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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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Related in: MedlinePlus

Exemple of ETOPO1 data downloaded with the marmap package, transformed with the raster package, and plotted with marmap.Orthographic projection, resolution of 10 minutes. R code is available in File S1.
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pone-0073051-g002: Exemple of ETOPO1 data downloaded with the marmap package, transformed with the raster package, and plotted with marmap.Orthographic projection, resolution of 10 minutes. R code is available in File S1.

Mentions: marmap interacts with multiple existing R packages for visualization and analysis, such as lattice for building three-dimensional plots (Figure 1C–D), and gdistance for least-cost path calculations (see above). marmap also contains functions to ease interactions with other packages dedicated to the analysis of spatial data. Data from class bathy can be transformed into raster objets for use in the raster package [10] (functions trans.mat and as.raster). Bathy objects can also be converted into the class SpatialGridDataFrame for use in the sp package [16], [17] (function as.SpatialGridDataFrame). These transformed objects can be converted back into objects of class bathy using the as.bathy function. In the example below, the package raster is used to change the projection of a dataset extracted from ETOPO1. The first line creates a raster object from a bathy object, the second defines the target projection (PROJ.4 format), the third creates a new projected raster object, and the last converts the new raster projection into a bathy object for plotting with marmap. Figure 2 provides an example of such transformed data.


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

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

Exemple of ETOPO1 data downloaded with the marmap package, transformed with the raster package, and plotted with marmap.Orthographic projection, resolution of 10 minutes. R code is available in File S1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3760912&req=5

pone-0073051-g002: Exemple of ETOPO1 data downloaded with the marmap package, transformed with the raster package, and plotted with marmap.Orthographic projection, resolution of 10 minutes. R code is available in File S1.
Mentions: marmap interacts with multiple existing R packages for visualization and analysis, such as lattice for building three-dimensional plots (Figure 1C–D), and gdistance for least-cost path calculations (see above). marmap also contains functions to ease interactions with other packages dedicated to the analysis of spatial data. Data from class bathy can be transformed into raster objets for use in the raster package [10] (functions trans.mat and as.raster). Bathy objects can also be converted into the class SpatialGridDataFrame for use in the sp package [16], [17] (function as.SpatialGridDataFrame). These transformed objects can be converted back into objects of class bathy using the as.bathy function. In the example below, the package raster is used to change the projection of a dataset extracted from ETOPO1. The first line creates a raster object from a bathy object, the second defines the target projection (PROJ.4 format), the third creates a new projected raster object, and the last converts the new raster projection into a bathy object for plotting with marmap. Figure 2 provides an example of such transformed data.

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