f.plot: Detection hazard plotting.

In david-borchers/hmltm: Line transect estimation with hidden Markov availability models

Detection hazard plotting.

Description

Plots detection hazard contours.

Plots the detection function (1- the survivor function) of a fitted model in two dimensions.

Usage

f.plot(
  hmltm,
  obs = 1:length(hmltm$hmltm.fit$xy$x),
  new.ymax = NULL,
  new.pars = NULL,
  theta.f = 0,
  theta.b = 90,
  xrange = c(0, max(hmltm$hmltm.fit$xy$x)),
  yrange = c(0, 1.5 * max(na.omit(hmltm$hmltm.fit$xy$y))),
  nx = 50,
  ny = nx,
  xlab = "Perpendicular distance",
  ylab = "Forward distance",
  type = "contour",
  nlevels = 20,
  add = FALSE,
  col = "black",
  logscale = FALSE,
  theta = 90,
  phi = 35,
  zlab = "pdf of first detections",
  values = FALSE,
  ...
)

Arguments

hmltm	output from est.hmltm
obs	row (observation) in data to use in plotting
new.ymax	a forward distance beyond which things can't be detected (used to override the ymax already in hmltm).
new.pars	model parameter vector (used to override the pars already in hmltm).
theta.f	REDUNDANT must = 0.
theta.b	REDUNDANT must = 90.
xrange	range of x-axis.
yrange	range of y-axis.
nx	number of points on x-axis at which to evaluate detection function.
ny	number of points on y-axis at which to evaluate detection function.
xlab	x label.
ylab	y label.
type	"contour", "persp", "image" or "both" (for image and contour).
nlevels	number of contour levels.
add	If TRUE, adds to current plot, else makes new plot.
col	colour of plot.
logscale	If TRUE, plots hazard values on log scale.
theta	argument for image.
phi	argument for image.
zlab	label in z-dimension for persp plots
values	If TRUE, returns hazard function values on nx by ny grid.
...	other arguments to image, contour or persp.
hfun	detection hazard function name
pars	detection hazard function parameter vector
dat	data frame.
models	model list, as for est.hmltm for example.

david-borchers/hmltm documentation built on Oct. 29, 2023, 9:07 p.m.