https://github.com/cadam00/seagraphs
Sea Currents to Connectivity Transformation
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Repository
Sea Currents to Connectivity Transformation
Basic Info
- Host: GitHub
- Owner: cadam00
- License: gpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://cadam00.github.io/SeaGraphs/
- Size: 6.22 MB
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- Watchers: 1
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Metadata Files
README.md
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This research was conducted at the Department of Marine Sciences, University of the Aegean, Greece, supported by the European Union’s Horizon 2020 research and innovation programme HORIZON-CL6–2021-BIODIV-01–12, under grant agreement No 101059407, “MarinePlan – Improved transdisciplinary science for effective ecosystem-based maritime spatial planning and conservation in European Seas”.
Introduction to the SeaGraphs Package (tutorial)
A plethora of sea current databases is typically available along many fields data (e.g. Lima et al. (2020)). However, transforming these data into a graph structure is not a straightforward implementation. This gap is attempted to be filled by SeaGraphs package. A further inspection of the methods used in this package is illustrated at Nagkoulis et al. (2025), where the whole Black Sea is examined.
Installation
Latest official version of the package can be installed using:
r
install.packages("SeaGraphs")
Development version of the package can be installed using:
r
if (!require(remotes)) install.packages("remotes")
remotes::install_github("cadam00/SeaGraphs")
Citation
Nagkoulis N, Adam C, Mamoutos I, Mazaris AD, Katsanevakis S, 2025. An ecological connectivity dataset for Black Sea obtained from sea currents. Data in Brief 58: 111268. https://doi.org/10.1016/j.dib.2024.111268
Illustration example
Currents information about the flow directions is usually split into horizontal
($u$) and vertical ($v$) components, regarding the horizontal and the vertical
flow of the currents, respectively. As an example we use a modified yearly
aggregated subset of the Black Sea site (Lima et al.,
2020; Schulzweida, 2023)
provided in the form of SpatRaster elements. This input can be plotted using
the following:
``` r
Import packages
library(SeaGraphs) library(terra)
Get example u and v components
componentu <- getcomponentu() componentv <- getcomponentv()
Plot each component
par(mfrow=c(1,2), las=1) plot(componentu, main="u") plot(componentv, main="v") ```
Figure 1: Currents $u$ and $v$ components.
In Figure 1 the two directions of components $u$ and $v$ are
presented, with higher currents values detected at the South-West direction.
A directed spatial graph in multiple forms (spatial network, shapefile, edge
list, adjacency matrix) based on these components is constructed, based on
these two components using the following process. This is doable by running the
seagraph command as follows:
``` r
Transform currents information to graph
graphresult <- seagraph(componentu = componentu, componentv = component_v) ```
Flow and antpath leaflet maps are two possible graphical representations of such
graphs using the SeaGraphs could be performed, but using graph_result
elements, like the shapefile one is possible as well. Note that the
South-Western directions of flows and magnitudes the final graphs are depicted
in both Figures 2 and 3. Note that these outputs
are dependent on the selected number of nearest neighbors in the seagraph
function.
r
flows_sfn(graph_result)
Figure 2: Flow leaflet map.
r
antpath_sfn(graph_result)
Figure 3: Antpath leaflet map.
References
Lima, L., Aydogdu, A., Escudier, R., Masina, S., Ciliberti, S. A., Azevedo, D., Peneva, E. L., Causio, S., Cipollone, A., Clementi, E., Cretí, S., Stefanizzi, L., Lecci, R., Palermo, F., Coppini, G., Pinardi, N., and Palazov, A. (2020). Black Sea Physical Reanalysis (CMEMS BS-Currents) (Version 1) [Data set]. Copernicus Monitoring Environment Marine Service (CMEMS). https://doi.org/10.25423/CMCC/BLKSEAMULTIYEARPHY007004. Last Access: 07/11/2024.
Nagkoulis, N., Adam, C., Mamoutos, I., Katsanevakis, S., and Mazaris, A. D. (2025). An ecological connectivity dataset for Black Sea obtained from sea currents. Data in Brief, 58, 111268. https://doi.org/10.1016/j.dib.2024.111268
Schulzweida, U. (2023). CDO User Guide (23.0). Zenodo. https://doi.org/10.5281/zenodo.10020800
Owner
- Login: cadam00
- Kind: user
- Repositories: 1
- Profile: https://github.com/cadam00
Citation (CITATION.cff)
# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
cff-version: 1.2.0
message: 'To cite package "SeaGraphs" in publications use:'
type: software
license: GPL-3.0-only
title: 'SeaGraphs: Sea Currents to Connectivity Transformation'
version: 0.1.1
doi: 10.1016/j.dib.2024.111268
abstract: Transformation of sea currents to connectivity data. Two files of horizontal
and vertical currents flows are transformed into connectivity data in the form of
sfnetwork, shapefile, edge list and adjacency matrix. An application example is
shown at Nagkoulis et al. (2025) <https://doi.org/10.1016/j.dib.2024.111268>.
authors:
- family-names: Nagkoulis
given-names: Nikolaos
email: nikolaosn@civil.auth.gr
orcid: https://orcid.org/0000-0002-1900-2634
- family-names: Adam
given-names: Christos
email: econp266@econ.soc.uoc.gr
orcid: https://orcid.org/0009-0003-3244-7034
- family-names: Mamoutos
given-names: Ioannis G.
email: i.mamoutos@marine.aegean.gr
orcid: https://orcid.org/0000-0002-2697-2620
- family-names: Mazaris
given-names: Antonios D.
email: amazaris@bio.auth.gr
orcid: https://orcid.org/0000-0002-4961-5490
- family-names: Katsanevakis
given-names: Stelios
email: stelios@katsanevakis.com
orcid: https://orcid.org/0000-0002-5137-7540
preferred-citation:
type: article
title: An ecological connectivity dataset for Black Sea obtained from sea currents
authors:
- family-names: Nagkoulis
given-names: Nikolaos
email: nikolaosn@civil.auth.gr
orcid: https://orcid.org/0000-0002-1900-2634
- family-names: Adam
given-names: Christos
email: econp266@econ.soc.uoc.gr
orcid: https://orcid.org/0009-0003-3244-7034
- family-names: Mamoutos
given-names: Ioannis
- family-names: Mazaris
given-names: Antonios D.
email: amazaris@bio.auth.gr
orcid: https://orcid.org/0000-0002-4961-5490
- family-names: Katsanevakis
given-names: Stelios
email: stelios@katsanevakis.com
orcid: https://orcid.org/0000-0002-5137-7540
journal: Data in Brief
year: '2025'
volume: '58'
doi: 10.1016/j.dib.2024.111268
start: '111268'
repository-code: https://github.com/cadam00/SeaGraphs
url: https://cadam00.github.io/SeaGraphs/
contact:
- family-names: Adam
given-names: Christos
email: econp266@econ.soc.uoc.gr
orcid: https://orcid.org/0009-0003-3244-7034
keywords:
- corridors
- ecological-modelling
- graph-theory
- r
- r-package
references:
- type: software
title: sfnetworks
abstract: 'sfnetworks: Tidy Geospatial Networks'
notes: Imports
url: https://luukvdmeer.github.io/sfnetworks/
repository: https://CRAN.R-project.org/package=sfnetworks
authors:
- family-names: Meer
given-names: Lucas
name-particle: van der
email: luukvandermeer@live.nl
orcid: https://orcid.org/0000-0001-6336-8628
- family-names: Abad
given-names: Lorena
email: lore.abad6@gmail.com
orcid: https://orcid.org/0000-0003-0554-734X
- family-names: Gilardi
given-names: Andrea
email: andrea.gilardi@unimib.it
orcid: https://orcid.org/0000-0002-9424-7439
- family-names: Lovelace
given-names: Robin
email: r.lovelace@leeds.ac.uk
orcid: https://orcid.org/0000-0001-5679-6536
year: '2025'
doi: 10.32614/CRAN.package.sfnetworks
- type: software
title: sf
abstract: 'sf: Simple Features for R'
notes: Imports
url: https://r-spatial.github.io/sf/
repository: https://CRAN.R-project.org/package=sf
authors:
- family-names: Pebesma
given-names: Edzer
email: edzer.pebesma@uni-muenster.de
orcid: https://orcid.org/0000-0001-8049-7069
year: '2025'
doi: 10.32614/CRAN.package.sf
- type: software
title: terra
abstract: 'terra: Spatial Data Analysis'
notes: Imports
url: https://rspatial.org/
repository: https://CRAN.R-project.org/package=terra
authors:
- family-names: Hijmans
given-names: Robert J.
email: r.hijmans@gmail.com
orcid: https://orcid.org/0000-0001-5872-2872
year: '2025'
doi: 10.32614/CRAN.package.terra
- type: software
title: leaflet
abstract: 'leaflet: Create Interactive Web Maps with the JavaScript ''Leaflet''
Library'
notes: Imports
url: https://rstudio.github.io/leaflet/
repository: https://CRAN.R-project.org/package=leaflet
authors:
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Schloerke
given-names: Barret
email: barret@posit.co
orcid: https://orcid.org/0000-0001-9986-114X
- family-names: Karambelkar
given-names: Bhaskar
- family-names: Xie
given-names: Yihui
year: '2025'
doi: 10.32614/CRAN.package.leaflet
- type: software
title: leaflet.minicharts
abstract: 'leaflet.minicharts: Mini Charts for Interactive Maps'
notes: Imports
repository: https://CRAN.R-project.org/package=leaflet.minicharts
authors:
- family-names: Bachelier
given-names: Veronique
email: veronique.bachelier@rte-france.com
- family-names: ZAWAM
given-names: Jalal-Edine
- family-names: Thieurmel
given-names: Benoit
email: benoit.thieurmel@datastorm.fr
- family-names: Guillem
given-names: Francois
year: '2025'
doi: 10.32614/CRAN.package.leaflet.minicharts
- type: software
title: leaflet.extras2
abstract: 'leaflet.extras2: Extra Functionality for ''leaflet'' Package'
notes: Imports
url: https://trafficonese.github.io/leaflet.extras2/
repository: https://CRAN.R-project.org/package=leaflet.extras2
authors:
- family-names: Sebastian
given-names: Gatscha
email: sebastian_gatscha@gmx.at
year: '2025'
doi: 10.32614/CRAN.package.leaflet.extras2
- type: software
title: methods
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2025'
- type: software
title: stats
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2025'
- type: software
title: 'R: A Language and Environment for Statistical Computing'
notes: Depends
url: https://www.R-project.org/
authors:
- name: R Core Team
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2025'
version: '>= 4.1.0'
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
notes: Suggests
url: https://yihui.org/knitr/
repository: https://CRAN.R-project.org/package=knitr
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2025'
doi: 10.32614/CRAN.package.knitr
- type: software
title: rmarkdown
abstract: 'rmarkdown: Dynamic Documents for R'
notes: Suggests
url: https://pkgs.rstudio.com/rmarkdown/
repository: https://CRAN.R-project.org/package=rmarkdown
authors:
- family-names: Allaire
given-names: JJ
email: jj@posit.co
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
- family-names: Dervieux
given-names: Christophe
email: cderv@posit.co
orcid: https://orcid.org/0000-0003-4474-2498
- family-names: McPherson
given-names: Jonathan
email: jonathan@posit.co
- family-names: Luraschi
given-names: Javier
- family-names: Ushey
given-names: Kevin
email: kevin@posit.co
- family-names: Atkins
given-names: Aron
email: aron@posit.co
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Chang
given-names: Winston
email: winston@posit.co
- family-names: Iannone
given-names: Richard
email: rich@posit.co
orcid: https://orcid.org/0000-0003-3925-190X
year: '2025'
doi: 10.32614/CRAN.package.rmarkdown
- type: software
title: testthat
abstract: 'testthat: Unit Testing for R'
notes: Suggests
url: https://testthat.r-lib.org
repository: https://CRAN.R-project.org/package=testthat
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2025'
doi: 10.32614/CRAN.package.testthat
version: '>= 3.0.0'
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cran.r-project.org: SeaGraphs
Sea Currents to Connectivity Transformation
- Homepage: https://github.com/cadam00/SeaGraphs
- Documentation: http://cran.r-project.org/web/packages/SeaGraphs/SeaGraphs.pdf
- License: GPL-3
-
Latest release: 0.1.3
published 7 months ago
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Dependencies
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- r-lib/actions/setup-r v2 composite
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- leaflet * imports
- leaflet.extras2 * imports
- leaflet.minicharts * imports
- methods * imports
- sf * imports
- sfnetworks * imports
- stats * imports
- terra * imports
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
- R >= 2.10 depends
- htmltools * imports
- leaflet >= 1.1.0 imports
- covr * suggests
- dplyr * suggests
- knitr * suggests
- manipulateWidget * suggests
- rmarkdown * suggests
- shiny * suggests
- testthat * suggests
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