plot_genealogy {ggsmc}

Plot an SMC or EnK genealogy from algorithm output.

Description

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)

Value

A particle genealogy in a ggplot figure.