2. Construct the potential landscapes from simulation results"

In simlandr: Simulation-Based Landscape Construction for Dynamical Systems

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
is_pkgdown <- identical(Sys.getenv("IN_PKGDOWN"), "true")

library(simlandr)

Introduction

Here comes the central purpose of simlandr: constructing the potential landscapes from simulation results.

The landscape function is calculated based on the steady-state distribution of the system:

$$U = -\ln P_\textrm{SS}$$

My colleagues and I recently wrote some papers about the theoretical background of this method. You can find them at https://doi.org/10.1080/00273171.2022.2119927 or https://osf.io/pzva3.

simlandr provides a set of tools to construct 2d, 3d, and 4d landscapes from single or multiple simulation results. These methods will be illustrated in the following sections.

---

Frequently used parameters for the family of landscape functions:

x,y,z,rols,cols,fr: the variable names for plot dimensions; from,to (for 2d landscapes), lims (for 3d and 4d landscapes): the range of axes; adjust (for 2d landscapes), h (for 3d and 4d landscapes): the level of smoothness; Umax: the maximum displayed value of potential.

---

Single simulation landscape

The landscapes in this section are only from a single simulation. We first make a simulation series for illustration.

single_test <- sim_fun_test(
  arg1 = list(ele1 = 1),
  arg2 = list(ele2 = 1, ele3 = 0)
)

The result of the landscape functions is a landscape object, which contains the landscape plot as well as the smooth distributions that are used to calculate the landscapes. Plots without z-axis are built with ggplot2 package, while plots with z-axis are built with plotly package. These plots can also be modified using ggplot2 or plotly functions.

You can use plot(l) to access those plots. For some types of landscapes, there are multiple types of plots available. Use plot(l, index = 2) or plot(l, index = 3), etc. to access those plots.

Below are the examples of available plots. The meaning of the parameters can be found on the helping page of each function.

2d (x, y) plot

l_single_2d <- make_2d_static(single_test, x = "out1")
plot(l_single_2d)

3d (x, y, z) or (x, y, color) plot

l_single_3d <- make_3d_static(single_test, x = "out1", y = "out2")

# This chunk will only run when building with pkgdown
plot(l_single_3d, 1)

plot(l_single_3d, 2)

4d (x, y, z, color) plot

# This chunk will only run when building with pkgdown
l_single_4d <- make_4d_static(single_test, x = "out1", y = "out2", z = "out3")
plot(l_single_4d) %>% plotly::layout(scene = list(zaxis = list(range = c(-3, 3))))

Multiple simulation landscape

The landscapes in the section are built from batch simulation results. The following two data sets will be used to illustrate the functions. The difference is that batch_test_result only contains one varying parameter, whereas batch_test_result2 contains two.

batch_test <- new_arg_set()

batch_test <- batch_test %>%
  add_arg_ele("arg2", "ele3", 0.2, 0.5, 0.1)

batch_test_grid <- make_arg_grid(batch_test)

batch_test_result <- batch_simulation(batch_test_grid, sim_fun_test,
  default_list = list(
    arg1 = list(ele1 = 0),
    arg2 = list(ele2 = 0, ele3 = 0)
  ),
  bigmemory = FALSE
)
batch_test_result

batch_test2 <- new_arg_set()
batch_test2 <- batch_test2 %>%
  add_arg_ele("arg1", "ele1", 0.2, 0.6, 0.2) %>%
  add_arg_ele("arg2", "ele2", 0.2, 0.6, 0.2)
batch_test_grid2 <- make_arg_grid(batch_test2)

batch_test_result2 <- batch_simulation(batch_test_grid2, sim_fun_test,
  default_list = list(
    arg1 = list(ele1 = 0),
    arg2 = list(ele2 = 0, ele3 = 0)
  ),
  bigmemory = FALSE
)
batch_test_result2

Below are the examples of available plots.

2d (x, y) plot series with one varying parameter or plot matrix with two varying parameters

l_batch_2d_m1 <- make_2d_matrix(batch_test_result, x = "out1", cols = "ele3")
plot(l_batch_2d_m1)

l_batch_2d_m2 <- make_2d_matrix(batch_test_result2, x = "out1", rows = "ele1", cols = "ele2")
plot(l_batch_2d_m2)

3d (x, y, color) plot series with one varying parameter or plot matrix with two varying parameters

l_batch_3d_m1 <- make_3d_matrix(batch_test_result, x = "out1", y = "out2", cols = "ele3")
plot(l_batch_3d_m1)

l_batch_3d_m2 <- make_3d_matrix(batch_test_result2, x = "out1", y = "out2", rows = "ele1", cols = "ele2")
plot(l_batch_3d_m2)

3d (x, y, z) or (x, y, color) animation and 3d (x, y, color) plot series with one varying parameter

This part is computational and storage expensive thus not evaluated in the released vignette. You can run it on your device to see how the function produces animations. gifski package is needed to show the 3d (x, y, color) animation.

l_batch_3d_a <- make_3d_animation(batch_test_result, x = "out1", y = "out2", fr = "ele3")

plot(l_batch_3d_a, 1)
plot(l_batch_3d_a, 2)

simlandr documentation built on April 4, 2025, 1:14 a.m.