Package: simlandr 0.4.1

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_0.4.1.tar.gz
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simlandr_0.4.1.tgz(r-4.6-x86_64)simlandr_0.4.1.tgz(r-4.6-arm64)simlandr_0.4.1.tgz(r-4.5-x86_64)simlandr_0.4.1.tgz(r-4.5-arm64)
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simlandr_0.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
simlandr/json (API)

# 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/docs site:https://sciurus365.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

research-tool cpp

6.08 score 7 stars 2 packages 19 scripts 403 downloads 42 exports 95 dependencies

Last updated from:6d353ca917. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	187
linux-devel-x86_64	OK	182
source / vignettes	OK	373
linux-release-arm64	OK	190
linux-release-x86_64	OK	188
macos-release-arm64	OK	120
macos-release-x86_64	OK	244
macos-oldrel-arm64	OK	111
macos-oldrel-x86_64	OK	346
windows-devel	OK	159
windows-release	OK	161
windows-oldrel	OK	165
wasm-release	OK	179

Exports:%>%add_arg_ele as_hash_big_matrix as.mcmc.list attach_all_matrices attach_hash_big_matrix autolayer autoplot batch_simulation calculate_barrier calculate_barrier_3d_core check_conv determine_lims fill_in_struct get_barrier_height get_dist get_geom make_2d_matrix make_2d_single make_2d_static make_2d_tidy_dist make_3d_animation make_3d_matrix make_3d_single make_3d_static make_4d_single make_4d_static make_arg_grid make_barrier_grid_2d make_barrier_grid_3d modified_simulation multi_init_simulation narg nele new_arg_set plotly_ld save_landscape sim_fun_grad sim_fun_nongrad sim_fun_test sim_fun_test2 sim_SDE

Dependencies:askpass base64enc BH bigmemory bigmemory.sri bslib cachem cli coda codetools cpp11 crayon crosstalk curl data.table Deriv digest dplyr evaluate farver fastmap FNN fontawesome forcats fs furrr future generics ggplot2 globals glue gtable highr hms htmltools htmlwidgets httr isoband jquerylib jsonlite kernlab KernSmooth knitr ks labeling later lattice lazyeval lifecycle listenv magrittr MASS Matrix mclust memoise mgcv mime multicool mvtnorm nlme openssl otel parallelly pillar pkgconfig plotly pracma prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales Sim.DiffProc stringi stringr sys tibble tidyr tidyselect tinytex utf8 uuid vctrs viridisLite withr xfun yaml

Construct the potential landscapes from simulation results

Introduction | Single simulation landscape | 2d (x, y) plot | 3d (x, y, z) or (x, y, color) plot | 4d (x, y, z, color) plot | Multiple simulation landscape | 2d (x, y) plot series with one varying parameter or plot matrix with two varying parameters | 3d (x, y, color) plot series with one varying parameter or plot matrix with two varying parameters | 3d (x, y, z) or (x, y, color) animation and 3d (x, y, color) plot series with one varying parameter

Rendered fromlandscape.Rmdusingknitr::rmarkdown

Last update: 2026-06-19
Started: 2021-04-12

Calculate the lowest elevation path and barrier height between stable states

Barrier calculation for 2d single landscape | Barrier calculation for 3d single landscape | Barrier calculation for 2d batch landscape | Barrier calculation for 3d batch landscape | Set the starting and end values for each landscape

Rendered frombarrier.Rmdusingknitr::rmarkdown

Last update: 2026-06-19
Started: 2021-04-12

Dynamic models and simulations

Introduction | Single simulation | Out-of-memory storage of the simulation output | Batch simulation

Rendered fromsimulation.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create and modify argument sets, then make an argument grid for batch simulation	add_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 object	as.mcmc.list.list
Attach all matrices in a batch simulation	attach_all_matrices
Get a ggplot2 layer from a barrier object	autolayer.barrier
Autoplot landscape objects	autoplot.landscape
Perform a batch simulation.	batch_simulation print.batch_simulation
Functions for calculating energy barrier from landscapes	calculate_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 converges	check_conv print.check_conv
Get the probability distribution from a landscape object	get_dist
Class "hash_big_matrix": big matrix with a md5 hash reference	as_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 parameters	make_2d_matrix
Make 2D static landscape plot for a single simulation output	make_2d_single make_2d_static
Make 3d animations from multiple simulations	make_3d_animation
Make a matrix of 3D static landscape plots for one or two parameters	make_3d_matrix
Make 3D static landscape plots from simulation output	make_3d_single make_3d_static
Make 4D static space-color plots from simulation output	make_4d_single make_4d_static
Make a grid for calculating barriers for 2d landscapes	make_barrier_grid_2d
Make a grid for calculating barriers for 3d landscapes	make_barrier_grid_3d
Simulate multiple 1-3D Markovian Stochastic Differential Equations	multi_init_simulation
Plot landscape objects	plot.landscape
Plot landscape objects interactively	plotly_ld
Save landscape plots	save_landscape
A simple gradient simulation function for testing	sim_fun_grad
A simple non-gradient simulation function for testing	sim_fun_nongrad
A simple simulation function for testing	sim_fun_test
Simulate 1-3D Markovian Stochastic Differential Equations	sim_SDE
Summarize the barrier height from a 'barrier' object	summary.barrier