Package: SDModels 1.0.6

Markus Ulmer

SDModels: Spectrally Deconfounded Models

Screen for and analyze non-linear sparse direct effects in the presence of unobserved confounding using the spectral deconfounding techniques (Ćevid, Bühlmann, and Meinshausen (2020)<jmlr.org/papers/v21/19-545.html>, Guo, Ćevid, and Bühlmann (2022) <doi:10.1214/21-AOS2152>). These methods have been shown to be a good estimate for the true direct effect if we observe many covariates, e.g., high-dimensional settings, and we have fairly dense confounding. Even if the assumptions are violated, it seems like there is not much to lose, and the deconfounded models will, in general, estimate a function closer to the true one than classical least squares optimization. 'SDModels' provides functions SDAM() for Spectrally Deconfounded Additive Models (Scheidegger, Guo, and Bühlmann (2025) <doi:10.1145/3711116>) and SDForest() for Spectrally Deconfounded Random Forests (Ulmer, Scheidegger, and Bühlmann (2025) <doi:10.48550/arXiv.2502.03969>).

Authors:Markus Ulmer [aut, cre, cph], Cyrill Scheidegger [aut]

SDModels_1.0.6.tar.gz
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SDModels.pdf |SDModels.html
SDModels/json (API)
NEWS

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

Bug tracker:https://github.com/markusul/sdmodels/issues

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

On CRAN:

Conda:

5.67 score 2 stars 15 scripts 202 downloads 22 exports 104 dependencies

Last updated 4 days agofrom:ba5caaafd4. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 11 2025
R-4.5-winOKMar 11 2025
R-4.5-macOKMar 11 2025
R-4.5-linuxOKMar 11 2025
R-4.4-winOKMar 11 2025
R-4.4-macOKMar 11 2025
R-4.4-linuxOKMar 11 2025
R-4.3-winOKMar 11 2025
R-4.3-macOKMar 11 2025

Exports:copycvSDTreef_fourfromListget_cp_seqget_Qget_WmergeForestpartDependenceplotOOBpredict_individual_fjpredictOOBpruneregPathSDAMSDForestSDTreesimulate_data_nonlinearsimulate_data_stepstabilitySelectiontoListvarImp

Dependencies:ashbase64encbitbit64bitopsbslibcachemclicliprclustercodetoolscolorspacecpp11crayondata.treedeSolveDiagrammeRdigestdoParalleldplyrevaluatefansifarverfastmapfdafdsFNNfontawesomeforeachfsgenericsggplot2glueGPUmatrixgridExtragrplassogtablehdrcdehighrhmshtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrkslabelinglatticelifecyclelocatexeclocfitmagrittrMASSMatrixmclustmemoisemgcvmimemulticoolmunsellmvtnormnlmepbapplypcaPPpillarpkgconfigpracmaprettyunitsprogresspurrrR6rainbowrappdirsrbibutilsRColorBrewerRcppRCurlRdpackreadrrlangrmarkdownrstudioapisassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyaml

Runtime

Rendered fromRuntime.Rmdusingknitr::rmarkdownon Mar 11 2025.

Last update: 2025-02-11
Started: 2024-06-17

Readme and manuals

Help Manual

Help pageTopics
Copy a forestcopy copy.SDForest
Copy a treecopy.SDTree
Cross-validation for the SDTreecvSDTree
Function of x on a fourier basisf_four
SDForest fromList methodfromList fromList.SDForest
SDTree fromList methodfromList.SDTree
Get the sequence of complexity parameters of an SDForestget_cp_seq get_cp_seq.SDForest
Get the sequence of complexity parameters of an SDTreeget_cp_seq.SDTree
Estimation of spectral transformationget_Q
Estimation of anchor transformationget_W
Merge two forestsmergeForest
Partial dependencepartDependence
Plot partial dependenceplot.partDependence
Visualize the paths of an SDTree or SDForestplot.paths
Plot SDTreeplot.SDTree
Visualize the out-of-bag performance of an SDForestplotOOB
Predictions of individual component functions for SDAMpredict_individual_fj
Predictions for SDAMpredict.SDAM
Predictions for the SDForestpredict.SDForest
Predictions for the SDTreepredict.SDTree
Out-of-bag predictions for the SDForestpredictOOB
Print partDependenceprint.partDependence
Print SDAMprint.SDAM
Print SDForestprint.SDForest
Print a SDTreeprint.SDTree
Prune an SDForestprune prune.SDForest
Prune an SDTreeprune.SDTree
Calculate the regularization path of an SDForestregPath regPath.SDForest
Calculate the regularization path of an SDTreeregPath.SDTree
Spectrally Deconfounded Additive ModelsSDAM
Spectrally Deconfounded Random ForestsSDForest
Spectrally Deconfounded TreeSDTree
Simulate data with linear confounding and non-linear causal effectsimulate_data_nonlinear
Simulate data with linear confounding and causal effect following a step-functionsimulate_data_step
Calculate the stability selection of an SDForeststabilitySelection stabilitySelection.SDForest
SDForest toList methodtoList toList.SDForest
SDTree toList methodtoList.SDTree
Extract Variable importance for SDAMvarImp.SDAM
Extract variable importance of an SDForestvarImp varImp.SDForest
Extract variable importance of an SDTreevarImp.SDTree