Package: Isinglandr 0.1.1.9000

Isinglandr: Landscape Construction and Simulation for Ising Networks

A toolbox for constructing potential landscapes for Ising networks. The parameters of the networks can be directly supplied by users or estimated by the 'IsingFit' package by van Borkulo and Epskamp (2016) <https://CRAN.R-project.org/package=IsingFit> from empirical data. The Ising model's Boltzmann distribution is preserved for the potential landscape function. The landscape functions can be used for quantifying and visualizing the stability of network states, as well as visualizing the simulation process.

Authors:Jingmeng Cui [aut, cre], Gabriela Lunansky [ctb]

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

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

Peer review:

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

Datasets:
  • MDDConnectivity - Estimation data for the Ising network of major depressive disorder
  • MDDThresholds - Estimation data for the Ising network of major depressive disorder

On CRAN:

3.30 score 1 stars 3 scripts 157 downloads 19 exports 169 dependencies

Last updated 1 months agofrom:e7c711c843. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winOKNov 09 2024
R-4.5-linuxOKNov 09 2024
R-4.4-winOKNov 09 2024
R-4.4-macOKNov 09 2024
R-4.3-winOKNov 09 2024
R-4.3-macOKNov 09 2024

Exports:%>%all_thresholdsautolayerbeta_listcalculate_barriercalculate_stabilitycalculate_stability_sechain_simulate_Isinglandcompare_stabilitymake_2d_Isinglandmake_2d_Isingland_matrixmake_3d_Isinglandmake_Ising_chainmake_Ising_gridshiny_Isingland_MDDsimulate_Isinglandsingle_thresholdsingle_weiwhole_weiadj

Dependencies:abindaskpassbackportsbase64encBHbigDbigmemorybigmemory.sribitopsbootboot.pvalbroombslibcachemcarcarDatacheckmateclassclassIntcliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIDerivdigestdoBydplyre1071evaluatefansifarverfastmapflextableFNNfontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeignFormulafsgdtoolsgenericsgganimateggplot2gluegridExtragtgtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonlitejuicyjuicekernlabKernSmoothknitrkslabelinglaterlatticelazyevallifecyclelme4lpSolvemagrittrmarkdownMASSMatrixMatrixModelsmclustmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompmulticoolmunsellmvtnormnlmenloptrnnetnumDerivofficeropensslpbkrtestpillarpkgconfigplotlypolsplinepracmaprettyunitsprogresspromisesproxypurrrquantregR6raggrappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreactablereactRrlangrmarkdownrmsrpartrstudioapis2sandwichsassscalessfshinyshinycssloadersshinythemessimlandrsourcetoolsSparseMstringistringrsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttinytextransformrtweenrunitsutf8uuidV8vctrsviridisviridisLitewithrwkxfunxml2xtableyamlzipzoo

Readme and manuals

Help Manual

Help pageTopics
Get ggplot2 layers of stability metrics to add to the landscape plotsautolayer.stability autolayer.stability_2d_Isingland autolayer.stability_2d_Isingland_matrix
Calculate energy barrier for Ising landscapescalculate_barrier.2d_Isingland calculate_barrier.2d_Isingland_matrix calculate_barrier.Isingland print.barrier_2d_Isingland summary.barrier_2d_Isingland summary.barrier_2d_Isingland_matrix
Calculate the stability metrics for Ising landscapescalculate_stability calculate_stability.2d_Isingland calculate_stability.2d_Isingland_matrix
Calculate the standard error, confidence interval, and p-value for the stability metrics of an Ising landscape using bootstrappingcalculate_stability_se compare_stability print.stability_se
Make Ising chains from (a series of) Ising grid(s) and perform a chain simulation.chain_simulate_Isingland make_Ising_chain
Make a 2D landscape for an Ising networkmake_2d_Isingland
Make a matrix of landscapes for multiple Ising networksmake_2d_Isingland_matrix
Make a 3D landscape for an Ising networkmake_3d_Isingland
Make a Grid to Specify Multiple Ising Networksmake_Ising_grid
Control Functions to Specify the Varying Parameters for an Ising Grid.all_thresholds beta_list make_Ising_grid-control-functions single_threshold single_wei whole_weiadj
Estimation data for the Ising network of major depressive disorderMDDConnectivity MDDNetwork MDDThresholds
A shiny app that shows the landscape for the Ising network of major depressive disordershiny_Isingland_MDD
Simulate a 2D Ising landscapesimulate_Isingland simulate_Isingland.2d_Isingland simulate_Isingland.2d_Isingland_matrix