All functions

attach_all_matrices()

Attach all matrices in a batch simulation

modified_simulation() batch_simulation()

Do the batch simulation

calculate_barrier calculate_barrier.2d_static_landscape calculate_barrier.2d_density_landscape calculate_barrier.density calculate_barrier.3d_static_landscape calculate_barrier.list calculate_barrier.3d_animation_landscape calculate_barrier.3d_matrix_landscape calculate_barrier.2d_matrix_landscape

General function for calculating energy barrier

calculate_barrier_2d()

Calculate barrier from a 2D landscape

calculate_barrier_2d_batch()

Calculate barrier from a 2D landscape with multiple simulations

calculate_barrier_3d()

Calculate barrier from a 3D landscape

calculate_barrier_3d_batch()

Calculate barrier from a 3D landscape with multiple simulations

check_conv()

Check density convergence of simulation

fill_in_struct()

Fill a vector of values into a structure list.

find_local_min_2d()

Find local minimum of a 2d distribution

find_local_min_3d()

Find local minimum of a 3d distribution

get_barrier_height()

Get the barrier height from a barrier object.

get_dist()

Get the probability distribution from a landscape object

get_geom()

Get a ggplot2 geom layer that can be added to a ggplot2 landscape plot

as.hash_big.matrix() attach.hash_big.matrix()

Class "hash_big.matrix": big matrix with a md5 hash reference

make_2d_density()

Make 2D density-based landscape plot for a single simulation output

make_2d_kernel_dist()

Make 2D kernel smooth distribution

make_2d_matrix()

Make a matrix of 2d graphs for two parameters

make_2d_static()

Make 2D static landscape plot for a single simulation output

make_2d_tidy_dist()

Make a tidy data.frame from smooth 2d distribution matrix

make_3d_animation()

Make 3d animations from multiple simulations

make_3d_kernel_dist()

Make 3D kernel smooth distribution

make_3d_matrix()

Make a matrix or vector of 3d heatmap graphs for two parameters

make_3d_static()

Make 3D static landscape plots from simulation output

make_3d_tidy_dist()

Make a tidy data.frame from smooth 3d distribution matrix

make_4d_static()

Make 4D static space-color plots from simulation output

make_arg_grid()

Make variable grids 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

make_var_grid()

Make variable grids for batch simulation

narg()

The number of arguments in an arg_set.

nele()

The number of elements in an arg_set.

new_arg_set() add_arg_ele()

Create and modify argument sets for batch simulation

new_var_set() add_var()

Create and modify variable sets for batch simulation

npar()

The number of parameters in a var_set.

nvar()

The number of variables in a var_set.

plot(<barrier>)

Plot the result of a barrier object

plot(<landscape>)

Make plots from landscape objects

print(<arg_grid>)

Print an arg_grid object

print(<arg_set>)

Print an arg_set object.

print(<batch_simulation>)

Print a batch_simulation object

print(<check_conv>)

Print a check_conv

print(<var_grid>)

Print a var_grid object

print(<var_set>)

Print a var_set object.

reverselog_trans()

A function for reversed log transformation

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