plot_fit: Plot a gibbonsecr fitted model

In dkidney/gibbonsecr: SECR Analysis for Acoustic Gibbon Surveys

Description

Plotting methods for gibbonsecr fitted model objects.

Usage

## S3 method for class 'gsecr'
plot(x, which = c("detfunc", "detsurf", "bearings",
  "distances", "densurf", "locations"), session = 1, ci = FALSE,
  level = 0.95, method = c("delta", "boot"), nboot = 999,
  newdata = NULL, add = FALSE, ...)

geom_fit(x, which = c("detfunc", "detsurf", "bearings", "distances",
  "densurf"), session = 1, ci = FALSE, level = 0.95,
  method = c("delta", "boot"), nboot = 999, contour = FALSE,
  newdata = NULL, ...)

Arguments

x	a gsecr object
which	plot type
session	session to plot (integer or session name)
ci	if TRUE, confidence intervals will be plotted
level	confidence level for confidence intervals
method	confidence interval estimation method
nboot	number of bootstrap samples to use when method = "boot"
newdata	optional dataframe of covariate values
add	if TRUE, adds to existing plot
...	additional arguments to be passed to the underlying plotting method (see Details)
contour	if TRUE, a contour plot will be drawn instead of a heatmap (for which = "detsurf" or which = "densurf")

Author(s)

Darren Kidney [e-mail]

Examples

## Not run: 

data(N.annamensis)
fit = N.annamensis.fit

# plot methods -----------------------------------------------------------------

# > detection function ----

par(mfrow = c(1,1), mar = c(4,4,2,1))
plot(fit)
plot(fit, ci = TRUE)
plot(fit, ci = TRUE, method = "boot")

# > bearing error ----

plot(fit, "bearings")
plot(fit, "bearings", ci = TRUE)
plot(fit, "bearings", ci = TRUE, method = "boot")

# > detection surface ----

plot(fit, "detsurf", session = 1)
points(fit$capthist, session = 1)

# > density surface ----

plot(fit, "densurf")

# ggplot methods ---------------------------------------------------------------

# > detection function ----

ggplot() +
    geom_fit(fit) +
    labs(x = "Radial distance (m)", y = "Detection probability")

ggplot() +
    geom_fit(fit) +
    geom_fit(fit, ci = TRUE) +
    labs(x = "Radial distance (m)", y = "Detection probability")

ggplot() +
    geom_fit(fit) +
    geom_fit(fit, ci = TRUE, method = "boot") +
    labs(x = "Radial distance (m)", y = "Detection probability")

# > bearing error ----

ggplot() +
    geom_fit(fit, "bearings") +
    labs(x = "Bearing error (degrees)", y = "Probability density")

ggplot() +
    geom_fit(fit, "bearings") +
    geom_fit(fit, "bearings", ci = TRUE) +
    labs(x = "Bearing error (degrees)", y = "Probability density")

ggplot() +
    geom_fit(fit, "bearings") +
    geom_fit(fit, "bearings", ci = TRUE, method = "boot") +
    labs(x = "Radial distance (m)", y = "Detection probability")

# > detection surface ----

ggplot() + coord_fixed() +
    geom_fit(fit, "detsurf", session = 1) +
    geom_fit(fit, "detsurf", session = 1, contour = TRUE) +
    geom_capthist(fit$capthist, session = 1) +
    scale_fill_distiller(palette = "Spectral", limits = c(0, 1)) +
    labs(x = "Longitude", y = "Latitude")

# > density surface ----

ggplot() + coord_fixed() +
    geom_fit(fit, "densurf") +
    geom_capthist(fit$capthist, "array") +
    scale_fill_distiller(palette = "Spectral") +
    labs(x = "Longitude", y = "Latitude")

## End(Not run)

dkidney/gibbonsecr documentation built on May 15, 2019, 9:11 a.m.