make_3d_matrix {simlandr}

Make a matrix of 3D static landscape plots for one or two parameters

Description

Currently only 3D (x, y, color) is supported. Matrices with 3D (x, y, z) plots are not supported.

Usage

make_3d_matrix(
  bs,
  x,
  y,
  rows = NULL,
  cols,
  lims,
  kde_fun = c("ks", "MASS"),
  n = 200,
  h,
  adjust = 1,
  Umax = 5,
  individual_landscape = TRUE
)

Arguments

bs

A batch_simulation object created by ⁠[batch_simulation()].⁠

x, y

The names of the target variables.

rows, cols

The names of the parameters. rows can be left blank if only one parameter is needed.

lims

The limits of the range for the density estimator as c(xl, xu) for 2D landscapes, c(xl, xu, yl, yu) for 3D landscapes, c(xl, xu, yl, yu, zl, zu) for 4D landscapes. If missing, the range of the data extended by 10% for both sides will be used. For landscapes based on multiple simulations, the largest range of all simulations (which means the lowest lower limit and the highest upper limit) will be used by default.

kde_fun

Which kernel estimator to use? Choices: "ks" ks::kde() (default; faster and using less memory); "base" base::density() (only for 2D landscapes); "MASS" MASS::kde2d() (only for 3D landscapes).

n

The number of equally spaced points in each axis, at which the density is to be estimated.

h

A number, or possibly a vector for 3D and 4D landscapes, specifying the smoothing bandwidth to be used. If missing, the default value of the kernel estimator will be used (but bw = "SJ" for base::density()). Note that the definition of bandwidth might be different for different kernel estimators. For landscapes based on multiple simulations, the largest h of all simulations will be used by default.

adjust

The multiplier to the bandwidth. The bandwidth used is actually adjust * h. This makes it easy to specify values like "half the default" bandwidth.

Umax

The maximum displayed value of potential.

individual_landscape

Make individual landscape for each simulation? Default is TRUE so that it is possible to calculate barriers. Set to FALSE to save time.

Value

A ⁠3d_matrix_landscape⁠ object that describes the landscape of the system, including the smoothed distribution and the landscape plot.