plot_outputs {binspp} | R Documentation |
Graphical output describing the posterior distributions
Description
A graphical representation of the posterior distributions in terms of histograms and trace plots.
Usage
plot_outputs(Output)
Arguments
Output |
list, output of the main function |
Details
If the covariate list z_beta was non-empty, the estimated
intensity function of the parent process is plotted. Then,
the estimated surface representing the location dependent
mean number of points in a cluster is plotted, and similarly,
the estimated surface representing the location dependent scale
of clusters is plotted.
After that, histograms of the sample posterior distributions
of the individual parameters are plotted, together with
the histograms of p-values giving significance of the individual
covariates in z_beta with respect to the population
of parent points.
Then, the trace plots for individual model parameters are plotted,
with highlighted sample median (full red line) and sample 2.5%
and 97.5% quantiles (dashed red lines), and similarly for
the p-values giving significance of the individual covariates
in z_beta with respect to the population of parent points.
Additionally, the following graphs are also plotted:
trace plot for the log-likelihood of the model,
trace plot for the number of parent points,
trace plot for the probability of accepting proposed updates of
(alpha, alpha_1, …, alpha_l)
,trace plot for the fraction of accepted updates of
alpha, alpha_1, …, alpha_l
in the last 1000 iterations,trace plot for the probability of accepting proposed updates of
omega, omega_1, …, omega_m
,trace plot for the fraction of accepted updates of
omega, omega_1, …, omega_m
in the last 1000 iterations,trace plot for the fraction of accepted updates of parent points in the last 1000 iterations.
Value
Series of plots providing a graphical representation of the posterior distributions in terms of histograms and trace plots.
Examples
library(spatstat)
# Prepare the dataset:
X = trees_N4
x_left = x_left_N4
x_right = x_right_N4
y_bottom = y_bottom_N4
y_top = y_top_N4
z_beta = list(refor = cov_refor, slope = cov_slope)
z_alpha = list(tmi = cov_tmi, tdensity = cov_tdensity)
z_omega = list(slope = cov_slope, reserv = cov_reserv)
# Determine the union of rectangles:
W = owin(c(x_left[1], x_right[1]), c(y_bottom[1], y_top[1]))
if (length(x_left) >= 2) {
for (i in 2:length(x_left)) {
W2 = owin(c(x_left[i], x_right[i]), c(y_bottom[i], y_top[i]))
W = union.owin(W, W2)
}
}
# Dilated observation window:
W_dil = dilation.owin(W, 100)
# Default parameters for prior distributions:
control = list(NStep = 100, BurnIn = 20, SamplingFreq = 5)
# MCMC estimation:
Output = estintp(X, control, x_left, x_right, y_bottom, y_top, W_dil,
z_beta, z_alpha, z_omega, verbose = FALSE)
# Text output + series of figures:
print_outputs(Output)
plot_outputs(Output)