Department of Geoecology
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spacetimeeco.bsky.social
Department of Geoecology
@spacetimeeco.bsky.social
3K followers 460 following 87 posts
We combine field measurements with geospatial technologies to understand plant distribution across time and space.

Led by Martin Kopecký, placed in @IBOTCZ
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spacetimeeco.bsky.social
Department of Geoecology @spacetimeeco.bsky.social · Nov 14
I created a feed for microclimate ecology and biogeography to capture posts with the hashtag #microclimate

bsky.app/profile/spac...
Reposted by Department of Geoecology
nowosad.fosstodon.org.ap.brid.gy
🗺️ fastfocal: fast moving-window and point extraction for rasters in R, optimized for large windows and common focal stats via FFT. Built on terra.

https://cran.r-project.org/package=fastfocal

#rstats #giscience #rspatial
January 21, 2026 at 4:12 PM
Reposted by Department of Geoecology
jitkaklimesova.bsky.social
New on the Belowground blog: How old do herbs live? plantlifebelowground.wordpress.com/2026/01/21/h...
How old do herbs live?
New research by Jitka Klimešová, from the Institute of Botany of the Czech Academy of Sciences. The picture above portrays one of the ways to determine the age of living parts of a clonal plant: fi…
plantlifebelowground.wordpress.com
January 21, 2026 at 7:14 AM
Reposted by Department of Geoecology
danlwarren.bsky.social
Back from holiday and it's finally time to post about this. I am taking on a section editor role for the new diamond open access journal Biogeography, put together by @biogeographyjfab.bsky.social. That means that it's free to publish and free to read. (thread)

biog.journals.sup.org/index.php/bi...
Biogeography
Biogeography is an academic-owned, diamond Open Access journal, published by the academic, non-profit, Stanford University Press (SUP), using the Public Knowledge Project’s Open Journal Systems platfo...
biog.journals.sup.org
January 20, 2026 at 2:48 AM
Reposted by Department of Geoecology
martinmacek.bsky.social
Forests in Šumava and Bavarian Forest NP are getting wild - describing their structure with #LiDAR was very helpful for #microclimate modelling.
Here are a just few pics from the #fieldwork:
January 15, 2026 at 1:40 PM
spacetimeeco.bsky.social
We paired #microclimate with #LiDAR to create 5m resolution temperature grids for the #BohemianForestEcosystem (NP Šumava and NP Bavarian Forest)🍁

Beside large microclimatic variability, our data reveals also systematic differences from #SoilTemp, #ForestTemp and #ERA5-Land

doi.org/10.1038/s415...
January 15, 2026 at 10:38 AM
Reposted by Department of Geoecology
giswqs.bsky.social
Introducing the NASA Earthdata Plugin for QGIS!

With the NASA Earthdata plugin, you can search, filter, preview, and download NASA datasets directly inside QGIS, no programming needed. It’s designed for anyone who wants fast, seamless access to NASA data within their existing GIS workflow.
January 6, 2026 at 4:36 PM
Reposted by Department of Geoecology
jakubnowosad.com
🚀 Exploring COGs (Cloud‑Optimized GeoTIFFs) in R with the terra package (e.g., visualizing the internal tile structure).

See: guide.cloudnativegeo.org/cloud-optimi...

#RStats #RSpatial #Geospatial #CloudNativeGeo #GISchat
December 17, 2025 at 2:02 PM
Reposted by Department of Geoecology
cedricscherer.com
I ignored the strip.clip argument in #ggplot2 for way too long 😲

Combined with a small negative margin tweak, you can place facet labels inside each panel. A tiny trick that makes small multiples feel so much cleaner.

🔵 no manual coordinates
🔵 inherits theme styling
🔵 scales nicely when resizing
Side-by-side comparison of two multi-panel bubble charts faceted by world region. The left column shows the default facet labels placed above each panel (“Africa”, “Americas”, “Asia”, “Europe”, “Oceania”). The right column shows the same charts, but the facet labels are moved inside each panel at the top-left using a negative margin. In the center, there is a title reading “Want to place your facet labels inside each panel?” with an arrow pointing right, followed by a short ggplot2 theme code snippet demonstrating how to move strip text inside the panel.
December 12, 2025 at 12:51 PM
Reposted by Department of Geoecology
jakubnowosad.com
A growing list of 2026 geospatial conferences is live 🌍

URL: github.com/Nowosad/conf...

If you know of additional GIS or remote-sensing events, please contribute. PRs and suggestions are welcome.

#GISchat #Geospatial #SpatialData #Conferences2026
December 14, 2025 at 2:01 PM
Reposted by Department of Geoecology
blasbenito.com
{collinear} 3.0 is now on CRAN (yay! 🥳)

This #rstats package automates multicollinearity management to improve model robustness and interpretability.

You can learn more at blasbenito.github.io/collinear/, but here's a summary of the most exciting new features: 🧵 1/5
collinear: Automated Multicollinearity Management
Provides a comprehensive and automated workflow for managing multicollinearity in data frames with numeric and/or categorical variables. The package integrates five robust methods into a single functi...
blasbenito.github.io
December 9, 2025 at 8:04 AM
Reposted by Department of Geoecology
martinmacek.bsky.social
Nice to have such a motivated excursion to our #microclimate research plot! @spacetimeeco.bsky.social
December 4, 2025 at 2:41 PM
spacetimeeco.bsky.social
wow. Science of the Total Environment is no longer indexed in Web of Science. Be aware when deciding where to submit your papers...
ptarroso.bsky.social Pedro Tarroso @ptarroso.bsky.social · Dec 3
The journal Science of the Total Environment has now been removed from the Web of Science index! A dramatic fall triggered by editorial practices that inflated number of articles, including some approved through fake peer reviews.

#Science #OpenScience #Research #OpenAccess #ScienceForAll

👇
December 3, 2025 at 1:05 PM
Reposted by Department of Geoecology
jakubnowosad.com
🌍 How trustworthy are your spatial predictions?

In my talk for the Rome R Users Group, I showed practical ways to evaluate where spatial predictions are trustworthy, and where they aren't.

Slides: jakubnowosad.com/rome2025
Video: youtu.be/uZe7thh80MI

#RSpatial #RStats #GISchat #SpatialModelling
Cover slide
December 1, 2025 at 2:00 PM
Reposted by Department of Geoecology
jakubnowosad.com
tmap or ggplot2 for maps? 🗺️

David O’Sullivan breaks down the trade-offs in a blog post.

URL: dosull.github.io/posts/2024-1...

#RStats #RSpatial #Maps #tmap #ggplot2
tmap vs. ggplot2 for mapping – Geospatial Stuff
For me at least the choice between ggplot2 and tmap is an ongoing question. Here are my latest thoughts on the subject (with code).
dosull.github.io
November 12, 2025 at 2:02 PM
Reposted by Department of Geoecology
gsimpson.bsky.social
A new release of the mgcv #RStats 📦 is out on CRAN and Simon Wood (U Edinburgh) has added some significant new features despite the small bump in version number:

🌟 scasm() for estimating GAMs with shape constrained smooths. Can be used with any family & smoothness selection is via the EFS method
Model is: b3 <- scasm( y ~ s(x0, bs = "bs", k= k) + s(x1, bs = "sc", xt = "m+", k = k) + s(x2, bs = "bs", k = k) + s(x3, bs = "bs", k = k), family=poisson, bs=200 ) The second smooth `s(x1) is a shape constrained smooth with a positive monotonicity constraint (xt = "m+"). The `bs = 200` arguments uses 200 boostrap samples, which generates bootstrap distributions for each coefficient in the model. These bootstrap samples respect the shape constraints, while the usual +/- 2 SE credible intervals may not. The uncertainty in the partial effects is shown by two credible interval bands; a dark blue central band is a 68% Bayesian credible interval, while the lighter blue outer interval is a 95% Bayesian credible interval. The background of each panel is light grey with white grid lines, in a similar style to ggplot2's default theme.
November 12, 2025 at 11:28 AM
Reposted by Department of Geoecology
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Department of Geoecology
spacetimeeco.bsky.social
Atmospheric #VaporPressureDeficit structures #forest #bryophyte communities across #landscape

our new #microclimate research in @egubg.bsky.social #Biogeosciences journal

BIG congratulation to the very first paper from our #bryophyte lover Anna Růžičková!

doi.org/10.5194/bg-2...
Graphical abstract of the paper shoving spatial variability in atmospheric vapor pressure deficit driven by the interplay between temperature-driven patterns in saturated water vapor pressure and actual water vapor pressure across topographically diverse landscape of the National Park Bohemian Switzerland in the Czech Republic.
November 4, 2025 at 8:25 AM
Reposted by Department of Geoecology
holisoils.bsky.social
#ForestSoils are more than dirt beneath our feet: they regulate water, store carbon, & support #biodiversity 🌱

On 18 November, the #HoliSoils Webinar Series continues with a session dedicated to understanding & mapping forest soils across Europe!

Sign up now ➡️ holisoils.eu/holisoils-we...
HoliSoils Webinar Series - Introductory lecture on forest soils, monitoring and mapping - HoliSoils
Don’t miss the HoliSoils webinar on 22 October (14:00–15:00 CEST) on monitoring forest soil biodiversity, ecosystem resilience, and microbial responses to management.
holisoils.eu
November 10, 2025 at 11:46 AM
spacetimeeco.bsky.social
Atmospheric #VaporPressureDeficit structures #forest #bryophyte communities across #landscape

our new #microclimate research in @egubg.bsky.social #Biogeosciences journal

BIG congratulation to the very first paper from our #bryophyte lover Anna Růžičková!

doi.org/10.5194/bg-2...
Graphical abstract of the paper shoving spatial variability in atmospheric vapor pressure deficit driven by the interplay between temperature-driven patterns in saturated water vapor pressure and actual water vapor pressure across topographically diverse landscape of the National Park Bohemian Switzerland in the Czech Republic.
November 4, 2025 at 8:25 AM
Reposted by Department of Geoecology
seanmichaletz.bsky.social
Submit an abstract to our #EGU2026 session "Microclimate Variation and Heat Impacts on Vegetation: From Molecules to the Biosphere"(meetingorganizer.copernicus.org/EGU26/sessio...) @kalimiddleby.bsky.social @santiagotrueba.bsky.social @sonyageange.bsky.social @egu.eu @egubg.bsky.social @hs.egu.eu
November 3, 2025 at 10:46 PM
Reposted by Department of Geoecology
xaviermorin.bsky.social
📣So happy to share the PhorEau model, combining models of forest dynamics, plant water relations, and process-based SDM = linking ecophysiology, ecology & biogeography 🌳📈💻
gmd.copernicus.org/articles/18/...
➡️ from Tanguy Postic's PhD, with many perspectives to simulate forests under CC
PHOREAU v1.0: a new process-based model to predict forest functioning, from tree ecophysiology to forest dynamics and biogeography
Abstract. Climate change impacts forest functioning and dynamics, but large uncertainties remain regarding the interactions between species composition, demographic processes and environmental drivers...
gmd.copernicus.org
October 23, 2025 at 4:07 PM
spacetimeeco.bsky.social
our new research - proximal #RemoteSensing below ground :)
boudalab.bsky.social Martin Bouda @boudalab.bsky.social · Oct 10
First images from our #HydroScale Průhonice site show a cluster of beech roots growing at a depth of 1.2m!

Michal Man there, using the new device to #GoBelowground. We may need to come up with a new name for it--doesn't feel like a "mini" rhizotron.
Short, thick segments of light-coloured roots woven into a brown soil with dark cracks and macropores. Glare at image top and bottom from LED light. Technician carefully inserting a camera on a very long rail into a transparent tube in the ground in a beech forest.
October 18, 2025 at 1:10 PM
Reposted by Department of Geoecology
zeileis.org
💡 Came across this nice tool today:

🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz

JOSS paper, online tool, R package #rstats

joss.theoj.org/papers/10.21...
Qualpal: Qualitative Color Palettes for Everyone
Larsson, J., (2025). Qualpal: Qualitative Color Palettes for Everyone. Journal of Open Source Software, 10(114), 8936, https://doi.org/10.21105/joss.08936
joss.theoj.org
October 17, 2025 at 9:12 AM
Reposted by Department of Geoecology
daxkellie.bsky.social
Still want to make cleaning biodiversity data shrimp-ler? 🦐

Good news: We just updated our Cleaning Biodiversity Data in R book, so you still can! We've updated data for 2025, added new content & fixed lots of silly typos 😀

Live the shrimp-le life:
cleaning-data-r.ala.org.au

#rstats #ecology 🧪🌏
The cover of the Cleaning Biodiversity Data in R book. It has an illustration of an Pacific Cleaner Shrimp in the middle of a navy background. The shrimp has a bright red-orange shell, pale-yellow body and white whiskers.
October 15, 2025 at 4:12 AM
Reposted by Department of Geoecology
biogeography.bsky.social
Dr. Brett Scheffers will be giving our October Funk lecture! If you are interested in how micro-scale variation in climate and habitat interact to shape biogeographic patterns, you won't want to miss this talk! Learn more here: www.biogeography.org/news/news/oc...
October 6, 2025 at 7:48 PM