attach_all_matrices     Attach all matrices in a batch simulation
calculate_barrier       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   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
