plot-methods: Methods for 'graphics' Function 'plot' in Package 'sampSurf'
In sampSurf: Sampling Surface Simulation for Areal Sampling Methods
Description
Methods
The “ArealSampling” Class
The “InclusionZone” Class
The “InclusionZoneGrid” Class
The “izContainer” Class
The “mirageInclusionZoneGrid” Class
The “sampSurf” Class
The “Stem” Class
The “StemContainer” Class
The “Tract” Class
The “MonteCarloSampling” Class
The “mcsContainer” Class
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...
add: TRUE: add the desired graphics to an
existing plot; FALSE: create a new plot.
asp: The plot asp aspect
parameter. Best to leave this at the default, which is good for
mapping displays.
axes: TRUE: plot axes; FALSE: no axes.
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$izCenterColor,
asp = 1,
... )
x: An object that is a subclass of “ArealSampling”.
pchIZCenter: The pch parameter for
the inclusion zone center.
izCenterColor: An R color to be used for the
inclusion zone center point location.
... : Other graphics arguments to be passed on to
plot or points.
signature(x = "circularPlot", y = "missing")-
This adds the necessary functionality to plot objects of class
"circularPlot".
usage...
plot(x,
axes = FALSE,
izColor = .StemEnv$izColor,
pchPlotCenter = 3,
showPlotCenter = FALSE,
showPerimeter = TRUE,
borderColor = .StemEnv$izBorderColor,
plotCenterColor = .StemEnv$izCenterColor,
asp = 1,
... )
x: An object that is of class “circularPlot” or any
subclass that might eventually be defined.
izColor: An R color for the interior of the plot's
inclusion zone.
pchPlotCenter: The pch value for the
plot center.
showPlotCenter: TRUE: show the plot center;
FALSE: do not plot it.
showPerimeter: TRUE: show the plot perimeter;
FALSE: do not plot it. Please note that the only way to
show the whole inclusion zone is to show th perimeter. If you
want either the interior of the zone or the perimeter but not
both, set the color for the one you do not want displayed to
NA.
borderColor: An R color for the border/perimeter
of the plot's inclusion zone.
plotCenterColor: An R color for the center point
of the plot's inclusion zone.
... : Other graphics arguments to be passed on to
plot.
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,
... )
x: An object that is of class “lineSegment” or any
subclass that might eventually be defined.
pchLineCenter: The pch value for the
line center.
showLineCenter: TRUE: show the line center;
FALSE: do not plot it.
lineColor: An R color for the line.
lineCenterColor: An R color for the line's center point.
... : Other graphics arguments to be passed on to
plot.
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,
... )
x: An object that is a subclass of “InclusionZone”.
... : Other graphics arguments to be passed on to
plot.
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,
... )
x: An object that is of class “standUpIZ” or
any subclass that might be eventualy defined.
showLog: TRUE: plot the log object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
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,
... )
x: An object that is of class “sausageIZ” or
any subclass that might be eventualy defined.
showLog: TRUE: plot the log object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
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,
... )
x: An object that is of class “chainSawIZ” or
any subclass that might be eventualy defined.
showLog: TRUE: plot the log object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
showSliver: TRUE: show the sliver
intersection area; FALSE: do not show it.
ltySliver: The line type (see: par)
for the delineation of the sliver.
sliverBorder: An R color for the border/perimeter
of the sliver section.
sliverColor: An R color for the interior of the
sliver section; remember, this will plot on top of the log
interior color.
showBolt: TRUE: show the minimal bounding bolt
area; FALSE: do not show it.
ltyBolt: The line type (see: par)
for the delineation of the bounding bolt.
boltBorder: An R color for the border/perimeter
of the bounding bolt section.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
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$izBorderColor,
... )
x: An object that is of class “pointRelascopeIZ” or
any subclass that might be eventualy defined.
showLog: TRUE: plot the log object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
showDualCenters: TRUE: mark the dual circle
centers; FALSE: nothing.
dcColor: An R color for the dual circle centers.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
signature(x = "perpendicularDistanceIZ", y = "missing")-
This adds the necessary functionality to plot objects of class
"perpendicularDistanceIZ" and subclasses (e.g.,
"omnibusPDSIZ").
usage...
plot(x,
axes = FALSE,
showLog = TRUE,
izColor = .StemEnv$izColor,
izBorder = .StemEnv$izBorderColor,
add = FALSE,
asp = 1,
... )
x: An object that is of class “perpendicularDistanceIZ” or
subclass.
showLog: TRUE: plot the log object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
signature(x = "distanceLimitedPDSIZ", y = "missing")-
This adds the necessary functionality to plot objects of class
"distanceLimitedPDSIZ" and subclasses (e.g.,
"omnibusDLPDSIZ" and
"hybridDLPDSIZ"). Please note that the
different components of the inclusion zone can be displayed to show
the transition between protocols (if any). In addition, the overall
"perpendicularDistanceIZ" zone can also be
displayed, showing what the inclusion zone would look like if the
entire log were treated under the PDS protocol.
usage...
plot(x,
axes = FALSE,
showLog = TRUE,
izColor = .StemEnv$izColor,
izBorder = .StemEnv$izBorderColor,
add = FALSE,
asp = 1,
showFullPDSIZ = FALSE,
showDLSPart = FALSE,
showPDSPart = FALSE,
... )
x: An object that is of class “distanceLimitedPDSIZ” or
subclass.
showLog: TRUE: plot the log object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
showFullPDSIZ: TRUE: display the full PDS
inclusion zone (as if the log were sampled fully with PDS);
FALSE: do not display it.
showDLSPart: TRUE: display the
"distanceLimitedIZ" portion of the
inclusion zone (if any); FALSE: do not display it.
showPDSPart: TRUE: display the
"perpendicularDistanceIZ" portion of the
inclusion zone (if any); FALSE: do not display it.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
signature(x = "distanceLimitedIZ", y = "missing")-
This adds the necessary functionality to plot objects of class
"distanceLimitedIZ" and subclass
"distanceLimitedMCIZ".
usage...
plot(x,
axes = FALSE,
showLog = TRUE,
izColor = .StemEnv$izColor,
izBorder = .StemEnv$izBorderColor,
add = FALSE,
asp = 1,
... )
x: An object that is of class “distanceLimitedIZ” or
subclass.
showLog: TRUE: plot the log object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
signature(x = "circularPlotIZ", y = "missing")-
This adds the necessary functionality to plot objects of class
"circularPlotIZ" as well as those of its
subclass "horizontalPointIZ". In addition, the
following subclasses derived from “horizontalPointIZ” also
use this method:
"horizontalPointCMCIZ",
"horizontalPointISIZ",
"horizontalPointCVIZ"
"criticalHeightIZ",
"importanceCHSIZ",
"antitheticICHSIZ", and
"pairedAICHSIZ".
usage...
plot(x,
axes = FALSE,
showTree = TRUE,
izColor = .StemEnv$izColor,
izBorder = .StemEnv$izBorderColor,
add = FALSE,
asp = 1,
... )
x: An object that is of class “circularPlotIZ” or
subclass.
showTree: TRUE: plot the tree object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
signature(x = "horizontalLineIZ", y = "missing")-
This adds the necessary functionality to plot objects of class
"horizontalLineIZ".
usage...
plot(x,
axes = FALSE,
showLineSegment = TRUE,
ltyLineSegment = 'dashed',
showTree = TRUE,
izColor = .StemEnv$izColor,
izBorder = .StemEnv$izBorderColor,
add = FALSE,
asp = 1,
... )
x: An object that is of class “horizontalLineIZ”.
showLineSegment:TRUE: show the line segment;
FALSE: do not show it.
ltyLineSegment: A valid lty value of the
plot parameter.
showTree: TRUE: plot the tree object;
FALSE: do not show it.
izColor: An R color for the interior of the
inclusion zone.
izBorder: An R color for the border/perimeter of
the inclusion zone.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
The “InclusionZoneGrid” Class
signature(x = "InclusionZoneGrid", y =
"missing")-
The base method for this class, it actually supplies all of the
functionality for all existing subclasses, since the internal
“InclusionZone” object will have its own plotting method
(see above), which will automatically be used, and this object is
all that really differentiates the objects of class
"InclusionZoneGrid".
usage...
plot(x,
axes = TRUE,
gridColor = .StemEnv$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,
... )
x: An object that is of class “InclusionZoneGrid” or
any subclass that might be eventualy defined.
gridColor: A valid R color for the background
grid. Note that a single color is fine for most sampling
methods, but for an inclusion zone whose surface varies within a
single object like the “chainSawIZ”, you must supply a
colorRampPalette in order to see the variation
correctly.
izColor: An R color for the interior of the
inclusion zone. Note that the default is set to NA so that no
filling is done within the inclusion zone to show the grid more
clearly.
gridLines: TRUE: show grid lines delineated
for more emphasis on the individual grid cells; FALSE: no
grid lines. Note that this can get busy if the area is
too large.
gridLineColor: An R color for the grid lines.
gridCenters: TRUE: show grid cell centers
within the individual grid cells; FALSE: no
grid cell centers. Note that this can get busy if the area is
too large.
gridCenterColor: An R color for the grid cell
centers.
estimate: A character variable corresponding to the
desired estimate attribute; these include 'volume', 'Length'
(logs), 'Density', 'surfaceArea', 'coverageArea' (logs),
'basalArea' (trees), 'biomass' and 'carbon'. The sample 'depth'
surface is now also available.
lwdGrid: The graphics parameter line width (see:
par) for the grid lines.
...: Other graphical arguments to be passed on to
plot, or to the plot methods for the
individual objects (i.e., “InclusionZone”,
“downLog”).
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,
... )
x: An object that is of subclass “izContainer”.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual objects.
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',
... )
x: An object that is of class “mirageInclusionZoneGrid” or
any subclass that might be eventualy defined.
tract: An object of class
"mirageTract".
tractBorder: The color to be used to plot the tract
border polygon.
lwdTract: The line width for the tract border
polygon.
showExtended: TRUE: show the extended grid
in the izGrid.extended slot of the object; FALSE:
show the actual grid object with only cells internal to the
tract.
showReflectedSlivers: TRUE: show the
polygons associated with the external portions of the inclusion
zone, but reflected back into the tract; FALSE: do not
show these polygons.
colReflections: The color to be used in displaying
the reflected sliver polygons if
showReflectedSlivers=TRUE.
...: Other graphical arguments to be passed on to
superclass method, or to plot, or to the
plot methods for the individual objects (i.e.,
“InclusionZone”, “downLog”).
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,
... )
x: An object that is of class “sampSurf” or
any subclass that might be eventualy defined.
showIZs: TRUE: plot the inclusion zones on
the surface; FALSE: just plot the surface.
izColor: This should always be NA or some
very transparent color so the interior of the inclusion zones
does not obscure the sampling surface details.
...: Other graphical arguments to be passed on to
the plot methods for the individual objects (e.g..,
“Tract”, “InclusionZone”, “downLog”).
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$logAttributeColor,
... )
x: An object that is of class “Stem” or
any subclass that might be eventualy defined.
pchStemLocation: The pch parameter
for the location of the stem center.
stemLocationColor: The color for the symbol marking
the stem/log location.
... : Other graphics arguments to be passed on to
points.
signature(x = "downLog", y = "missing")-
This adds the necessary functionality to plot objects of class
"downLog".
usage...
plot(x,
axes = FALSE,
logColor = .StemEnv$logColor,
showLogCenter = FALSE,
pchLogCenter = 3,
logCenterColor = .StemEnv$logAttributeColor,
showNeedle = FALSE,
logNeedleColor = .StemEnv$logAttributeColor,
logBorderColor = .StemEnv$logBorderColor,
asp = 1,
... )
x: An object of class “downLog” or any
subclass that might eventually be defined.
logColor: An R color to be used for shading the log.
showLogCenter: TRUE: plot log center
location; FALSE: do not plot it.
pchLogCenter: The pch value for the
log center.
logCenterColor: An R color to be used for the log
center point location.
showNeedle: TRUE: plot log ‘needle;’
FALSE: do not plot it.
logNeedleColor: An R color to be used for the log
'needle.'
logBorderColor: An R color to be used for drawing
the perimeter of the log.
...: Other graphical arguments to be passed on to
plot.
signature(x = "standingTree", y = "missing")-
This adds the necessary functionality to plot objects of class
"standingTree".
usage...
plot(x,
axes = FALSE,
treeColor = .StemEnv$treeColor,
showLocation = TRUE,
pchLocation = 3, #20 is also good
locationColor = .StemEnv$treeAttributeColor,
treeBorderColor = .StemEnv$treeBorderColor, #log perimeter color
asp = 1,
... )
x: An object of class “downLog” or any
subclass that might eventually be defined.
treeColor: An R color to be used for shading the tree.
showLocation: TRUE: plot tree center
location; FALSE: do not plot it.
pchLocation: The pch value for the
tree center.
locationColor: An R color to be used for the tree
center point location.
treeBorderColor: An R color to be used for drawing
the perimeter of the tree.
...: Other graphical arguments to be passed on to
plot.
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,
... )
x: An object that is of class “Stem” or
any subclass that might be eventualy defined.
... : Other graphics arguments to be passed on.
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,
... )
x: An object that is of class
“downLogs” or subclass thereof.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual downLog objects (please see above).
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,
... )
x: An object that is of class
“standingTrees” or subclass thereof.
... : Other graphics arguments to be passed on to
plot, or to the plot methods for the
individual standingTree objects (please see above).
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$blue.colors(1000),
asp = 1,
useImage = TRUE,
... )
x: An object that is of class “Tract” or
subclass thereof.
gridColor: A valid R color for the background grid. Note
that a single color is fine for initial blank grids, but you can
also supply a function from colorRampPalette in
order to see and surface variation that is in the tract
correctly; this is the default in shades of blue.
useImage: TRUE: use the
raster::image command to draw the tract
(default); FALSE: use the
raster::plot command instead, which gives
the gradient legend. This is an option because the latter will
not rezise the graphics correctly on a graphics window, though
it is fine for a hardcopy and if you do not resize the
device. This may be fixed in raster eventually
(Dec-2010).
...: Other graphical arguments to be passed on to
raster::plot. In addition, one can add
grid lines to the tract via arguments passed to
gridCellEnhance.
signature(x = "bufferedTract", y = "missing")-
This is the plot method for objects of class
"bufferedTract" and subclasses. It essentially
calls the bas “Tract” method for all of the work and adds the
buffer.
usage...
plot(x,
bufferColor = transparentColorBase('blanchedalmond', .StemEnv$alphaTrans),
axes = TRUE,
gridColor = .StemEnv$blue.colors(1000),
lwd = 2,
asp = 1,
... )
x: An object that is of class “bufferedTract” or
subclass thereof.
bufferColor: The color for the buffer area.
gridColor: A valid R color for the background grid. Note
that a single color is fine for initial blank grids, but you can
also supply a function from colorRampPalette in
order to see and surface variation that is in the tract
correctly; this is the default in shades of blue.
lwd: The line width for the border (see:
par).
...: Other graphical arguments to be passed on to
raster::plot. In addition, one can add
grid lines to the tract via arguments passed to
gridCellEnhance.
The “MonteCarloSampling” Class
signature(x = "crudeMonteCarlo", y = "missing")-
The “importanceSampling” and “controlVariate” sampling
classes use this method as well.
usage...
plot(x,
axes = FALSE,
renderAs = c('profile', 'crossSection'),
isHeightColor = .StemEnv$isHeightColor,
... )
x: An object that is of class “crudeMonteCarlo” or
subclass thereof.
renderAs: 'profile' to see the sampling locations
along the stem in a profile view; 'crossSection' will display a
cross-sectional view of the same information.
isHeightColor: A legal R color to use for drawing
the sampling point locations.
...: Other graphical arguments to be passed on to
plot.
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,
... )
x: An object that is of class “mcsContainer”.
showDiagonal: TRUE: Plot the 1:1 line for
reference.
...: Other graphical arguments to be passed on to
plot.
sampSurf documentation built on March 5, 2021, 5:06 p.m.
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Description Methods The “ArealSampling” Class The “InclusionZone” Class The “InclusionZoneGrid” Class The “izContainer” Class The “mirageInclusionZoneGrid” Class The “sampSurf” Class The “Stem” Class The “StemContainer” Class The “Tract” Class The “MonteCarloSampling” Class The “mcsContainer” Class
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...
add:TRUE: add the desired graphics to an existing plot;FALSE: create a new plot.asp: Theplotaspaspect parameter. Best to leave this at the default, which is good for mapping displays.axes:TRUE: plot axes;FALSE: no axes.
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
locationslot 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 throughcallNextMethod). usage...
plot(x, pchIZCenter = 20, izCenterColor = .StemEnv$izCenterColor, asp = 1, ... )x: An object that is a subclass of “ArealSampling”.pchIZCenter: Thepchparameter for the inclusion zone center.izCenterColor: An R color to be used for the inclusion zone center point location.... : Other graphics arguments to be passed on to
plotorpoints.
signature(x = "circularPlot", y = "missing")-
This adds the necessary functionality to plot objects of class "
circularPlot". usage...
plot(x, axes = FALSE, izColor = .StemEnv$izColor, pchPlotCenter = 3, showPlotCenter = FALSE, showPerimeter = TRUE, borderColor = .StemEnv$izBorderColor, plotCenterColor = .StemEnv$izCenterColor, asp = 1, ... )x: An object that is of class “circularPlot” or any subclass that might eventually be defined.izColor: An R color for the interior of the plot's inclusion zone.pchPlotCenter: Thepchvalue for the plot center.showPlotCenter:TRUE: show the plot center;FALSE: do not plot it.showPerimeter:TRUE: show the plot perimeter;FALSE: do not plot it. Please note that the only way to show the whole inclusion zone is to show th perimeter. If you want either the interior of the zone or the perimeter but not both, set the color for the one you do not want displayed toNA.borderColor: An R color for the border/perimeter of the plot's inclusion zone.plotCenterColor: An R color for the center point of the plot's inclusion zone.... : Other graphics arguments to be passed on to
plot.
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, ... )x: An object that is of class “lineSegment” or any subclass that might eventually be defined.pchLineCenter: Thepchvalue for the line center.showLineCenter:TRUE: show the line center;FALSE: do not plot it.lineColor: An R color for the line.lineCenterColor: An R color for the line's center point.... : Other graphics arguments to be passed on to
plot.
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, ... )x: An object that is a subclass of “InclusionZone”.... : Other graphics arguments to be passed on to
plot.
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, ... )x: An object that is of class “standUpIZ” or any subclass that might be eventualy defined.showLog:TRUE: plot the log object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
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, ... )x: An object that is of class “sausageIZ” or any subclass that might be eventualy defined.showLog:TRUE: plot the log object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
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, ... )x: An object that is of class “chainSawIZ” or any subclass that might be eventualy defined.showLog:TRUE: plot the log object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.showSliver:TRUE: show the sliver intersection area;FALSE: do not show it.ltySliver: The line type (see:par) for the delineation of the sliver.sliverBorder: An R color for the border/perimeter of the sliver section.sliverColor: An R color for the interior of the sliver section; remember, this will plot on top of the log interior color.showBolt:TRUE: show the minimal bounding bolt area;FALSE: do not show it.ltyBolt: The line type (see:par) for the delineation of the bounding bolt.boltBorder: An R color for the border/perimeter of the bounding bolt section.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
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$izBorderColor, ... )x: An object that is of class “pointRelascopeIZ” or any subclass that might be eventualy defined.showLog:TRUE: plot the log object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.showDualCenters: TRUE: mark the dual circle centers; FALSE: nothing.dcColor: An R color for the dual circle centers.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
signature(x = "perpendicularDistanceIZ", y = "missing")-
This adds the necessary functionality to plot objects of class "
perpendicularDistanceIZ" and subclasses (e.g., "omnibusPDSIZ"). usage...
plot(x, axes = FALSE, showLog = TRUE, izColor = .StemEnv$izColor, izBorder = .StemEnv$izBorderColor, add = FALSE, asp = 1, ... )x: An object that is of class “perpendicularDistanceIZ” or subclass.showLog:TRUE: plot the log object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
signature(x = "distanceLimitedPDSIZ", y = "missing")-
This adds the necessary functionality to plot objects of class "
distanceLimitedPDSIZ" and subclasses (e.g., "omnibusDLPDSIZ" and "hybridDLPDSIZ"). Please note that the different components of the inclusion zone can be displayed to show the transition between protocols (if any). In addition, the overall "perpendicularDistanceIZ" zone can also be displayed, showing what the inclusion zone would look like if the entire log were treated under the PDS protocol. usage...
plot(x, axes = FALSE, showLog = TRUE, izColor = .StemEnv$izColor, izBorder = .StemEnv$izBorderColor, add = FALSE, asp = 1, showFullPDSIZ = FALSE, showDLSPart = FALSE, showPDSPart = FALSE, ... )x: An object that is of class “distanceLimitedPDSIZ” or subclass.showLog:TRUE: plot the log object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.showFullPDSIZ:TRUE: display the full PDS inclusion zone (as if the log were sampled fully with PDS);FALSE: do not display it.showDLSPart:TRUE: display the "distanceLimitedIZ" portion of the inclusion zone (if any);FALSE: do not display it.showPDSPart:TRUE: display the "perpendicularDistanceIZ" portion of the inclusion zone (if any);FALSE: do not display it.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
signature(x = "distanceLimitedIZ", y = "missing")-
This adds the necessary functionality to plot objects of class "
distanceLimitedIZ" and subclass "distanceLimitedMCIZ". usage...
plot(x, axes = FALSE, showLog = TRUE, izColor = .StemEnv$izColor, izBorder = .StemEnv$izBorderColor, add = FALSE, asp = 1, ... )x: An object that is of class “distanceLimitedIZ” or subclass.showLog:TRUE: plot the log object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
signature(x = "circularPlotIZ", y = "missing")-
This adds the necessary functionality to plot objects of class "
circularPlotIZ" as well as those of its subclass "horizontalPointIZ". In addition, the following subclasses derived from “horizontalPointIZ” also use this method: "horizontalPointCMCIZ", "horizontalPointISIZ", "horizontalPointCVIZ" "criticalHeightIZ", "importanceCHSIZ", "antitheticICHSIZ", and "pairedAICHSIZ". usage...
plot(x, axes = FALSE, showTree = TRUE, izColor = .StemEnv$izColor, izBorder = .StemEnv$izBorderColor, add = FALSE, asp = 1, ... )x: An object that is of class “circularPlotIZ” or subclass.showTree:TRUE: plot the tree object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
signature(x = "horizontalLineIZ", y = "missing")-
This adds the necessary functionality to plot objects of class "
horizontalLineIZ". usage...
plot(x, axes = FALSE, showLineSegment = TRUE, ltyLineSegment = 'dashed', showTree = TRUE, izColor = .StemEnv$izColor, izBorder = .StemEnv$izBorderColor, add = FALSE, asp = 1, ... )x: An object that is of class “horizontalLineIZ”.showLineSegment:TRUE: show the line segment;FALSE: do not show it.ltyLineSegment: A validltyvalue of theplotparameter.showTree:TRUE: plot the tree object;FALSE: do not show it.izColor: An R color for the interior of the inclusion zone.izBorder: An R color for the border/perimeter of the inclusion zone.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
The “InclusionZoneGrid” Class
signature(x = "InclusionZoneGrid", y = "missing")-
The base method for this class, it actually supplies all of the functionality for all existing subclasses, since the internal “InclusionZone” object will have its own plotting method (see above), which will automatically be used, and this object is all that really differentiates the objects of class "
InclusionZoneGrid". usage...
plot(x, axes = TRUE, gridColor = .StemEnv$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, ... )x: An object that is of class “InclusionZoneGrid” or any subclass that might be eventualy defined.gridColor: A valid R color for the background grid. Note that a single color is fine for most sampling methods, but for an inclusion zone whose surface varies within a single object like the “chainSawIZ”, you must supply acolorRampPalettein order to see the variation correctly.izColor: An R color for the interior of the inclusion zone. Note that the default is set toNAso that no filling is done within the inclusion zone to show the grid more clearly.gridLines:TRUE: show grid lines delineated for more emphasis on the individual grid cells;FALSE: no grid lines. Note that this can get busy if the area is too large.gridLineColor: An R color for the grid lines.gridCenters:TRUE: show grid cell centers within the individual grid cells;FALSE: no grid cell centers. Note that this can get busy if the area is too large.gridCenterColor: An R color for the grid cell centers.estimate: A character variable corresponding to the desired estimate attribute; these include 'volume', 'Length' (logs), 'Density', 'surfaceArea', 'coverageArea' (logs), 'basalArea' (trees), 'biomass' and 'carbon'. The sample 'depth' surface is now also available.lwdGrid: The graphics parameter line width (see:par) for the grid lines....: Other graphical arguments to be passed on toplot, or to the plot methods for the individual objects (i.e., “InclusionZone”, “downLog”).
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, ... )x: An object that is of subclass “izContainer”.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual objects.
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', ... )x: An object that is of class “mirageInclusionZoneGrid” or any subclass that might be eventualy defined.tract: An object of class "mirageTract".tractBorder: The color to be used to plot the tract border polygon.lwdTract: The line width for the tract border polygon.showExtended:TRUE: show the extended grid in theizGrid.extendedslot of the object;FALSE: show the actual grid object with only cells internal to the tract.showReflectedSlivers:TRUE: show the polygons associated with the external portions of the inclusion zone, but reflected back into the tract;FALSE: do not show these polygons.colReflections: The color to be used in displaying the reflected sliver polygons ifshowReflectedSlivers=TRUE....: Other graphical arguments to be passed on to superclass method, or toplot, or to the plot methods for the individual objects (i.e., “InclusionZone”, “downLog”).
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, ... )x: An object that is of class “sampSurf” or any subclass that might be eventualy defined.showIZs:TRUE: plot the inclusion zones on the surface;FALSE: just plot the surface.izColor: This should always beNAor some very transparent color so the interior of the inclusion zones does not obscure the sampling surface details....: Other graphical arguments to be passed on to the plot methods for the individual objects (e.g.., “Tract”, “InclusionZone”, “downLog”).
The “Stem” Class
signature(x = "Stem", y = "missing")-
The base method for this class, it only plots the
locationslot 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 throughcallNextMethod). usage...
plot(x, pchStemLocation = 20, stemLocationColor = .StemEnv$logAttributeColor, ... )x: An object that is of class “Stem” or any subclass that might be eventualy defined.pchStemLocation: Thepchparameter for the location of the stem center.stemLocationColor: The color for the symbol marking the stem/log location.... : Other graphics arguments to be passed on to
points.
signature(x = "downLog", y = "missing")-
This adds the necessary functionality to plot objects of class "
downLog". usage...
plot(x, axes = FALSE, logColor = .StemEnv$logColor, showLogCenter = FALSE, pchLogCenter = 3, logCenterColor = .StemEnv$logAttributeColor, showNeedle = FALSE, logNeedleColor = .StemEnv$logAttributeColor, logBorderColor = .StemEnv$logBorderColor, asp = 1, ... )x: An object of class “downLog” or any subclass that might eventually be defined.logColor: An R color to be used for shading the log.showLogCenter:TRUE: plot log center location;FALSE: do not plot it.pchLogCenter: Thepchvalue for the log center.logCenterColor: An R color to be used for the log center point location.showNeedle:TRUE: plot log ‘needle;’FALSE: do not plot it.logNeedleColor: An R color to be used for the log 'needle.'logBorderColor: An R color to be used for drawing the perimeter of the log....: Other graphical arguments to be passed on toplot.
signature(x = "standingTree", y = "missing")-
This adds the necessary functionality to plot objects of class "
standingTree". usage...
plot(x, axes = FALSE, treeColor = .StemEnv$treeColor, showLocation = TRUE, pchLocation = 3, #20 is also good locationColor = .StemEnv$treeAttributeColor, treeBorderColor = .StemEnv$treeBorderColor, #log perimeter color asp = 1, ... )x: An object of class “downLog” or any subclass that might eventually be defined.treeColor: An R color to be used for shading the tree.showLocation:TRUE: plot tree center location;FALSE: do not plot it.pchLocation: Thepchvalue for the tree center.locationColor: An R color to be used for the tree center point location.treeBorderColor: An R color to be used for drawing the perimeter of the tree....: Other graphical arguments to be passed on toplot.
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, ... )x: An object that is of class “Stem” or any subclass that might be eventualy defined.... : Other graphics arguments to be passed on.
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, ... )x: An object that is of class “downLogs” or subclass thereof.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual downLog objects (please see above).
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, ... )x: An object that is of class “standingTrees” or subclass thereof.... : Other graphics arguments to be passed on to
plot, or to the plot methods for the individual standingTree objects (please see above).
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$blue.colors(1000), asp = 1, useImage = TRUE, ... )x: An object that is of class “Tract” or subclass thereof.gridColor: A valid R color for the background grid. Note that a single color is fine for initial blank grids, but you can also supply a function fromcolorRampPalettein order to see and surface variation that is in the tract correctly; this is the default in shades of blue.useImage:TRUE: use the raster::imagecommand to draw the tract (default);FALSE: use the raster::plotcommand instead, which gives the gradient legend. This is an option because the latter will not rezise the graphics correctly on a graphics window, though it is fine for a hardcopy and if you do not resize the device. This may be fixed inrastereventually (Dec-2010)....: Other graphical arguments to be passed on to raster::plot. In addition, one can add grid lines to the tract via arguments passed togridCellEnhance.
signature(x = "bufferedTract", y = "missing")-
This is the plot method for objects of class "
bufferedTract" and subclasses. It essentially calls the bas “Tract” method for all of the work and adds the buffer. usage...
plot(x, bufferColor = transparentColorBase('blanchedalmond', .StemEnv$alphaTrans), axes = TRUE, gridColor = .StemEnv$blue.colors(1000), lwd = 2, asp = 1, ... )x: An object that is of class “bufferedTract” or subclass thereof.bufferColor: The color for the buffer area.gridColor: A valid R color for the background grid. Note that a single color is fine for initial blank grids, but you can also supply a function fromcolorRampPalettein order to see and surface variation that is in the tract correctly; this is the default in shades of blue.lwd: The line width for the border (see:par)....: Other graphical arguments to be passed on to raster::plot. In addition, one can add grid lines to the tract via arguments passed togridCellEnhance.
The “MonteCarloSampling” Class
signature(x = "crudeMonteCarlo", y = "missing")-
The “importanceSampling” and “controlVariate” sampling classes use this method as well.
usage...
plot(x, axes = FALSE, renderAs = c('profile', 'crossSection'), isHeightColor = .StemEnv$isHeightColor, ... )x: An object that is of class “crudeMonteCarlo” or subclass thereof.renderAs: 'profile' to see the sampling locations along the stem in a profile view; 'crossSection' will display a cross-sectional view of the same information.isHeightColor: A legal R color to use for drawing the sampling point locations....: Other graphical arguments to be passed on toplot.
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, ... )x: An object that is of class “mcsContainer”.showDiagonal:TRUE: Plot the 1:1 line for reference....: Other graphical arguments to be passed on toplot.
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