} and {bayestestR} from easystats must drive a lot of downloads...

Reposted by Francisco Rodriguez-Sanchez

Alfredo Sánchez-Tójar @asanchez-tojar.bsky.social · 21d

📣 Hot off the press at #ProcB!

🔍 Our study checked data/code-sharing policies in 275 eco/evo journals and compliance in Proc B (n=2,340) & Ecology Letters (n=571). Policies exist, but clarity and strictness vary, affecting reproducibility.

🔗 doi.org/10.1098/rspb...

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Reposted by Francisco Rodriguez-Sanchez

MC Stan @mc-stan.org · 21d

MC Stan is here! Follow for the latest Stan news, and tag if you want us to repost your posts about new papers, packages, courses, etc. about Stan

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Reposted by Francisco Rodriguez-Sanchez

Jakub Nowosad @jakubnowosad.com · 24d

🚀 Book in progress: Spatial Data Visualization with tmap

A guide to creating thematic maps in R with the tmap package.
Covers everything from loading data to interactive and animated maps, with reproducible code.

Read online: tmap.geocompx.org

#rstats #rspatial #geocompx #gischat #maps

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 28d

Here's an example of the master document approach. Just move or silence chunks at will. Easier than copy-pasting full contents IMO

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 28d

You could create a master qmd that calls child documents, and reorder them in the master document at will, see bookdown.org/yihui/rmarkd...

Or use Quarto includes: quarto.org/docs/authori...

If a book, can arrange chapters in _quarto.yml: quarto.org/docs/books/b...

16.4 Child documents (*) | R Markdown Cookbook

This book showcases short, practical examples of lesser-known tips and tricks to helps users get the most out of these tools. After reading this book, you will understand how R Markdown documents are ...

bookdown.org

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 28d

it should work fine (please let me know otherwise).

You could ignore certain files or folders (see pakillo.github.io/grateful/#pr...)

Or use `skip.missing` arg to skip packages not currently installed, see pakillo.github.io/grateful/ref... (after your suggestion)

Facilitate Citation of R Packages

Facilitates the citation of R packages used in analysis projects. Scans project for packages used, gets their citations, and produces a document with citations in the preferred bibliography format, re...

pakillo.github.io

Francisco Rodriguez-Sanchez @frodsan.bsky.social · 29d

🤣 no need to cite grateful (it's omitted by default)... unless you're writing about software citation practices 😉

Reposted by Francisco Rodriguez-Sanchez

Bluesky @bsky.app · Sep 8

v1.108 is rolling out today 🚚

Now live, at long last: Bookmarks, aka Saved Posts. For all those posts you'll definitely plan to come back to!

Update the app and give it a try. The button is right down there 👇

1.1K 6.2K 24K

Reposted by Francisco Rodriguez-Sanchez

James Bartlett @bartlettje.bsky.social · Sep 8

Our contribution to an upcoming book on teaching open science was "how to teach reproducible research". There are plenty of lesson plans or individual courses out there but less on how you can build skills across a whole degree.

osf.io/preprints/ps...

OSF

osf.io

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 29d

{grateful} 0.3.0 is now on CRAN. Hope it makes citing #rstats packages even easier!

pakillo.github.io/grateful/

New features 👇

Now possible to scan and cite dependencies from a package DESCRIPTION file (#62). Use pkgs = c("Depends", "Imports", "Suggests", "LinkingTo") or combinations of them to choose which dependencies to cite.

Now possible to scan and cite dependencies from a single R script, ‘Rmarkdown’ or ‘Quarto’ document #65. Just provide the path to the file to the pkgs argument.

Now possible to customise the language of citation paragraphs (#55), thanks to new arguments to cite_packages: text.start, text.pks and text.RStudio.

New logical argument skip.missing allows the user to skip missing packages (those used somewhere in the project but not currently installed) #54.

Slow down requests when querying dependencies for a large number of packages #61.

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 29d

Thanks! My DM are open now (I think)

Francisco Rodriguez-Sanchez @frodsan.bsky.social · 29d

Interesting! Is it possible to watch online?

Francisco Rodriguez-Sanchez @frodsan.bsky.social · Sep 8

An extension of joint SDM to jointly model species abundances and intraspecific trait variation. #ecopubs @esajournals.bsky.social

doi.org/10.1002/ecy....

Joint species-trait distribution modeling: The role of intraspecific trait variation in community assembly

The links between intraspecific trait variation and community assembly remain little studied, partially due to the lack of statistical methods to jointly model intraspecific trait variation and species abundances at the community level. Here, we extend the joint species distribution modeling (JSDM) framework into the joint species-trait distribution modeling (JSTDM) framework to explicitly link species abundances to phenotypic variation in traits for multiple species simultaneously. Using a case study of 65 tundra plant species abundances and 3 key functional traits measured across 325 sites, we show how the JSTDM approach (1) estimates the statistical associations among species abundances, species-level traits, and site-level traits, relative to environmental variation; (2) improves predictions on trait variation by using information on species abundances; and (3) generates hypotheses about trait-driven community assembly mechanisms. The JSTDM methodology presented in this study allows assessing the interplay between species abundances and traits at the community level, providing the much needed modeling tools to quantify the role of phenotypic trait variation in eco-evolutionary community assembly.

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · Sep 5

Before LLMs Josiah Parry started a package to automate many 'extrachecks' github.com/JosiahParry/... #rstats

GitHub - JosiahParry/extrachecks: Extra R package checks to save you from a headache. A package to accompany https://github.com/DavisVaughan/extrachecks

Extra R package checks to save you from a headache. A package to accompany https://github.com/DavisVaughan/extrachecks - JosiahParry/extrachecks

github.com