Package: causalBatch 1.3.0
Eric W. Bridgeford
causalBatch: Causal Batch Effects
Software which provides numerous functionalities for detecting and removing group-level effects from high-dimensional scientific data which, when combined with additional assumptions, allow for causal conclusions, as-described in our manuscripts Bridgeford et al. (2024) <doi:10.1101/2021.09.03.458920> and Bridgeford et al. (2023) <arxiv:2307.13868>. Also provides a number of useful utilities for generating simulations and balancing covariates across multiple groups/batches of data via matching and propensity trimming for more than two groups.
Authors:
causalBatch_1.3.0.tar.gz
causalBatch_1.3.0.zip(r-4.5)causalBatch_1.3.0.zip(r-4.4)causalBatch_1.3.0.zip(r-4.3)
causalBatch_1.3.0.tgz(r-4.4-any)causalBatch_1.3.0.tgz(r-4.3-any)
causalBatch_1.3.0.tar.gz(r-4.5-noble)causalBatch_1.3.0.tar.gz(r-4.4-noble)
causalBatch_1.3.0.tgz(r-4.4-emscripten)causalBatch_1.3.0.tgz(r-4.3-emscripten)
causalBatch.pdf |causalBatch.html✨
causalBatch/json (API)
| # Install 'causalBatch' in R: |
| install.packages('causalBatch', repos = c('https://neurodata.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/neurodata/causal_batch/issues
Last updated 3 months agofrom:15d17582f4. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 26 2024 |
| R-4.5-win | NOTE | Aug 26 2024 |
| R-4.5-linux | NOTE | Aug 26 2024 |
| R-4.4-win | NOTE | Aug 26 2024 |
| R-4.4-mac | NOTE | Jul 27 2024 |
| R-4.3-win | NOTE | Aug 26 2024 |
| R-4.3-mac | NOTE | Aug 26 2024 |
Exports:cb.align.kway_matchcb.align.vm_trimcb.correct.apply_cComBatcb.correct.caus_cComBatcb.detect.caus_cdcorrcb.sims.sim_impulsecb.sims.sim_impulse_asycovcb.sims.sim_linearcb.sims.sim_sigmoid
Dependencies:annotateAnnotationDbiaskpassbackportsBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcdcsischkclicodetoolscpp11crayoncurlDBIdplyredgeRfansifastmapFNNformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTkernlabKernSmoothkslambda.rlatticelifecyclelimmalocfitmagrittrMatchItMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimemulticoolmvtnormnlmennetopensslpillarpkgconfigplogrpngpracmaR6RcppRcppProgressrlangRSQLiteS4VectorssnowstatmodsurvivalsvasystibbletidyselectUCSC.utilsutf8vctrswithrXMLxtableXVectorzlibbioc
Causal Balancing
Rendered fromcausal_balancing.Rmdusingknitr::rmarkdownon Aug 26 2024.Last update: 2024-06-18
Started: 2024-01-22
Causal Conditional ComBat
Rendered fromcausal_ccombat.Rmdusingknitr::rmarkdownon Aug 26 2024.Last update: 2024-06-17
Started: 2024-01-22
Causal Conditional Distance Correlation
Rendered fromcausal_cdcorr.Rmdusingknitr::rmarkdownon Aug 26 2024.Last update: 2024-01-22
Started: 2024-01-22
Simulations for Causal Batch/Group Effects
Rendered fromcausal_simulations.Rmdusingknitr::rmarkdownon Aug 26 2024.Last update: 2024-01-22
Started: 2024-01-22
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| K-Way matching | cb.align.kway_match |
| Vector Matching | cb.align.vm_trim |
| Adjust for batch effects using an empirical Bayes framework | cb.correct.apply_cComBat |
| Causal Conditional ComBat | cb.correct.caus_cComBat |
| Causal Conditional Distance Correlation | cb.detect.caus_cdcorr |
| Covariate generator function | cb.sims.covar_generator |
| Compute overlap of two beta distributions | cb.sims.get_beta_overlap |
| Impulse Simulation | cb.sims.sim_impulse |
| Impulse Simulation with Asymmetric Covariates | cb.sims.sim_impulse_asycov |
| Linear Simulation | cb.sims.sim_linear |
| Sigmoidal Simulation | cb.sims.sim_sigmoid |
| Sigmoid function | sigmoid |
