plot_star: Plot a matrix or an *_ipm object
In levisc8/ipmr: Integral Projection Models

plot.ipmr_matrix

R Documentation

Plot a matrix or an *_ipm object

Description

Plot a matrix or an *_ipm object

Usage

## S3 method for class 'ipmr_matrix'
plot(
  x = NULL,
  y = NULL,
  A,
  col = grDevices::rainbow(100, start = 0.67, end = 0),
  bw = FALSE,
  do_contour = FALSE,
  do_legend = FALSE,
  contour_cex = 1,
  ...
)

## S3 method for class 'simple_di_det_ipm'
plot(
  x = NULL,
  y = NULL,
  ipm = NULL,
  col = rainbow(100, start = 0.67, end = 0),
  bw = FALSE,
  do_contour = FALSE,
  do_legend = FALSE,
  exponent = 1,
  n_row = 1,
  n_col = 1,
  ...
)

## S3 method for class 'simple_di_stoch_param_ipm'
plot(
  x = NULL,
  y = NULL,
  ipm = NULL,
  col = rainbow(100, start = 0.67, end = 0),
  bw = FALSE,
  do_contour = FALSE,
  do_legend = FALSE,
  exponent = 1,
  n_row = 1,
  n_col = 1,
  ...
)

## S3 method for class 'simple_di_stoch_kern_ipm'
plot(
  x = NULL,
  y = NULL,
  ipm = NULL,
  col = rainbow(100, start = 0.67, end = 0),
  bw = FALSE,
  do_contour = FALSE,
  do_legend = FALSE,
  exponent = 1,
  n_row = 1,
  n_col = 1,
  ...
)

## S3 method for class 'general_di_det_ipm'
plot(
  x = NULL,
  y = NULL,
  ipm = NULL,
  mega_mat = NA_character_,
  col = rainbow(100, start = 0.67, end = 0),
  bw = FALSE,
  do_contour = FALSE,
  do_legend = FALSE,
  exponent = 1,
  n_row = 1,
  n_col = 1,
  ...
)

Arguments

`x, y`	Either the values of the meshpoints or `NULL`. If `NULL`, then a sequence is generated so that meshpoints are given sequential bin numbers.
`A, ipm`	A matrix or a result from `make_ipm`, or `NULL` if `x` is specified as the matrix or IPM object.
`col`	A vector of colors to use for plotting
`bw`	A logical indicating whether to use a greyscale palette for plotting
`do_contour`	A logical indicating whether or not draw contour lines on the plot
`do_legend`	A logical indicating whether to draw a legend for the plot
`contour_cex`	A numeric specifying how large to make labels for the contour lines.
`...`	further arguments passed to legend
`exponent`	The exponent to raise each kernel to. Setting this to a low number can help visualize kernels that are overwhelmed by a few very large numbers.
`n_row, n_col`	If plotting multiple (sub-)kernels, how many rows and columns to arrange them in.
`mega_mat`	A vector with symbols, I's, and/or 0s representing the matrix blocks. They should be specified in ROW MAJOR order! Can also be a character string specifying the call. Parameter set index syntax is supported. When used, `format_mega_kernel` will produce as many mega-matrices as there are combinations of `par_set_indices` in the `proto_ipm`.

Details

If an IPM kernel is overwhelmed by information in say, a fecundity sub-kernel, use the exponent argument in plot.*_ipm to make it more visually appealing.