plot-methods {sampSurf}R Documentation

Methods for graphics Function plot in Package ‘sampSurf’

Description

The methods described here are for the plot generic as used in the sampSurf package. Each of the methods shown below has different arguments that customize it for a different class of objects found in this package. Method dispatch is based on the signature x,y arguments, and often, the latter is "missing" so only the first argument is necessary to associate the appropriate method.

Methods

The methods below are catagorized by their main signature argument, which corresponds to one of the classes in package “sampSurf”.

The following arguments may be used in all of the routines below. They share the same definition in each method and are defined as...

Some of the routines may specify a different default for these depending upon the desired outcome. Obviously, the defaults can be overridden, and they can be used in routines where they are not explicitly part of the argument definition for the most part.

For the most part, the methods below are organized alphabetically in sections based on the class. The exception is the stem-based Monte Carlo subsampling methods, which are at the end (areal versions are, however, treated within the “InclusionZone” section).

The “ArealSampling” Class

signature(x = "ArealSampling", y = "missing")

The base method for this class, it only plots the location slot of subclass objects. Note that since “ArealSampling” is a virtual class, this method just provides very generic capabilities that will eventually be shared among all subclasses and will never therefore be called outright based on its signature (but only through callNextMethod).

usage...

plot(x, 
     pchIZCenter = 20,
     izCenterColor = .StemEnv$izCenterColor,
     asp = 1,
     ... )
signature(x = "circularPlot", y = "missing")

This adds the necessary functionality to plot objects of class "circularPlot".

usage...

plot(x, 
     axes = FALSE, 
     izColor = .StemEnv$izColor,
     pchPlotCenter = 3, 
     showPlotCenter = FALSE,
     showPerimeter = TRUE,
     borderColor = .StemEnv$izBorderColor, 
     plotCenterColor = .StemEnv$izCenterColor, 
     asp = 1,
     ... )
signature(x = "lineSegment", y = "missing")

This adds the necessary functionality to plot objects of class "lineSegment".

usage...

plot(x,
     axes = FALSE, 
     pchLineCenter = 20,
     showLineCenter = FALSE,
     showLineSegment = TRUE,
     lineColor = .StemEnv$izBorderColor, 
     lineCenterColor = .StemEnv$izCenterColor,
     asp = 1,
     ... ) 

The “InclusionZone” Class

signature(x = "InclusionZone", y = "missing")

The base method for this class, it does not plot anything visible other than axes if desired; its role is to set up the extents of the plot from a subclass object's bounding box. Note that since “InclusionZone” is a virtual class, this method just provides very generic capabilities that will eventually be shared among all subclasses and will never therefore be called outright based on its signature (but only through callNextMethod).

usage...

plot(x, 
     axes = FALSE,        
     asp = 1,
     ... )
signature(x = "standUpIZ", y = "missing")

This adds the necessary functionality to plot objects of class "standUpIZ".

usage...

plot(x, 
     axes = FALSE, 
     showLog = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE,  
     asp = 1,
     ... )
signature(x = "sausageIZ", y = "missing")

This adds the necessary functionality to plot objects of class "sausageIZ".

usage...

plot(x, 
     axes = FALSE,
     showLog = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE, 
     asp = 1,
     ... )
signature(x = "chainSawIZ", y = "missing")

This adds the necessary functionality to plot objects of class "chainSawIZ".

usage...

plot(x, 
     axes = FALSE,  
     showLog = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     showSliver = TRUE,
     ltySliver = 'dashed',
     sliverBorder = 'black',
     sliverColor = transparentColorBase('coral', .StemEnv$alphaTrans),
     showBolt = TRUE,
     ltyBolt = 'dotted',
     boltBorder =  transparentColorBase('grey20', .StemEnv$alphaTrans),
     add = FALSE,
     asp = 1,
     ... )
signature(x = "pointRelascopeIZ", y = "missing")

This adds the necessary functionality to plot objects of class "pointRelascopeIZ".

usage...

plot(x, 
     axes = FALSE,    
     showLog = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE,    
     asp = 1,
     showDualCenters = FALSE, 
     dcColor = .StemEnv$izBorderColor, 
     ... )
signature(x = "perpendicularDistanceIZ", y = "missing")

This adds the necessary functionality to plot objects of class "perpendicularDistanceIZ" and subclasses (e.g., "omnibusPDSIZ").

usage...

plot(x, 
     axes = FALSE,  
     showLog = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE,  
     asp = 1,
     ... )
signature(x = "distanceLimitedPDSIZ", y = "missing")

This adds the necessary functionality to plot objects of class "distanceLimitedPDSIZ" and subclasses (e.g., "omnibusDLPDSIZ" and "hybridDLPDSIZ"). Please note that the different components of the inclusion zone can be displayed to show the transition between protocols (if any). In addition, the overall "perpendicularDistanceIZ" zone can also be displayed, showing what the inclusion zone would look like if the entire log were treated under the PDS protocol.

usage...

plot(x, 
     axes = FALSE,  
     showLog = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE,  
     asp = 1,
     showFullPDSIZ = FALSE,
     showDLSPart = FALSE,
     showPDSPart = FALSE,
     ... )
signature(x = "distanceLimitedIZ", y = "missing")

This adds the necessary functionality to plot objects of class "distanceLimitedIZ" and subclass "distanceLimitedMCIZ".

usage...

plot(x, 
     axes = FALSE,  
     showLog = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE,  
     asp = 1,
     ... )
signature(x = "circularPlotIZ", y = "missing")

This adds the necessary functionality to plot objects of class "circularPlotIZ" as well as those of its subclass "horizontalPointIZ". In addition, the following subclasses derived from “horizontalPointIZ” also use this method: "horizontalPointCMCIZ", "horizontalPointISIZ", "horizontalPointCVIZ" "criticalHeightIZ", "importanceCHSIZ", "antitheticICHSIZ", and "pairedAICHSIZ".

usage...

plot(x, 
     axes = FALSE,  
     showTree = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE,  
     asp = 1,
     ... )
signature(x = "horizontalLineIZ", y = "missing")

This adds the necessary functionality to plot objects of class "horizontalLineIZ".

usage...

plot(x, 
     axes = FALSE,  
     showLineSegment = TRUE,
     ltyLineSegment = 'dashed',
     showTree = TRUE,
     izColor = .StemEnv$izColor,
     izBorder = .StemEnv$izBorderColor,
     add = FALSE,
     asp = 1,
     ... ) 

The “InclusionZoneGrid” Class

signature(x = "InclusionZoneGrid", y = "missing")

The base method for this class, it actually supplies all of the functionality for all existing subclasses, since the internal “InclusionZone” object will have its own plotting method (see above), which will automatically be used, and this object is all that really differentiates the objects of class "InclusionZoneGrid".

usage...

plot(x, 
     axes = TRUE,
     gridColor = .StemEnv$blue.colors(1000),
     asp = 1,
     izColor = NA,
     gridLines = TRUE,
     gridLineColor = .StemEnv$gridLineColor,
     gridCenters = FALSE, 
     gridCenterColor = .StemEnv$gridCenterColor,
     estimate = names(c(.StemEnv$puaEstimates, .StemEnv$ppEstimates)),
     lwdGrid = 1, 
     ... )

The “izContainer” Class

signature(x = "izContainer", y = "missing")

This adds the necessary functionality to plot subclass objects of container class "izContainer", including both "downLogIZs" and "standingTreeIZs" . Note that arguments passed in this call that are destined for individual “downLogIZ” or “downLog” objects within the collection will apply to all objects of that class within the collection; similarly for standing tree components.

usage...

plot(x, 
     axes = FALSE,  
     add = FALSE, 
     asp = 1,
     ... )

The “mirageInclusionZoneGrid” Class

signature(x = "mirageInclusionZoneGrid", y = "missing")

This method will call the superclass method for the desired “InclusionZoneGrid” object (see below). Please see the superclass method for other arguments that can be passed on.

usage...

plot(x,
     tract = NULL,
     tractBorder = 'red',
     lwdTract = 1.25,
     showExtended = FALSE,
     showReflectedSlivers = FALSE,
     colReflections = 'blue',
     ... )

The “sampSurf” Class

signature(x = "sampSurf", y = "missing")

This is the only extant method for plotting objects of class "sampSurf." It makes use of many of the plotting methods for the other objects in the sampSurf package, some of which also rely on plot methods from the raster package.

usage...

plot(x, 
     showIZs = TRUE,
     izColor = NA,  
     ... )

The “Stem” Class

signature(x = "Stem", y = "missing")

The base method for this class, it only plots the location slot of subclass objects. Note that since “Stem” is a virtual class, this method just provides very generic capabilities that will eventually be shared among all subclasses and will never therefore be called outright based on its signature (but only through callNextMethod).

usage...

plot(x, 
     pchStemLocation = 20,    
     stemLocationColor = .StemEnv$logAttributeColor,
     ... )
signature(x = "downLog", y = "missing")

This adds the necessary functionality to plot objects of class "downLog".

usage...

plot(x,
     axes = FALSE, 
     logColor = .StemEnv$logColor,	 
     showLogCenter = FALSE,
     pchLogCenter = 3,     
     logCenterColor = .StemEnv$logAttributeColor,
     showNeedle = FALSE,
     logNeedleColor = .StemEnv$logAttributeColor,
     logBorderColor = .StemEnv$logBorderColor,   
     asp = 1,
     ... )
signature(x = "standingTree", y = "missing")

This adds the necessary functionality to plot objects of class "standingTree".

usage...

plot(x,
     axes = FALSE,
     treeColor = .StemEnv$treeColor,
     showLocation = TRUE,
     pchLocation = 3,       #20 is also good
     locationColor = .StemEnv$treeAttributeColor,
     treeBorderColor = .StemEnv$treeBorderColor,   #log perimeter color
     asp = 1,
     ... )

The “StemContainer” Class

signature(x = "StemContainer", y = "missing")

The base method for this class. Note that since “StemContainer” is a virtual class, this method just provides very generic capabilities that are shared among all subclasses and will never therefore be called outright based on its signature (but only through callNextMethod). Currently, it just sets up the overall extents for the plot area.

usage...

plot(x, 
     axes = FALSE, 
     add = FALSE, 
     asp = 1,
     ... )
signature(x = "downLogs", y = "missing")

This adds the necessary functionality to plot objects of container class "downLogs". Note that arguments passed in this call that are destined for individual “downLog” objects within the collection will apply to all logs within the collection.

usage...

plot(x, 
     axes = FALSE,
     add = FALSE,
     asp = 1,
     ... )
signature(x = "standingTrees", y = "missing")

This adds the necessary functionality to plot objects of container class "standingTrees". Note that arguments passed in this call that are destined for individual “standingTree” objects within the collection will apply to all trees within the collection.

usage...

plot(x, 
     axes = FALSE,
     add = FALSE,
     asp = 1,
     ... )

The “Tract” Class

signature(x = "Tract", y = "missing")

This method is the base plot method for objects of class "Tract" and subclasses. Because “Tract” objects are a subclass of "RasterLayer," all of the plotting is done through calls to those methods.

usage...

plot(x,
     axes = TRUE,  
     gridColor = .StemEnv$blue.colors(1000),
     asp = 1,
     useImage = TRUE,
     ... )
signature(x = "bufferedTract", y = "missing")

This is the plot method for objects of class "bufferedTract" and subclasses. It essentially calls the bas “Tract” method for all of the work and adds the buffer.

usage...

plot(x,
     bufferColor = transparentColorBase('blanchedalmond', .StemEnv$alphaTrans),
     axes = TRUE, 
     gridColor = .StemEnv$blue.colors(1000),      
     lwd = 2,
     asp = 1,
     ... )

The “MonteCarloSampling” Class

signature(x = "crudeMonteCarlo", y = "missing")

The “importanceSampling” and “controlVariate” sampling classes use this method as well.

usage...

plot(x,
     axes = FALSE,
     renderAs = c('profile', 'crossSection'),
     isHeightColor = .StemEnv$isHeightColor,
     ... )

The “mcsContainer” Class

signature(x = "mcsContainer", y = "missing")

Display the true versus estimated volumes graphically. Please note that this method applies to objects of class “antitheticContainer” as well.

usage...

plot(x,
     xlab = 'Estimated volume',
     ylab = 'True volume',
     showDiagonal = TRUE,
     ... )

[Package sampSurf version 0.7-5 Index]