Package: simlandr 0.4.0

simlandr: Simulation-Based Landscape Construction for Dynamical Systems

A toolbox for constructing potential landscapes for dynamical systems using Monte Carlo simulation. The method is based on the potential landscape definition by Wang et al. (2008) <doi:10.1073/pnas.0800579105> (also see Zhou & Li, 2016 <doi:10.1063/1.4943096> for further mathematical discussions) and can be used for a large variety of models.

Authors:Jingmeng Cui [aut, cre]

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simlandr.pdf |simlandr.html✨
simlandr/json (API)
NEWS

# Install 'simlandr' in R:
install.packages('simlandr', repos = c('https://sciurus365.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sciurus365/simlandr/issues

Pkgdown site:https://sciurus365.github.io

On CRAN:

research-tool

6.41 score 6 stars 2 packages 12 scripts 369 downloads 38 exports 109 dependencies

Last updated 6 days agofrom:219033f61c. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 16 2025
R-4.5-winOKFeb 16 2025
R-4.5-macOKFeb 16 2025
R-4.5-linuxOKFeb 16 2025
R-4.4-winOKFeb 16 2025
R-4.4-macOKFeb 16 2025
R-4.3-winOKFeb 16 2025
R-4.3-macOKFeb 16 2025

Exports:%>%add_arg_eleas_hash_big_matrixas.mcmc.listattach_all_matricesattach_hash_big_matrixautolayerbatch_simulationcalculate_barriercheck_convfill_in_structget_barrier_heightget_distget_geommake_2d_matrixmake_2d_singlemake_2d_staticmake_2d_tidy_distmake_3d_animationmake_3d_matrixmake_3d_singlemake_3d_staticmake_4d_singlemake_4d_staticmake_arg_gridmake_barrier_grid_2dmake_barrier_grid_3dmodified_simulationmulti_init_simulationnargnelenew_arg_setsave_landscapesim_fun_gradsim_fun_nongradsim_fun_testsim_fun_test2sim_SDE

Dependencies:askpassbase64encBHbigmemorybigmemory.sribslibcachemclassclassIntclicodacodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDerivdigestdplyre1071evaluatefansifarverfastmapFNNfontawesomeforcatsfsfurrrfuturegenericsgganimateggplot2globalsgluegtablehighrhmshtmltoolshtmlwidgetshttrisobandjquerylibjsonlitekernlabKernSmoothknitrkslabelinglaterlatticelazyevallifecyclelistenvlpSolvemagrittrMASSMatrixmclustmemoisemgcvmimemulticoolmunsellmvtnormnlmeopensslparallellypillarpkgconfigplotlypracmaprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcpprlangrmarkdowns2sassscalessfSim.DiffProcstringistringrsystibbletidyrtidyselecttinytextransformrtweenrunitsutf8uuidvctrsviridisLitewithrwkxfunyaml

Dynamic models and simulations

Jingmeng Cui

Rendered fromsimulation.Rmdusingknitr::rmarkdownon Feb 16 2025.

Last update: 2025-01-29
Started: 2021-04-07

Construct the potential landscapes from simulation results

Jingmeng Cui

Rendered fromlandscape.Rmdusingknitr::rmarkdownon Feb 16 2025.

Last update: 2025-02-12
Started: 2021-04-12

Calculate the lowest elevation path and barrier height between stable states

Jingmeng Cui

Rendered frombarrier.Rmdusingknitr::rmarkdownon Feb 16 2025.

Last update: 2025-01-29
Started: 2021-04-12

simlandr: Simulation-Based Landscape Construction for Dynamical Systems

Rendered fromsimlandr.Rnwusingutils::Sweaveon Feb 16 2025.

Last update: 2025-01-29
Started: 2022-03-16

Readme and manuals

Help Manual

Help pageTopics
Create and modify argument sets, then make an argument grid for batch simulationadd_arg_ele arg_set-class make_arg_grid narg nele new_arg_set print.arg_grid print.arg_set
Convert a list of simulation output to a mcmc.list objectas.mcmc.list.list
Attach all matrices in a batch simulationattach_all_matrices
Get a ggplot2 layer from a barrier objectautolayer.barrier
Perform a batch simulation.batch_simulation print.batch_simulation
Functions for calculating energy barrier from landscapescalculate_barrier calculate_barrier.2d_landscape calculate_barrier.2d_landscape_batch calculate_barrier.3d_landscape calculate_barrier.3d_landscape_batch
Graphical diagnoses to check if the simulation convergescheck_conv print.check_conv
Get the probability distribution from a landscape objectget_dist
Class "hash_big_matrix": big matrix with a md5 hash referenceas_hash_big_matrix attach_hash_big_matrix hash_big_matrix hash_big_matrix-class
Make a matrix of 2D static landscape plots for one or two parametersmake_2d_matrix
Make 2D static landscape plot for a single simulation outputmake_2d_single make_2d_static
Make 3d animations from multiple simulationsmake_3d_animation
Make a matrix of 3D static landscape plots for one or two parametersmake_3d_matrix
Make 3D static landscape plots from simulation outputmake_3d_single make_3d_static
Make 4D static space-color plots from simulation outputmake_4d_single make_4d_static
Make a grid for calculating barriers for 2d landscapesmake_barrier_grid_2d
Make a grid for calculating barriers for 3d landscapesmake_barrier_grid_3d
Simulate multiple 1-3D Markovian Stochastic Differential Equationsmulti_init_simulation
Make plots from landscape objectsplot.landscape
Save landscape plotssave_landscape
A simple gradient simulation function for testingsim_fun_grad
A simple non-gradient simulation function for testingsim_fun_nongrad
A simple simulation function for testingsim_fun_test
Simulate 1-3D Markovian Stochastic Differential Equationssim_SDE
Summarize the barrier height from a 'barrier' objectsummary.barrier