Package index

All functions

new_arg_set() add_arg_ele() nele() narg() print(<arg_set>) make_arg_grid() print(<arg_grid>)

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

attach_all_matrices()

Attach all matrices in a batch simulation

autolayer(<barrier>)

Get a ggplot2 layer from a barrier object

batch_simulation() print(<batch_simulation>)

Perform a batch simulation.

calculate_barrier()

Functions for calculating energy barrier from landscapes

check_conv() print(<check_conv>)

Graphical diagnoses to check if the simulation converges

get_dist()

Get the probability distribution from a landscape object

as_hash_big_matrix() attach_hash_big_matrix()

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_static() make_2d_single()

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_static() make_3d_single()

Make 3D static landscape plots from simulation output

make_4d_static() make_4d_single()

Make 4D static space-color plots from simulation output

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

plot(<landscape>)

Make plots from landscape objects

save_landscape()

Save landscape plots

sim_SDE()

Simulate 1-3D Markovian Stochastic Differential Equations

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

summary(<barrier>)

Summarize the barrier height from a barrier object