Department of Geoecology
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spacetimeeco.bsky.social
Department of Geoecology
@spacetimeeco.bsky.social
2.9K followers 440 following 81 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
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
spacetimeeco.bsky.social
very interesting reading about #macroecology patterns emerging...just everywhere :) and what biological mechanisms we can (or rather can not) infer from such patterns
October 1, 2025 at 8:51 AM
Reposted by Department of Geoecology
markuseichhorn.bsky.social
Occlusion in forest laser scanning is often seen as a problem, but it can also be an opportunity. Our new preprint tries to find the positives in the things we haven't seen. 🌲🌳🧪 eartharxiv.org/repository/view/10336/
Proportion of occluded voxels across the forest canopy from a mobile terrestrial laser scanner. Data collected by Daniel Kuekenbrink.
September 26, 2025 at 10:15 AM
Reposted by Department of Geoecology
tomhengl.bsky.social
If you maybe missed the #EOSummerSchool2025 at WICC, video-recordings 📼 and lecture materials are now available: youtube.com/playlist?lis...
The event was organized in collaboration with EO Council (www.eo-council.nl), Netherlands Space Office (www.spaceoffice.nl/en/) and SURF (www.surf.nl/en/).
OpenGeoHub Summer School 2025 at WICC "Data Science for Earth Observation" - YouTube
Data Science for Earth Observation: Hands-on Training in Python, R and Julia Date: 1—6 September 2025 Location: Wageningen, Netherlands IMPORTANT NOTICE: Som...
youtube.com
September 26, 2025 at 11:38 AM
Reposted by Department of Geoecology
cts.cuni.cz
📖 Book release! Hinterland. Archeologie severočeských pískovcových krajin. Co-edited by Petr Pokorný, contributions from Jindra Prach and Jan Hošek (CTS).

An illustrated journey (100+ images) through 20,000 years of sandstone landscapes, from the Ice Age to today.

🔗 www.kosmas.cz/knihy/559021...
September 25, 2025 at 11:20 AM
Reposted by Department of Geoecology
copernicusecmwf.bsky.social
🔔 Register now for the #C3S User Workshop on 20 Oct. in Prague, an in-person event for users to explore climate data tools and real-world applications, with hands-on training and networking opportunities. 📅 Sign up by 30 September: climate.copernicus.eu/c3s-user-eng...
September 25, 2025 at 8:32 AM
spacetimeeco.bsky.social
interesting method to measure #microclimate:

about fiber-optics use in #microclimatology see also e.g.

Tyler et al. (2008) Journal of Glaciology doi.org/10.3189/0022...

Lutz et al. (2012) Northwest Science doi.org/10.3955/046....

Seyfried et al. (2016) Vadose Zone Journal doi.org/10.2136/vzj2...
September 23, 2025 at 8:12 AM
Reposted by Department of Geoecology
jasonpevans.bsky.social
We just published a paper that shows including lateral flow of soil moisture matters for climate once you get down to km-scale modelling of the land surface. More and more of our work is at these scales so we need to start including processes like this. 🧪
hess.copernicus.org/articles/29/...
The influence of lateral flow on land surface fluxes in southeast Australia varies with model resolution
Abstract. Land surface models (LSMs) used in climate models typically represent surface hydrology as one-dimensional vertical fluxes, neglecting the lateral movement of water within and between grids....
hess.copernicus.org
September 21, 2025 at 10:28 PM
spacetimeeco.bsky.social
#microclimate
leed-greifswald.bsky.social Landscape Ecology and Ecosystem Dynamics @leed-greifswald.bsky.social · Sep 16
In this study, we attempt to shift the perspective on near-ground forest microclimate towards smaller organisms. We aimed to quantify how ground cover type further modifies air temp., air humidity and soil temp. on small scales. Our initial findings were presented at this year's GFÖ in Würzburg!
Poster from Daniel Harnisch for the GFÖ, about soil micro climate
September 16, 2025 at 7:41 AM
Reposted by Department of Geoecology
tomhengl.bsky.social
Had a privilege and pleasure to teach terra pkg (created by @roberthijmans.bsky.social et al.) and spatial sampling with R together with Alexandre Wadoux at the #EOSummerSchool2025 at WICC. You can follow the terra tutorial from here: differ.blog/p/processing...
📹: youtu.be/q9sQkg7BeAc?...
Processing large rasters using terra package for R: combining tiling and time-series modeling
Processing large rasters using terra package for R: combining tiling and time-series modeling
differ.blog
September 15, 2025 at 8:53 PM
Reposted by Department of Geoecology
cranupdates.bsky.social
New on CRAN: mlr3spatiotempcv (2.3.4). View at https://CRAN.R-project.org/package=mlr3spatiotempcv
mlr3spatiotempcv: Spatiotemporal Resampling Methods for 'mlr3'
Extends the mlr3 machine learning framework with spatio-temporal resampling methods to account for the presence of spatiotemporal autocorrelation (STAC) in predictor variables. STAC may cause highly biased performance estimates in cross-validation if ignored. A JSS article is available at &lt;<a href="https://doi.org/10.18637%2Fjss.v111.i07" target="_top">doi:10.18637/jss.v111.i07</a>&gt;.
CRAN.R-project.org
September 12, 2025 at 1:18 PM
spacetimeeco.bsky.social
Like #microclimate, #tundra, #plants and experiments? Then apply for this position with @juliakemppinen.bsky.social
Highly recommended....
juliakemppinen.bsky.social Julia Kemppinen @juliakemppinen.bsky.social · Sep 12
I am recruiting a postdoctoral researcher to conduct experiments on tundra plants and microclimates 🌱🌡️💧❄️ Call ends October 7! jobs.helsinki.fi/job/Helsinki...
Postdoctoral Researcher, Biodiversity Change
Postdoctoral Researcher, Biodiversity Change
jobs.helsinki.fi
September 12, 2025 at 1:40 PM
Reposted by Department of Geoecology
jakubnowosad.com
📢 Materials from the OpenGeoHub Summer School 2025 (“Data Science for Earth Observation”) by Krzysztof Dyba are now online.

Discuss how to access, process, and analyze satellite data with #RStats.

👉 github.com/kadyb/OGH2025

#RSpatial #RemoteSensing #GISchat
September 10, 2025 at 2:00 PM
Reposted by Department of Geoecology
tomhengl.bsky.social
Our paper now in @nature.com Scientific Data
"Global 30-m annual median vegetation height maps (2000–2022) based on ICESat-2 data and ML"
doi.org/10.1038/s415...
🌍 stac.openlandmap.org/gpw_gsvh-30m...
📱 global-pasture-watch.projects.earthengine.app/view/gsvh-30m
📰 landcarbonlab.org/insights/glo...
Global 30-m annual median vegetation height maps (2000–2022) based on ICESat-2 data and Machine Learning - Scientific Data
Scientific Data - Global 30-m annual median vegetation height maps (2000–2022) based on ICESat-2 data and Machine Learning
doi.org
September 7, 2025 at 4:07 PM