5 Funding disclaimer

This study was financially supported by the SponGES project from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 679849. This document reflects only the authors’ view and the Executive Agency for Small and Medium-sized Enterprises (EASME) is not responsible for any use that may be made of the information it contains.
For more information, please visit the SponGES website.

# automatically create a bib database for R packages
knitr::write_bib(c(.packages(), "bookdown", "knitr", "rmarkdown", "kableExtra", "ggplot2", "ggmap", "maps", "mapdata", "marmap", "ggrepel", "lattice", "sf", "rnaturalearth", 
    "rnaturalearthdata", "vegan", "xcms", "camera", "ropls", "tidyverse", "stringr", "usdm", "reshape2", "gridExtra", "dplyr", "plotly", "phyloseq", "seqinr", 
    "igraph"), "packages.bib")

Maps were made with the pacakges marmap (Pante and Simon-Bouhet 2013), ggmap (Kahle and Wickham 2013), maps (Brownrigg 2018), mapdata (Richard A. Becker and Ray Brownrigg. 2018), sf (Pebesma 2018), rnaturalearth (South 2017b), rnaturalearthdata (South 2017a), lattice (Sarkar 2008). Analyses used the functionalities from R (R Core Team 2018) as well as the packages usdm (Naimi et al. 2014), tidyverse (Wickham et al. 2019), plotly (Sievert et al. 2020), dplyr (Wickham et al. 2020), stringr (Wickham 2019), kableExtra (Zhu 2019), GridExtra (Auguie 2017), ggrepel (Slowikowski 2020), reshape2 (Wickham 2017), knitr (Xie 2015), Rmarkadown (Xie, Allaire, and Grolemund 2018) and bookdown (Xie 2020). Specifically, metabolomics relied on XCMS (Smith et al. 2006), (Tautenhahn, Boettcher, and Neumann 2008), (Benton, Want, and Ebbels 2010) with CAMERA (Kuhl et al. 2012) ROPLS (Thevenot et al. 2015), and the microbiome analyses on vegan (Oksanen et al. 2019), phyloseq (McMurdie and Holmes 2013), seqinr (Charif and Lobry 2019), and igraph (Csardi and Nepusz 2006).

References

Auguie, Baptiste. 2017. GridExtra: Miscellaneous Functions for "Grid" Graphics. https://CRAN.R-project.org/package=gridExtra.

Benton, H. Paul, Elizabeth J. Want, and Timothy M. D. Ebbels. 2010. “Correction of Mass Calibration Gaps in Liquid Chromatography-Mass Spectrometry Metabolomics Data.” BIOINFORMATICS 26: 2488.

Brownrigg, Ray. 2018. Maps: Draw Geographical Maps. https://CRAN.R-project.org/package=maps.

Charif, Delphine, and Jean R. Lobry. 2019. Seqinr: Biological Sequences Retrieval and Analysis. https://CRAN.R-project.org/package=seqinr.

Csardi, Gabor, and Tamas Nepusz. 2006. “The Igraph Software Package for Complex Network Research.” InterJournal Complex Systems: 1695. http://igraph.org.

Kahle, David, and Hadley Wickham. 2013. “Ggmap: Spatial Visualization with Ggplot2.” The R Journal 5 (1): 144–61. https://journal.r-project.org/archive/2013-1/kahle-wickham.pdf.

Kuhl, C., R. Tautenhahn, C. Boettcher, T. R. Larson, and S. Neumann. 2012. “CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets.” Analytical Chemistry 84: 283–89. http://pubs.acs.org/doi/abs/10.1021/ac202450g.

McMurdie, Paul J., and Susan Holmes. 2013. “Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data.” PLoS ONE 8 (4): e61217. http://dx.plos.org/10.1371/journal.pone.0061217.

Naimi, Babak, Nicholas a.s. Hamm, Thomas A. Groen, Andrew K. Skidmore, and Albertus G. Toxopeus. 2014. “Where Is Positional Uncertainty a Problem for Species Distribution Modelling.” Ecography 37: 191–203. https://doi.org/10.1111/j.1600-0587.2013.00205.x.

Oksanen, Jari, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, et al. 2019. Vegan: Community Ecology Package. https://CRAN.R-project.org/package=vegan.

Pante, Eric, and Benoit Simon-Bouhet. 2013. “Marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R.” PLoS ONE 8 (9): e73051.

Pebesma, Edzer. 2018. “Simple Features for R: Standardized Support for Spatial Vector Data.” The R Journal 10 (1): 439–46. https://doi.org/10.32614/RJ-2018-009.

R Core Team. 2018. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

Richard A. Becker, Original S code by, and Allan R. Wilks. R version by Ray Brownrigg. 2018. Mapdata: Extra Map Databases. https://CRAN.R-project.org/package=mapdata.

Sarkar, Deepayan. 2008. Lattice: Multivariate Data Visualization with R. New York: Springer. http://lmdvr.r-forge.r-project.org.

Sievert, Carson, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec, and Pedro Despouy. 2020. Plotly: Create Interactive Web Graphics via ’Plotly.js’. https://CRAN.R-project.org/package=plotly.

Slowikowski, Kamil. 2020. Ggrepel: Automatically Position Non-Overlapping Text Labels with ’Ggplot2’. https://CRAN.R-project.org/package=ggrepel.

Smith, C.A., Want, E.J., O’Maille, G., Abagyan,R., Siuzdak, and G. 2006. “XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching and Identification.” Analytical Chemistry 78: 779–87.

South, Andy. 2017a. Rnaturalearthdata: World Vector Map Data from Natural Earth Used in ’Rnaturalearth’. https://CRAN.R-project.org/package=rnaturalearthdata.

South, Andy. 2017b. Rnaturalearth: World Map Data from Natural Earth. https://CRAN.R-project.org/package=rnaturalearth.

Tautenhahn, Ralf, Christoph Boettcher, and Steffen Neumann. 2008. “Highly Sensitive Feature Detection for High Resolution Lc/Ms.” BMC Bioinformatics 9: 504.

Thevenot, E. A., A. Roux, Y. Xu, E. Ezan, and C. Junot. 2015. “Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index and Gender by Implementing a Comprehensive Workflow for Univariate and Opls Statistical Analyses.” Journal of Proteome Research 14: 3322–35. http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354.

Wickham, Hadley. 2017. Reshape2: Flexibly Reshape Data: A Reboot of the Reshape Package. https://CRAN.R-project.org/package=reshape2.

Wickham, Hadley. 2019. Stringr: Simple, Consistent Wrappers for Common String Operations. https://CRAN.R-project.org/package=stringr.

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.

Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2020. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.

Xie, Yihui. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.

Xie, Yihui. 2020. Bookdown: Authoring Books and Technical Documents with R Markdown. https://CRAN.R-project.org/package=bookdown.

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.

Zhu, Hao. 2019. KableExtra: Construct Complex Table with ’Kable’ and Pipe Syntax.