| add_arg_ele | Create and modify argument sets for batch simulation |
| add_var | Create and modify variable sets for batch simulation |
| as.hash_big.matrix | Class "hash_big.matrix": big matrix with a md5 hash reference |
| attach.hash_big.matrix | Class "hash_big.matrix": big matrix with a md5 hash reference |
| attach_all_matrices | Attach all matrices in a batch simulation |
| batch_simulation | Do the batch simulation |
| calculate_barrier | General function for calculating energy barrier |
| calculate_barrier.2d_density_landscape | General function for calculating energy barrier |
| calculate_barrier.2d_matrix_landscape | General function for calculating energy barrier |
| calculate_barrier.2d_static_landscape | General function for calculating energy barrier |
| calculate_barrier.3d_animation_landscape | General function for calculating energy barrier |
| calculate_barrier.3d_matrix_landscape | General function for calculating energy barrier |
| calculate_barrier.3d_static_landscape | General function for calculating energy barrier |
| calculate_barrier.density | General function for calculating energy barrier |
| calculate_barrier.list | 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 |
| 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_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 |
| modified_simulation | Do the batch simulation |
| narg | The number of arguments in an 'arg_set'. |
| nele | The number of elements in an 'arg_set'. |
| new_arg_set | Create and modify argument sets for batch simulation |
| new_var_set | 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 |