sjedrp: Density recovery profile

In sje30/sjedrp: Density Recovery Profile for Retinal Mosaics

Density recovery profile

Description

Compute Rodieck's density recovery profile.

Usage

autodrp(xs, ys, nbins, r, a)
crossdrp(xs1, ys1, xs2, ys2, nbins, r, a,auto)
## S3 method for class 'sjedrp'
plot(x, scale = 1, title = NULL, mirror = FALSE,
     show.title = TRUE, ylab = "density", ylim=NULL, xlab = "distance", ...)
drp.makestf(x, y, file)

Arguments

xs, xs1, xs2, x	vector of x coordinates
ys, ys1, ys2, y	vector of y coordinates
nbins	Number of bins
r	Width of each bin
a	Bounds of region. Either NULL if you want to make the boundary exactly fit all the data points; or a vector of length 4 with elements (lowx, highx, lowy, highy). Cells outside the bounds are rejected. If a is omitted, packing factors may be slightly higher than when giving bounds.
auto	A boolean, FALSE by default. This is set to TRUE if autodrp has called crossdrp to do the correlations, so the user won't need to worry about setting this.
file	File output (with Macintosh end of lines) for Bob Rodieck's program. This has extra columns, as needed by pre-2001 versions of his program.
scale	Scaling factor for multiplying values on y-axis. For example, if scale=1e6, this converts the density from $um^-2$ to $mm^-2$, which is more readable.
mirror	A boolean, FALSE by default. If true, the DRP is plotted symmetrically around the y-axis.
title	Title to place on top of the plot.
show.title	A boolean, TRUE by default. If TRUE, show the title.
xlab	Label to show on the x axis.
ylab	Label to show on the y axis.
ylim	If non-NULL, then the (lo, hi) values to use for y axis.
...	Extra arguments to pass to plotting functions.

Details

Follow the Rodieck prescription for finding the effective radius and the packing factor. Note this method is very close to that of the Ripley method for computing Khat.

drp.makestf takes a set of data points and will output a text file (with Macintosh end of lines) that can then be input into the MacDRP program from Bob Rodieck. This serves as a useful comparison. His 2001 version of the program now accepts just two-column files, so this function is no longer required.

Value

res	A list with the following components:
effrad	the effective radius
p	the packing factor
maxr	the maximum radius
k	reliability factor
Dc	critical density

Author(s)

Stephen Eglen

References

Rodieck RW (1991). The density recovery profile: A method for the analysis of points in the plane applicable to retinal studies. Visual Neuroscience 6: 95-111.

See Also

khat and other functions by Ripley and Diggle. See also rodieckach for the data and code to generate the DRP from Rodieck (1992). Various data files have been tested, see sjedrp.d10 for details.

Examples

data(sjedrp.d20)
bb <- c(0, 700, 0, 700)
res <- autodrp(sjedrp.d20$x, sjedrp.d20$y, nbins=20, r=10, a=bb)
par(mfrow=c(2,1), las=1)
plot(res, scale=1e6)
plot(res, mirror=TRUE, scale=1e6)
title(xlab=expression(paste("distance (", mu, "m)")),
      ylab=expression(paste("density (cells/",mm^2, ")")))
plot(res, scale=1e6, ylim=c(0, 800))

sje30/sjedrp documentation built on May 1, 2024, 5:20 p.m.