Plot an SMC or EnK genealogy from algorithm output.
Usage
plot_genealogy(
output,
parameter,
dimension = 1,
target = NULL,
external_target = NULL,
use_initial_points = TRUE,
use_weights = TRUE,
alpha_points = 0.1,
alpha_lines = 0.1,
axis_limits = NULL,
vertical = TRUE,
arrows = TRUE,
default_title = FALSE
)Arguments
- output
Output from the SMC or EnK algorithm.
- parameter
The parameter we wish to see the evolution of.
- dimension
(optional) The dimension of the parameter we wish to see the evolution of. (default is 1)
- target
(optional) The target to plot. (default is to use all targets)
- external_target
(optional) The external target to plot. (default is to use all external targets, or to ignore if the column is not present)
- use_initial_points
(optional) If target is not specified and this argument is TRUE, will add the initial unweighted proposed points to the output to be plotted. (default is TRUE)
- use_weights
(optional) If FALSE, will ignore particle weights in the line graph. If TRUE, will use the particle weights. (defaults to TRUE)
- alpha_points
(optional) The transparency of the points in the plot. (default=0.1)
- alpha_lines
(optional) The transparency of the lines in the plot. (default=0.1)
- axis_limits
(optional) Input of the form c(start,end), which specifies the ends of the parameter axis.
- vertical
(optional) If TRUE (default), plots a genealogy vertically. If FALSE, plots horizontally.
- arrows
(optional) If TRUE (default), includes arrowheads. If FALSE, arrowheads are omitted.
- default_title
(optional) If TRUE, will provide a default title for the figure. If FALSE, no title is used. (defaults to FALSE)