Simulation-Based Landscape Construction for Dynamical Systems

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Documentation for package ‘simlandr’ version 0.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.mcmc.list.list	Convert a list of simulation output to a mcmc.list object
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
multi_init_simulation	Simulate multiple 1-3D Markovian Stochastic Differential Equations
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
sim_SDE	Simulate 1-3D Markovian Stochastic Differential Equations
summary.barrier	Summarize the barrier height from a 'barrier' object