Package: simlandr 0.3.1

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]

simlandr_0.3.1.tar.gz
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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'))

Peer review:

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

On CRAN:

research-tool

5.56 score 6 stars 2 packages 3 scripts 260 downloads 35 exports 100 dependencies

Last updated 6 months agofrom:7f902377fc. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-winOKNov 23 2024
R-4.5-linuxOKNov 23 2024
R-4.4-winOKNov 23 2024
R-4.4-macOKNov 23 2024
R-4.3-winOKNov 23 2024
R-4.3-macOKNov 23 2024

Exports:%>%add_arg_eleas_hash_big_matrixattach_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_simulationnargnelenew_arg_setsave_landscapesim_fun_gradsim_fun_nongradsim_fun_testsim_fun_test2

Dependencies:askpassbase64encBHbigmemorybigmemory.sribslibcachemclassclassIntclicolorspacecpp11crayoncrosstalkcurldata.tableDBIdigestdplyre1071evaluatefansifarverfastmapFNNfontawesomeforcatsfsgenericsgganimateggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrisobandjquerylibjsonlitekernlabKernSmoothknitrkslabelinglaterlatticelazyevallifecyclelpSolvemagrittrMASSMatrixmclustmemoisemgcvmimemulticoolmunsellmvtnormnlmeopensslpillarpkgconfigplotlypracmaprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcpprlangrmarkdowns2sassscalessfstringistringrsystibbletidyrtidyselecttinytextransformrtweenrunitsutf8uuidvctrsviridisLitewithrwkxfunyaml

simlandr: Simulation-Based Landscape Construction for Dynamical Systems

Rendered fromsimlandr.Rnwusingutils::Sweaveon Nov 23 2024.

Last update: 2022-03-16
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
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
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
Summarize the barrier height from a 'barrier' objectsummary.barrier