plotsparr: Plotting sparr objects

In tilmandavies/sparr: Spatial and Spatiotemporal Relative Risk

Plotting sparr objects

Description

plot methods for classes bivden, stden, rrs, rrst and msden.

Usage

## S3 method for class 'bivden'
plot(
  x,
  what = c("z", "edge", "bw"),
  add.pts = FALSE,
  auto.axes = TRUE,
  override.par = TRUE,
  ...
)

## S3 method for class 'msden'
plot(x, what = c("z", "edge", "bw"), sleep = 0.2, override.par = TRUE, ...)

## S3 method for class 'rrs'
plot(
  x,
  auto.axes = TRUE,
  tol.show = TRUE,
  tol.type = c("upper", "lower", "two.sided"),
  tol.args = list(levels = 0.05, lty = 1, drawlabels = TRUE),
  ...
)

## S3 method for class 'rrst'
plot(
  x,
  tselect = NULL,
  type = c("joint", "conditional"),
  fix.range = FALSE,
  tol.show = TRUE,
  tol.type = c("upper", "lower", "two.sided"),
  tol.args = list(levels = 0.05, lty = 1, drawlabels = TRUE),
  sleep = 0.2,
  override.par = TRUE,
  expscale = FALSE,
  ...
)

## S3 method for class 'stden'
plot(
  x,
  tselect = NULL,
  type = c("joint", "conditional"),
  fix.range = FALSE,
  sleep = 0.2,
  override.par = TRUE,
  ...
)

Arguments

x	An object of class bivden, stden, rrs, rrst, or msden.
what	A character string to select plotting of result ("z"; default); edge-correction surface ("edge"); or variable bandwidth surface ("bw").
add.pts	Logical value indicating whether to add the observations to the image plot using default points.
auto.axes	Logical value indicating whether to display the plot with automatically added x-y axes and an ‘L’ box in default styles.
override.par	Logical value indicating whether to override the existing graphics device parameters prior to plotting, resetting mfrow and mar. See ‘Details’ for when you might want to disable this.
...	Additional graphical parameters to be passed to plot.im, or in one instance, to plot.ppp (see ‘Details’).
sleep	Single positive numeric value giving the amount of time (in seconds) to Sys.sleep before drawing the next image in the animation.
tol.show	Logical value indicating whether to show pre-computed tolerance contours on the plot(s). The object x must already have the relevant p-value surface(s) stored in order for this argument to have any effect.
tol.type	A character string used to control the type of tolerance contour displayed; a test for elevated risk ("upper"), decreased risk ("lower"), or a two-tailed test (two.sided).
tol.args	A named list of valid arguments to be passed directly to contour to control the appearance of plotted contours. Commonly used items are levels, lty, lwd and drawlabels.
tselect	Either a single numeric value giving the time at which to return the plot, or a vector of length 2 giving an interval of times over which to plot. This argument must respect the stored temporal bound in x$tlim, else an error will be thrown. By default, the full set of images (i.e. over the entire available time span) is plotted.
type	A character string to select plotting of joint/unconditional spatiotemporal estimate (default) or conditional spatial density given time.
fix.range	Logical value indicating whether use the same color scale limits for each plot in the sequence. Ignored if the user supplies a pre-defined colourmap to the col argument, which is matched to ... above and passed to plot.im. See ‘Examples’.
expscale	Logical value indicating whether to force a raw-risk scale. Useful for users wishing to plot a log-relative risk surface, but to have the raw-risk displayed on the colour ribbon.

Details

In all instances, visualisation is deferred to plot.im, for which there are a variety of customisations available the user can access via .... The one exception is when plotting observation-specific "diggle" edge correction factors—in this instance, a plot of the spatial observations is returned with size proportional to the influence of each correction weight.

When plotting a rrs object, a pre-computed p-value surface (see argument tolerate in risk) will automatically be superimposed at a significance level of 0.05. Greater flexibility in visualisation is gained by using tolerance in conjunction with contour.

An msden, stden, or rrst object is plotted as an animation, one pixel image after another, separated by sleep seconds. If instead you intend the individual images to be plotted in an array of images, you should first set up your plot device layout, and ensure override.par = FALSE so that the function does not reset these device parameters itself. In such an instance, one might also want to set sleep = 0.

Value

Plots to the relevant graphics device.

Author(s)

T.M. Davies

Examples

data(pbc)
data(fmd)
data(burk)

# 'bivden' object
pbcden <- bivariate.density(split(pbc)$case,h0=3,hp=2,adapt=TRUE,davies.baddeley=0.05,verbose=FALSE)
plot(pbcden)
plot(pbcden,what="bw",main="PBC cases\n variable bandwidth surface",xlab="Easting",ylab="Northing")

# 'stden' object
burkden <- spattemp.density(burk$cases,tres=128) # observation times are stored in marks(burk$cases)
plot(burkden,fix.range=TRUE,sleep=0.1) # animation
plot(burkden,tselect=c(1000,3000),type="conditional") # spatial densities conditional on each time

# 'rrs' object
pbcrr <- risk(pbc,h0=4,hp=3,adapt=TRUE,tolerate=TRUE,davies.baddeley=0.025,edge="diggle")
plot(pbcrr) # default
plot(pbcrr,tol.args=list(levels=c(0.05,0.01),lty=2:1,col="seagreen4"),auto.axes=FALSE)

# 'rrst' object
f <- spattemp.density(fmd$cases,h=6,lambda=8)
g <- bivariate.density(fmd$controls,h0=6)
fmdrr <- spattemp.risk(f,g,tolerate=TRUE)
plot(fmdrr,sleep=0.1,fix.range=TRUE)
plot(fmdrr,type="conditional",sleep=0.1,tol.type="two.sided",
     tol.args=list(levels=0.05,drawlabels=FALSE))

# 'msden' object
pbcmult <- multiscale.density(split(pbc)$case,h0=4,h0fac=c(0.25,2.5))
plot(pbcmult) # densities
plot(pbcmult,what="edge") # edge correction surfaces
plot(pbcmult,what="bw") # bandwidth surfaces

tilmandavies/sparr documentation built on March 21, 2023, 11:34 a.m.