# Simulation-Based Landscape Construction for Dynamical Systems

## Documentation for package ‘simlandr’ version 0.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

add_arg_ele | Create and modify argument sets, then make an argument grid for batch simulation
arg_set-class | Create and modify argument sets, then make an argument grid for batch simulation
as.mcmc.list.list | Convert a list of simulation output to a mcmc.list object
as_hash_big_matrix | Class "hash_big_matrix": big matrix with a md5 hash reference
attach_all_matrices | Attach all matrices in a batch simulation
attach_hash_big_matrix | Class "hash_big_matrix": big matrix with a md5 hash reference
autolayer.barrier | Get a ggplot2 layer from a barrier object
batch_simulation | Perform a batch simulation.
calculate_barrier | Functions for calculating energy barrier from landscapes
calculate_barrier.2d_landscape | Functions for calculating energy barrier from landscapes
calculate_barrier.2d_landscape_batch | Functions for calculating energy barrier from landscapes
calculate_barrier.3d_landscape | Functions for calculating energy barrier from landscapes
calculate_barrier.3d_landscape_batch | Functions for calculating energy barrier from landscapes
check_conv | Graphical diagnoses to check if the simulation converges
get_dist | Get the probability distribution from a landscape object
hash_big_matrix | Class "hash_big_matrix": big matrix with a md5 hash reference
hash_big_matrix-class | Class "hash_big_matrix": big matrix with a md5 hash reference
make_2d_matrix | Make a matrix of 2D static landscape plots for one or two parameters
make_2d_single | Make 2D static landscape plot for a single simulation output
make_2d_static | Make 2D static landscape plot for a single simulation output
make_3d_animation | Make 3d animations from multiple simulations
make_3d_matrix | Make a matrix of 3D static landscape plots for one or two parameters
make_3d_single | Make 3D static landscape plots from simulation output
make_3d_static | Make 3D static landscape plots from simulation output
make_4d_single | Make 4D static space-color plots from simulation output
make_4d_static | Make 4D static space-color plots from simulation output
make_arg_grid | Create and modify argument sets, then make an argument grid for batch simulation
make_barrier_grid_2d | Make a grid for calculating barriers for 2d landscapes
make_barrier_grid_3d | Make a grid for calculating barriers for 3d landscapes
multi_init_simulation | Simulate multiple 1-3D Markovian Stochastic Differential Equations
narg | Create and modify argument sets, then make an argument grid for batch simulation
nele | Create and modify argument sets, then make an argument grid for batch simulation
new_arg_set | Create and modify argument sets, then make an argument grid for batch simulation
plot.landscape | Make plots from landscape objects
print.arg_grid | Create and modify argument sets, then make an argument grid for batch simulation
print.arg_set | Create and modify argument sets, then make an argument grid for batch simulation
print.batch_simulation | Perform a batch simulation.
print.check_conv | Graphical diagnoses to check if the simulation converges
save_landscape | Save landscape plots
sim_fun_grad | A simple gradient simulation function for testing
sim_fun_nongrad | A simple non-gradient simulation function for testing
sim_fun_test | A simple simulation function for testing
sim_SDE | Simulate 1-3D Markovian Stochastic Differential Equations
summary.barrier | Summarize the barrier height from a 'barrier' object