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marmap: A package for importing, plotting and analyzing bathymetric and topographic data in R.

Pante E, Simon-Bouhet B - PLoS ONE (2013)

Bottom Line: In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps.Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances.Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.

View Article: PubMed Central - PubMed

Affiliation: Littoral, Environnement et Sociétés Joint Research Unit 7266 Centre National de la Recherche Scientifique, Université de La Rochelle, La Rochelle, France.

ABSTRACT
In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps. Functions to query data (bathymetry, sampling information…) are available interactively by clicking on marmap maps. Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances. Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.

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Examples of two and three dimensional plots created using marmap tools.Left panel (A): data from the NW Atlantic Ocean, showing the NE coast of the USA and the New England and Corner Rise seamounts chains. The blue line represents the position of two- (B) and three- (C) dimensional cross sections, the red rectangle delimiting the area covered by the belt transect. The bottom left figure (D) represents the NW Atlantic data as plotted with the wireframe function from package lattice [21], based on data imported with marmap. Right panel: map of Papua New Guinea and satellite islands (E; see text). The middle figure (F) represents the results of a least-cost path analysis around the Hawaiian islands (coastline in thick black, dark grey: 1000 m isobath, light grey 4000 m isobath; red line: path avoiding waters shallower than 1000 m, blue line: path avoiding waters shallower than 4000 m). The bottom figure (G) represents the results of projected surface area calculations for the bathyal and abyssal areas around the Hawaiian islands. R code is available in File S1.
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pone-0073051-g001: Examples of two and three dimensional plots created using marmap tools.Left panel (A): data from the NW Atlantic Ocean, showing the NE coast of the USA and the New England and Corner Rise seamounts chains. The blue line represents the position of two- (B) and three- (C) dimensional cross sections, the red rectangle delimiting the area covered by the belt transect. The bottom left figure (D) represents the NW Atlantic data as plotted with the wireframe function from package lattice [21], based on data imported with marmap. Right panel: map of Papua New Guinea and satellite islands (E; see text). The middle figure (F) represents the results of a least-cost path analysis around the Hawaiian islands (coastline in thick black, dark grey: 1000 m isobath, light grey 4000 m isobath; red line: path avoiding waters shallower than 1000 m, blue line: path avoiding waters shallower than 4000 m). The bottom figure (G) represents the results of projected surface area calculations for the bathyal and abyssal areas around the Hawaiian islands. R code is available in File S1.

Mentions: Once loaded into R, bathymetric data are re-organized as a matrix that is used for manipulation, plotting and exporting. These data are represented as an R class called “bathy”, valid within a marmap session. The creation of a custom R class allows the use of generic functions such as plot and summary. Bathymetric data of class “bathy” can be plotted with the streamlined marmap plotting tools, or used with other geographic analysis packages (e.g. “maps” [9]). Bathymetric data can be plotted as simple contour plots, with control over the range, density and look of isobaths, or with automatic isobath choice and placement. Contour plots can be coupled with heat maps with built-in and customizable color ramps (Figure 1A,E). Sampling data (GPS points, tracks, polygons, etc…) and text (legends, labels, scales, etc…) can simply be added to marmap maps using R low-level functions.


marmap: A package for importing, plotting and analyzing bathymetric and topographic data in R.

Pante E, Simon-Bouhet B - PLoS ONE (2013)

Examples of two and three dimensional plots created using marmap tools.Left panel (A): data from the NW Atlantic Ocean, showing the NE coast of the USA and the New England and Corner Rise seamounts chains. The blue line represents the position of two- (B) and three- (C) dimensional cross sections, the red rectangle delimiting the area covered by the belt transect. The bottom left figure (D) represents the NW Atlantic data as plotted with the wireframe function from package lattice [21], based on data imported with marmap. Right panel: map of Papua New Guinea and satellite islands (E; see text). The middle figure (F) represents the results of a least-cost path analysis around the Hawaiian islands (coastline in thick black, dark grey: 1000 m isobath, light grey 4000 m isobath; red line: path avoiding waters shallower than 1000 m, blue line: path avoiding waters shallower than 4000 m). The bottom figure (G) represents the results of projected surface area calculations for the bathyal and abyssal areas around the Hawaiian islands. R code is available in File S1.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3760912&req=5

pone-0073051-g001: Examples of two and three dimensional plots created using marmap tools.Left panel (A): data from the NW Atlantic Ocean, showing the NE coast of the USA and the New England and Corner Rise seamounts chains. The blue line represents the position of two- (B) and three- (C) dimensional cross sections, the red rectangle delimiting the area covered by the belt transect. The bottom left figure (D) represents the NW Atlantic data as plotted with the wireframe function from package lattice [21], based on data imported with marmap. Right panel: map of Papua New Guinea and satellite islands (E; see text). The middle figure (F) represents the results of a least-cost path analysis around the Hawaiian islands (coastline in thick black, dark grey: 1000 m isobath, light grey 4000 m isobath; red line: path avoiding waters shallower than 1000 m, blue line: path avoiding waters shallower than 4000 m). The bottom figure (G) represents the results of projected surface area calculations for the bathyal and abyssal areas around the Hawaiian islands. R code is available in File S1.
Mentions: Once loaded into R, bathymetric data are re-organized as a matrix that is used for manipulation, plotting and exporting. These data are represented as an R class called “bathy”, valid within a marmap session. The creation of a custom R class allows the use of generic functions such as plot and summary. Bathymetric data of class “bathy” can be plotted with the streamlined marmap plotting tools, or used with other geographic analysis packages (e.g. “maps” [9]). Bathymetric data can be plotted as simple contour plots, with control over the range, density and look of isobaths, or with automatic isobath choice and placement. Contour plots can be coupled with heat maps with built-in and customizable color ramps (Figure 1A,E). Sampling data (GPS points, tracks, polygons, etc…) and text (legends, labels, scales, etc…) can simply be added to marmap maps using R low-level functions.

Bottom Line: In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps.Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances.Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.

View Article: PubMed Central - PubMed

Affiliation: Littoral, Environnement et Sociétés Joint Research Unit 7266 Centre National de la Recherche Scientifique, Université de La Rochelle, La Rochelle, France.

ABSTRACT
In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps. Functions to query data (bathymetry, sampling information…) are available interactively by clicking on marmap maps. Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances. Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.

Show MeSH
Related in: MedlinePlus