Simulation-Based Landscape Construction for Dynamical Systems


[Up] [Top]

Documentation for package ‘simlandr’ version 0.2.0

Help Pages

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