BayesSUR v1.1-2
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Bayesian Seemingly Unrelated Regression
Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Banterle et al. (2018) <doi:10.1101/467019>.
Functions in BayesSUR
| Name | Description | |
| coef.BayesSUR | extract the posterior mean of the coefficients of a "BayesSUR" class object | |
| plot.CPO | plot the conditional predictive ordinate | |
| example_GDSC | Preprocessed data set to mimic a small pharmacogenetic example | |
| fitted.BayesSUR | fitted response values corresponds to the posterior mean estimates | |
| elpd | measure the prediction accuracy by the expected log pointwise predictive density | |
| plot.Estimator | plot the posterior mean estimators | |
| plot.Network | plot the network representation of the associations between responses and predictors | |
| plot.Manhattan | plot Manhattan-like plots for marginal posterior inclusion probabilities (mPIP) and numbers of responses of association for predictors | |
| plot.MCMCdiag | show trace plots and diagnostic density plots | |
| print.BayesSUR | print a short summary of the Bayesian Seemingly Unrelated Regressions Fits | |
| summary.BayesSUR | summarizing Bayesian Seemingly Unrelated Regressions Fits | |
| targetGene | targetGene | |
| predict.BayesSUR | predict responses corresponding to the posterior mean of the coefficients, return posterior mean of coefficients or indices of nonzero coefficients | |
| plot.ResponseGraph | plot the estimated graph for multiple response variables | |
| BayesSUR_internal | BayesSUR_internal | |
| getEstimator | extract the posterior mean of the parameters | |
| BayesSUR | main function of the package | |
| example_eQTL | Simulated data set to mimic a small expression quantitative trait loci (eQTL) example | |
| plot.BayesSUR | create a selection of plots for a "BayesSUR" class object | |
| No Results! | ||
Vignettes of BayesSUR
| Name | ||
| BayesSUR.pdf.asis | ||
| No Results! | ||
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Details
| Type | Package |
| Date | 2020-04-25 |
| License | MIT + file LICENSE |
| Copyright | The C++ files pugixml.cpp, pugixml.hpp and pugiconfig.hpp are Copyright (C) 2006-2018 by Arseny Kapoulkine (arseny.kapoulkine@gmail.com) and Copyright (C) 2003 by Kristen Wegner (kristen@tima.net). The R function vertical.image.legend() has Copyright (C) 2013 by Jenise Swall (jswall@vcu.edu). |
| VignetteBuilder | R.rsp |
| RoxygenNote | 7.1.0 |
| Encoding | UTF-8 |
| LinkingTo | Rcpp, RcppArmadillo (>= 0.9.000) |
| LazyData | true |
| NeedsCompilation | yes |
| SystemRequirements | C++11 |
| Packaged | 2020-04-25 15:43:23 UTC; zhiz |
| Repository | CRAN |
| Date/Publication | 2020-04-27 14:00:18 UTC |
| suggests | BDgraph , data.table , plyr , R.rsp , scrime |
| imports | graphics , grDevices , igraph , Matrix , Rcpp , stats , tikzDevice , utils , xml2 |
| depends | R (>= 3.5.0) |
| linkingto | RcppArmadillo (>= 0.9.000) |
| Contributors | Sylvia Richardson, Leonardo Bottolo, Marco Banterle, Alex Lewin, Manuela Zucknick, Waldir Leoncio |
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