| plot.secr {secr} | R Documentation |
Plot detection functions using estimates of parameters in an secr object, or as provided by the user.
## S3 method for class 'secr':
plot(x, newdata = NULL, add = FALSE,
sigmatick = FALSE, rgr = FALSE, limits = TRUE, alpha = 0.05,
xval = 0:200, ylim = NULL, xlab = NULL, ylab = NULL, ...)
detectfnplot(detectfn, pars, details = NULL, add = FALSE,
sigmatick = FALSE, rgr = FALSE, xval = 0:200, ylim = NULL,
xlab = NULL, ylab = NULL, ...)
x |
an secr object |
newdata |
dataframe of data to form estimates |
add |
logical to add curve(s) to an existing plot |
sigmatick |
logical; if TRUE the scale parameter sigma is shown by a vertical line |
rgr |
logical; if TRUE a scaled curve r.g(r) is plotted instead of g(r) |
limits |
logical; if TRUE pointwise confidence limits are drawn |
alpha |
alpha level for confidence intervals |
xval |
vector of distances at for which detection to be plotted |
ylim |
vector length 2 giving limits of y axis |
xlab |
label for x axis |
ylab |
label for y axis |
... |
arguments to pass to lines |
detectfn |
integer code for detection function 0 halfnormal, 1 hazard-rate etc. |
pars |
vector or matrix of parameter values |
details |
list of ancillary parameters |
newdata is usually NULL, in which case one curve is plotted for
each session and group. Otherwise, predict.secr is used to form
estimates and plot a curve for each row in newdata.
If axis labels are not provided they default to 'Distance (m)' and 'Detection probability' or 'Detection lambda'.
detectfnplot is an alternative in which the user nominates the
type of function and provides parameter values. If pars is a matrix then
a separate curve is plotted with the parameter values in each row.
For detectfnplot the signal threshold parameters 'cutval' and
'spherical' should be provided in details (see examples).
Approximate confidence limits for g(r) are calculated using a numerical
first-order delta-method approximation to the standard error at each
xval. The distribution is assumed to be normal on the logit scale;
limits are back-transformed from that scale.
plot.secr invisibly returns a dataframe of the plotted values (or
a list of dataframes in the case that newdata has more than one
row).
Murray Efford murray.efford@otago.ac.nz
detection functions, plot, secr
data(secrdemo)
plot (secrdemo.b, xval = 0:100, ylim = c(0, 0.4))
## Add recapture probability
plot (secrdemo.b, newdata = data.frame(b = 1), add = TRUE,
col='red')
## signal strength detection: 70dB at source, attenuation
## 0.3dB/m, sdS 5dB; detection threshold 40 dB.
detectfnplot (detectfn = 10, c(70, -0.3, 5), details =
list(cutval = 40, spherical = FALSE))
## add a function with louder source and spherical spreading...
detectfnplot (detectfn = 10, c(110, -0.3, 5), details =
list(cutval = 40, spherical = TRUE), add = TRUE, col='red')