plot.secr: Plot Detection Functions

In secr: Spatially Explicit Capture-Recapture

Plot Detection Functions

Description

Plot detection functions using estimates of parameters in an secr object, or as provided by the user.

Usage

## S3 method for class 'secr'
plot(x, newdata = NULL, add = FALSE,
    sigmatick = FALSE, rgr = FALSE, limits = FALSE, alpha = 0.05,
    xval = 0:200, ylim = NULL, xlab = NULL, ylab = NULL, ...)

## S3 method for class 'secrlist'
plot(x, newdata = NULL, add = FALSE,
    sigmatick = FALSE, rgr = FALSE, limits = FALSE, alpha = 0.05,
    xval = 0:200, ylim = NULL, xlab = NULL, ylab = NULL, ...,
    overlay = TRUE)

detectfnplot (detectfn, pars, details = NULL, add = FALSE,
    sigmatick = FALSE, rgr = FALSE, hazard = FALSE, xval = 0:200, ylim = NULL,
    xlab = NULL, ylab = NULL, ...)

attenuationplot (pars, add = FALSE, spherical = TRUE,
    xval = 0:200, ylim = NULL, xlab = NULL, ylab = NULL, ...)

Arguments

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)
hazard	logical; if TRUE the hazard of detection is plotted instead of probability
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
overlay	logical; if TRUE then automatically add = TRUE for plots after the first
detectfn	integer code or character string for shape of detection function 0 = halfnormal etc. – see detectfn
pars	list, vector or matrix of parameter values
details	list of ancillary parameters
spherical	logical for whether to include spherical spreading term

Details

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. pars maybe a list as from detectpar; it is first coerced to a numeric vector with unlist. Parameter values must be in the expected order (e.g. g0, sigma, z). 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 of g(r) is assumed to be normal on the logit scale for non-hazard functions (detectfn 0:13). For hazard detection functions (detectfn 14:18) the hazard is assumed (from version 3.1.1) to be distributed normally on the log scale. Limits are back-transformed to the probability scale g(r).

attenuationplot plots the expected decline in signal strength with distance, given parameters \beta_0 and \beta_1 for a log-linear model of sound attenuation.

Value

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).

See Also

Detection functions, plot, secr

Examples

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))

## add a function with louder source and spherical spreading...
detectfnplot (detectfn = 11, c(110, -0.3, 5), details =
    list(cutval = 40), add = TRUE, col = "red")

## matching sound attenuation curves; `spherical-only' dashed line
attenuationplot (c(70, -0.3), spherical = FALSE, ylim=c(-10,110))
attenuationplot (c(110, 0), spherical = TRUE, add=TRUE, lty=2)
attenuationplot (c(110, -0.3), spherical = TRUE, add = TRUE,
    col = "red")

secr documentation built on Nov. 4, 2024, 9:06 a.m.