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.

Moitinho-Silva, L, G Steinert, S Nielsen, C C P Hardoim, Y-C Wu, G P McCormack, S López-Legentil, et al. 2017. “Predicting the Hma-Lma Status in Marine Sponges by Machine Learning.” Frontiers in Microbiology 8: 752. https://doi.org/10.3389/fmicb.2017.00752.

Murillo, Fj, E Kenchington, G Tompkins, L Beazley, E Baker, A Knudby, and W Walkusz. 2018. “Sponge Assemblages and Predicted Archetypes in the Eastern Canadian Arctic.” Marine Ecology Progress Series 597 (June): 115–35. https://doi.org/10.3354/meps12589.

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.

———. 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.

———. 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/.

———. 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.