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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
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 calculate_barrier.2d_landscape calculate_barrier.3d_landscape calculate_barrier.2d_landscape_batch calculate_barrier.3d_landscape_batch
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
plot(<landscape>)
Make plots from landscape objects
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
summary(<barrier>)
Summarize the barrier height from a barrier object