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_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 |
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 |
summary.barrier |
Summarize the barrier height from a 'barrier' object |