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. 2014 Jun 16;9(6):e100195. doi: 10.1371/journal.pone.0100195

Table 3. List of dependencies (other R add-on packages) for VMSbase.

Package Name Scope Reference
CairoDevice: Cairo-basedcross-platform antialiasedgraphics device driver Cairo/GTK graphics device driver withoutput to screen, file (png, svg, pdf, and ps)or memory (arbitrary GdkDrawable orCairo context). [46]
chron: Chronological objects whichcan handle dates and times Chronological objects which can handledates and times [47]
cluster: Cluster Analysis ExtendedRousseeuw et al Cluster Analysis, extended original fromPeter Rousseeuw, Anja Struyf and MiaHubert. [21], [48]
Ecodist: Dissimilarity-based functionsfor ecological analysis Dissimilarity-based analysis functionsincluding ordination and Mantel testfunctions, intended for use with spatialand community data. [49]
Fields: Tools for spatial data Fields is for curve, surface and functionfitting with an emphasis on splines, spatialdata and spatial statistics. Implementationof sparse matrix methods for large data setsand currently requires the sparse matrix(spam) package for testing and use withlarge data sets. [50]
Ggmap: A package for spatialvisualization with Google Mapsand OpenStreetMap Visualization of spatial data and modelson top of Google Maps, OpenStreetMaps,Stamen Maps, or CloudMade Maps usingggplot2. [14]
Gwidgets:gWidgets API for buildingtoolkit-independent, interactive GUIs Toolkit-independent API for buildinginteractive GUIs. [51]
GWidgetsRGtk: Toolkit implementationof gWidgets for RGtk2 Port of gWidgets API to RGtk2 [52]
Intervals: Weighted Logrank Testsand NPMLE for interval censored data Functions to fit nonparametric survivalcurves, plot them, and perform logrankor Wilcoxon type tests. [53]
Mapdata: Extra Map Databases Supplement to maps package, providingthe larger and/or higher-resolution databases. [54]
Maps:Draw Geographical Maps Display of maps. Projection code andlarger maps are in separate packages(mapproj and mapdata) [55]
Maptools: Tools for reading andhandling spatial objects Set of tools for manipulating and readinggeographic data, in particular ESRIshapefiles; C code used from shapelib.It includes binary access to GSHHSshoreline files. The package also providesinterface wrappers for exchanging spatialobjects with packages such asPBSmapping, spatstat, maps, RArcInfo,Stata tmap, WinBUGS, Mondrian, andothers. [56]
marmap: Import, plot and analyzebathymetric and topographic data Import, plot and analyze bathymetric andtopographic data [12]
Outliers: Tests for outliers A collection of some tests commonlyused for identifying outliers [57]
PBSmapping: Mapping FisheriesData and Spatial Analysis Tools Two-dimensional plotting featuressimilar to those commonly availablein a Geographic Information System(GIS). Embedded C code speedsalgorithms from computational geometry,such as finding polygons that containspecified point events or convertingbetween longitude-latitude andUniversal Transverse Mercator (UTM)coordinates. [13], [58]
Plotrix: Various plotting functions Lots of plots, various labeling, axis andcolor scaling functions [59]
Sp: classes and methodsfor spatial data Classes and methods for spatial data.The classes document where the spatiallocation information resides, for 2Dor 3D data. [60]
Sqldf: Perform SQL Selects onR Data Frames Manipulate R data frames using SQL. [11]