Plot method for an estimated distance function. Estimated distance functions are of class 'dfunc'
# S3 method for dfunc
plot(x, include.zero = FALSE, nbins = "Sturges",
newdata = NULL, legend = TRUE, vertLines = TRUE, plotBars = TRUE,
density = NULL, xlab = "Distance", ylab = if (x$pointSurvey)
"Observation density" else "Probability of detection", border = "blue",
col = 0, col.dfunc = "red", lty.dfunc = 1, lwd.dfunc = 2, ...)An estimated distance function resulting from a call to
dfuncEstim.
Boolean value specifying whether to include 0 in the plot. A value of TRUE will include 0 on the left hand end of the x-axis regardless of the range of distances. A value of FALSE will plot only the range on input distanced.
Internally, this function uses hist to compute histogram
bars for the plot. This argument is the breaks argument to
hist. This can be either a vector giving the breakpoints between
bars, a single number giving the suggested number of bars, a string naming
an algorithm to compute the number of bars, or a function to compute the
number of bars. See help(hist) for all options.
Matrix containing values of covariates to plot. Each row is a set of covariate values (i.e. each column contains all values of each covariate)
Logical scalar for whether to include legend. If TRUE, a legend will be included on plot detailing covariate values plotted.
Logical scalar specifying whether to plot vertical
lines at w.lo and w.hi from 0 to the
distance function.
Logical scalar for whether to plot the histogram of distances behind the distance function. If FALSE, no histogram is plotted, only the distance function line(s).
If plotBars=TRUE, a vector giving the density of
shading lines, in lines per inch, for the bars underneath
the distance function. Values of NULL or a number strictly less than 0
mean solid fill using colors from parameter col. If
density =0 , bars are not filled with any color or lines.
Label for the x-axis
Label for the y-axis
The color of bar borders when bars are plotted. A
value of NA means no borders. If there are shading lines
(i.e., density>0), border = TRUE uses the same
color for the border as for the shading lines.
A vector of bar fill colors or line colors when bars are
drawn and density != 0, replicated
to the correct length. A value of 0 is the background color.
Color of the distance function(s), replicated to
the required length. If covariates or newdata is present
and length(col.dfunc)==1,
col.dfunc is expanded to
to number of plotted distance functions by setting it equal
to graphics::rainbow(n), where n is the number
of plotted distance functions. If you want to plot all
distance functions in the same color, set col.dfunc to
a constant vector having length at least 2 (e.g.,
col.dfunc = c(1,1)) will
plot all curves in black).
Line type of the distance function(s), replicated
to the required length. If covariates or newdata is present
and length(lty.dfunc)==1,
lty.dfunc is expanded to
to number of plotted distance functions by setting it equal
to lty.dfunc + 0:(n-1), where n is the number
of plotted distance functions. If you want to plot all
distance functions using the same line type, set lty.dfunc to
a constant vector having length at least 2 (e.g.,
lty.dfunc = c(1,1)) will
plot all solid lines).
Line width of the distance function(s), replicated to the required length.
When bars are plotted, this routine
uses graphics::barplot for setting up the
plotting region and plotting bars. When bars are not plotted,
this routine sets up the plot with graphics::plot.
… can be any other
argument to barplot or plot EXCEPT
width, ylim, xlim, and space.
The input distance function is returned, with two additional components related to the plot that may be needed if additional lines or text is to added to the plot by the user. These additional components are:
Scaling factor for horizontal coordinates. Due to the way
barplot works, the x-axis has been scaled. The internal coordinates
of the bars are 1, 2, …, nbars. To plot something at a distance
coordinate of x, x must be divided by this value. For example, to draw a
vertical line at a value of 10 on the x-axis, the correct call is
abline(v=10/obj$xscl.plot).
Scaling factor for vertical coordinates. The histogram and
distance function plotted by this routine are scaled so that height of the
distance function at w.lo is g0. Usually, this means the
distance curve is scaled so that the y-intercept is 1, or that g(0) = 1.
To add a plot feature at a real coordinate of y, y must be divided by this
returned parameters. For example, to draw a horizontal line at y-axis
coordinate of 1.0, issue abline(h=1/obj$yscl).
If plotBars is TRUE, a scaled histogram is plotted
and the estimated distance function
is plotted over the top of it. When bars are plotted,
this routine uses graphics::barplot
for setting up the initial plotting region and
most parameters to graphics::barplot can
be specified (exceptions noted above in description of '…').The form of the likelihood and any series
expansions is printed in the main title (overwrite this with
main="<my title>"). Convergence of the distance
function is checked. If the distance function did not converge, a warning
is printed over the top of the histogram. If one or more parameter
estimates are at their limits (likely indicating non-convergence or poor
fit), another warning is printed.
# NOT RUN {
set.seed(87654)
x <- rnorm(1000, mean=0, sd=20)
x <- x[x >= 0]
dfunc <- dfuncEstim(x~1, likelihood="halfnorm")
plot(dfunc)
plot(dfunc, nbins=25)
# showing effects of plot params
plot(dfunc, col=c("red","blue","orange"),
border="black", xlab="Dist (m)", ylab="Prob",
vertLines = FALSE, main="Showing plot params")
plot(dfunc, col="wheat", density=30, angle=c(-45,0,45),
cex.axis=1.5, cex.lab=2, ylab="Probability")
plot(dfunc, col=c("grey","lightgrey"), border=NA)
plot(dfunc, col="grey", border=0, col.dfunc="blue",
lty.dfunc = 2, lwd.dfunc=4, vertLines=FALSE)
plot(dfunc, plotBars=FALSE, cex.axis=1.5, col.axis="blue")
rug(dfunc$dist)
# }
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