==572179== Memcheck, a memory error detector ==572179== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==572179== Using Valgrind-3.16.1 and LibVEX; rerun with -h for copyright info ==572179== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R --vanilla ==572179== R Under development (unstable) (2021-04-15 r80174) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "mixggm" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('mixggm') Package 'mixggm' version 1.0 Type 'citation("mixggm")' for citing this R package in publications. > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("control-parameters") > ### * control-parameters > > flush(stderr()); flush(stdout()) > > ### Name: control-parameters > ### Title: Set control parameters for various purposes > ### Aliases: ctrlICF ctrlSTEP ctrlGA ctrlEM ctrlREG > > ### ** Examples > > > ## Not run: > ##D > ##D # ga search with increased mutation probability > ##D data(banknote, package = "mclust") > ##D mod1 <- searchGGM(banknote[,-1], model = "concentration", search = "ga", > ##D ctrlGa = ctrlGA(pmutation = 0.3)) > ##D > ##D > ##D # regularization > ##D library(MASS) > ##D V <- 10 > ##D N <- 20 > ##D mu <- rep(0, V) > ##D sigma <- matrix(0.9, V,V) > ##D diag(sigma) <- 1 > ##D x <- cbind( MASS::mvrnorm(N, mu, sigma), > ##D MASS::mvrnorm(N, mu, sigma), > ##D MASS::mvrnorm(N, mu, sigma)) # high-dimensional data V = 30, N = 20 > ##D # > ##D hyperPar <- ctrlREG(x, K = 1, scaleType = "diag") > ##D mod2 <- searchGGM(x, model = "covariance", penalty = "ebic") # throws an error > ##D mod2 <- searchGGM(x, model = "covariance", penalty = "ebic", # regularization > ##D regularize = TRUE, regHyperPar = hyperPar) > ##D plot(mod2, "adjacency") > ##D > ##D > ##D # occam's window > ##D library(MASS) > ##D V <- 20 > ##D N <- 500 > ##D mu <- rep(0, V) > ##D sigma <- matrix(0.9, V,V) > ##D diag(sigma) <- 1 > ##D edges <- rbinom(choose(V,2), 1, 0.3) > ##D A <- matrix(0, V,V) > ##D A[lower.tri(A)] <- edges > ##D A <- A + t(A) > ##D fit <- fitGGM(S = sigma, N = N, graph = A, model = "concentration", > ##D ctrlIcf = ctrlICF(tol = 1e-06)) > ##D sigma <- fit$sigma > ##D # > ##D x <- MASS:::mvrnorm(N, mu, sigma) > ##D # > ##D mod3 <- searchGGM(x, model = "concentration", search = "step-back", > ##D ctrlStep = ctrlSTEP(occamAdd = 5, occamRem = 5)) > ##D par(mfrow = c(1,2)) > ##D plot(fit, what = "adjacency") > ##D plot(mod3, what = "adjacency") > ##D > ## End(Not run) > > > > > cleanEx() > nameEx("fitGGM") > ### * fitGGM > > flush(stderr()); flush(stdout()) > > ### Name: fitGGM > ### Title: Fit a Gaussian graphical model > ### Aliases: fitGGM print.fitGGM > > ### ** Examples > > > # Gaussian covariance graph model > data(mtcars) > x <- mtcars[,c(1,3:7)] > R <- cor(x) > # > # model where variables with correlation less than 0.5 are marginally independent > graph <- ( abs(R) < 0.5 )*1 > diag(graph) <- 0 > fit1 <- fitGGM(data = x, graph = graph) > plot(fit1) > > > # Gaussian concentration graph model > data(swiss) > # > # fit a conditional independence model: > V <- ncol(swiss) > graph <- matrix( c(0,1,0,1,1,1, + 1,0,1,1,0,0, + 0,1,0,1,1,0, + 1,1,1,0,1,0, + 1,0,1,1,0,0, + 1,0,0,0,0,0), V,V, byrow = TRUE ) > fit2 <- fitGGM(swiss, graph = graph, model = "concentration") > plot(fit2) > > > ## Not run: > ##D > ##D data(marks, package = "ggm") > ##D # > ##D # the conditional independence model of Whittaker (1990), pag. 6 > ##D V <- ncol(marks) > ##D graph <- matrix( c(0,1,1,0,0, > ##D 1,0,1,0,0, > ##D 1,1,0,1,1, > ##D 0,0,1,0,1, > ##D 0,0,1,1,0), V,V, byrow = TRUE ) > ##D fit3 <- fitGGM(marks, graph = graph, model = "concentration") > ##D plot(fit3) > ## End(Not run) > > > > > cleanEx() > nameEx("mixGGM") > ### * mixGGM > > flush(stderr()); flush(stdout()) > > ### Name: mixGGM > ### Title: Mixture of Gaussian graphical models > ### Aliases: mixGGM print.mixGGM > > ### ** Examples > > > # fit a mixture of concentration graph models > data(iris) > mod1 <- mixGGM(iris[,-5], model = "concentration") | | | 0%==572179== Conditional jump or move depends on uninitialised value(s) ==572179== at 0x4DB2F4: bcEval (svn/R-devel/src/main/eval.c:7173) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51C6A0: do_logic (svn/R-devel/src/main/logic.c:43) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51C70B: lbinary (svn/R-devel/src/main/logic.c:74) ==572179== by 0x51C70B: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51C7FB: Rf_isNumber (svn/R-devel/src/include/Rinlinedfuns.h:979) ==572179== by 0x51C7FB: lbinary (svn/R-devel/src/main/logic.c:77) ==572179== by 0x51C7FB: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51C8DD: XLENGTH_EX (svn/R-devel/src/include/Rinlinedfuns.h:204) ==572179== by 0x51C8DD: Rf_xlength (svn/R-devel/src/include/Rinlinedfuns.h:572) ==572179== by 0x51C8DD: lbinary (svn/R-devel/src/main/logic.c:82) ==572179== by 0x51C8DD: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51C9E4: XLENGTH_EX (svn/R-devel/src/include/Rinlinedfuns.h:204) ==572179== by 0x51C9E4: Rf_xlength (svn/R-devel/src/include/Rinlinedfuns.h:572) ==572179== by 0x51C9E4: lbinary (svn/R-devel/src/main/logic.c:83) ==572179== by 0x51C9E4: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x446DD8: Rf_getAttrib (svn/R-devel/src/main/attrib.c:164) ==572179== by 0x51CA30: Rf_isArray (svn/R-devel/src/include/Rinlinedfuns.h:927) ==572179== by 0x51CA30: lbinary (svn/R-devel/src/main/logic.c:85) ==572179== by 0x51CA30: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x446DF6: Rf_getAttrib (svn/R-devel/src/main/attrib.c:167) ==572179== by 0x51CA30: Rf_isArray (svn/R-devel/src/include/Rinlinedfuns.h:927) ==572179== by 0x51CA30: lbinary (svn/R-devel/src/main/logic.c:85) ==572179== by 0x51CA30: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51CAA8: Rf_isVector (svn/R-devel/src/include/Rinlinedfuns.h:875) ==572179== by 0x51CAA8: Rf_isTs (svn/R-devel/src/include/Rinlinedfuns.h:938) ==572179== by 0x51CAA8: lbinary (svn/R-devel/src/main/logic.c:87) ==572179== by 0x51CAA8: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x446DD8: Rf_getAttrib (svn/R-devel/src/main/attrib.c:164) ==572179== by 0x51CAE0: Rf_isTs (svn/R-devel/src/include/Rinlinedfuns.h:938) ==572179== by 0x51CAE0: lbinary (svn/R-devel/src/main/logic.c:87) ==572179== by 0x51CAE0: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x446DF6: Rf_getAttrib (svn/R-devel/src/main/attrib.c:167) ==572179== by 0x51CAE0: Rf_isTs (svn/R-devel/src/include/Rinlinedfuns.h:938) ==572179== by 0x51CAE0: lbinary (svn/R-devel/src/main/logic.c:87) ==572179== by 0x51CAE0: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x446DD8: Rf_getAttrib (svn/R-devel/src/main/attrib.c:164) ==572179== by 0x51CE5E: lbinary (svn/R-devel/src/main/logic.c:109) ==572179== by 0x51CE5E: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x446DF6: Rf_getAttrib (svn/R-devel/src/main/attrib.c:167) ==572179== by 0x51CE5E: lbinary (svn/R-devel/src/main/logic.c:109) ==572179== by 0x51CE5E: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51D009: lbinary (svn/R-devel/src/main/logic.c:138) ==572179== by 0x51D009: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x465E41: Rf_coerceVector (svn/R-devel/src/main/coerce.c:1177) ==572179== by 0x51D32E: lbinary (svn/R-devel/src/main/logic.c:145) ==572179== by 0x51D32E: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Conditional jump or move depends on uninitialised value(s) ==572179== at 0x52678E: SETCAR (svn/R-devel/src/main/memory.c:4207) ==572179== by 0x51D339: lbinary (svn/R-devel/src/main/logic.c:145) ==572179== by 0x51D339: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51D068: XLENGTH_EX (svn/R-devel/src/include/Rinlinedfuns.h:204) ==572179== by 0x51D068: binaryLogic (svn/R-devel/src/main/logic.c:329) ==572179== by 0x51D068: lbinary (svn/R-devel/src/main/logic.c:150) ==572179== by 0x51D068: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51D07E: XLENGTH_EX (svn/R-devel/src/include/Rinlinedfuns.h:204) ==572179== by 0x51D07E: binaryLogic (svn/R-devel/src/main/logic.c:329) ==572179== by 0x51D07E: lbinary (svn/R-devel/src/main/logic.c:150) ==572179== by 0x51D07E: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Use of uninitialised value of size 8 ==572179== at 0x51D0C6: DATAPTR (svn/R-devel/src/include/Rinlinedfuns.h:120) ==572179== by 0x51D0C6: binaryLogic (svn/R-devel/src/main/logic.c:338) ==572179== by 0x51D0C6: lbinary (svn/R-devel/src/main/logic.c:150) ==572179== by 0x51D0C6: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D4D7B: bcEval (svn/R-devel/src/main/eval.c:7174) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4DF7DD: bcEval (svn/R-devel/src/main/eval.c:7083) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== by 0x4F0E17: FORCE_PROMISE (svn/R-devel/src/main/eval.c:5136) ==572179== by 0x4F0E17: getvar (svn/R-devel/src/main/eval.c:5177) ==572179== by 0x4D9CF8: bcEval (svn/R-devel/src/main/eval.c:6867) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F0B6F: forcePromise (svn/R-devel/src/main/eval.c:555) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Conditional jump or move depends on uninitialised value(s) ==572179== at 0x51E073: binaryLogic (svn/R-devel/src/main/logic.c:357) ==572179== by 0x51E073: lbinary (svn/R-devel/src/main/logic.c:150) ==572179== by 0x51E073: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D3F31: bcEval (svn/R-devel/src/main/eval.c:7175) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4F0403: Rf_eval (svn/R-devel/src/main/eval.c:850) ==572179== by 0x4F4459: do_set (svn/R-devel/src/main/eval.c:2969) ==572179== by 0x4F0684: Rf_eval (svn/R-devel/src/main/eval.c:802) ==572179== by 0x5214EC: Rf_ReplIteration (svn/R-devel/src/main/main.c:264) ==572179== by 0x521837: R_ReplConsole (svn/R-devel/src/main/main.c:314) ==572179== by 0x5218C4: run_Rmainloop (svn/R-devel/src/main/main.c:1117) ==572179== by 0x52190D: Rf_mainloop (svn/R-devel/src/main/main.c:1124) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Conditional jump or move depends on uninitialised value(s) ==572179== at 0x51E07D: binaryLogic (svn/R-devel/src/main/logic.c:357) ==572179== by 0x51E07D: lbinary (svn/R-devel/src/main/logic.c:150) ==572179== by 0x51E07D: do_logic (svn/R-devel/src/main/logic.c:63) ==572179== by 0x4D3F31: bcEval (svn/R-devel/src/main/eval.c:7175) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4F0403: Rf_eval (svn/R-devel/src/main/eval.c:850) ==572179== by 0x4F4459: do_set (svn/R-devel/src/main/eval.c:2969) ==572179== by 0x4F0684: Rf_eval (svn/R-devel/src/main/eval.c:802) ==572179== by 0x5214EC: Rf_ReplIteration (svn/R-devel/src/main/main.c:264) ==572179== by 0x521837: R_ReplConsole (svn/R-devel/src/main/main.c:314) ==572179== by 0x5218C4: run_Rmainloop (svn/R-devel/src/main/main.c:1117) ==572179== by 0x52190D: Rf_mainloop (svn/R-devel/src/main/main.c:1124) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%==572179== Conditional jump or move depends on uninitialised value(s) ==572179== at 0x51F087: checkValues (svn/R-devel/src/main/logic.c:427) ==572179== by 0x51F087: do_logic3 (svn/R-devel/src/main/logic.c:483) ==572179== by 0x4D3726: bcEval (svn/R-devel/src/main/eval.c:7115) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4F0403: Rf_eval (svn/R-devel/src/main/eval.c:850) ==572179== by 0x4F4459: do_set (svn/R-devel/src/main/eval.c:2969) ==572179== by 0x4F0684: Rf_eval (svn/R-devel/src/main/eval.c:802) ==572179== by 0x5214EC: Rf_ReplIteration (svn/R-devel/src/main/main.c:264) ==572179== by 0x521837: R_ReplConsole (svn/R-devel/src/main/main.c:314) ==572179== by 0x5218C4: run_Rmainloop (svn/R-devel/src/main/main.c:1117) ==572179== by 0x52190D: Rf_mainloop (svn/R-devel/src/main/main.c:1124) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Conditional jump or move depends on uninitialised value(s) ==572179== at 0x5B16DC: do_first_min (svn/R-devel/src/main/summary.c:1060) ==572179== by 0x4D3726: bcEval (svn/R-devel/src/main/eval.c:7115) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4F0403: Rf_eval (svn/R-devel/src/main/eval.c:850) ==572179== by 0x4F4459: do_set (svn/R-devel/src/main/eval.c:2969) ==572179== by 0x4F0684: Rf_eval (svn/R-devel/src/main/eval.c:802) ==572179== by 0x5214EC: Rf_ReplIteration (svn/R-devel/src/main/main.c:264) ==572179== by 0x521837: R_ReplConsole (svn/R-devel/src/main/main.c:314) ==572179== by 0x5218C4: run_Rmainloop (svn/R-devel/src/main/main.c:1117) ==572179== by 0x52190D: Rf_mainloop (svn/R-devel/src/main/main.c:1124) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== ==572179== Conditional jump or move depends on uninitialised value(s) ==572179== at 0x5B16C4: do_first_min (svn/R-devel/src/main/summary.c:1060) ==572179== by 0x4D3726: bcEval (svn/R-devel/src/main/eval.c:7115) ==572179== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==572179== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==572179== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==572179== by 0x4F0403: Rf_eval (svn/R-devel/src/main/eval.c:850) ==572179== by 0x4F4459: do_set (svn/R-devel/src/main/eval.c:2969) ==572179== by 0x4F0684: Rf_eval (svn/R-devel/src/main/eval.c:802) ==572179== by 0x5214EC: Rf_ReplIteration (svn/R-devel/src/main/main.c:264) ==572179== by 0x521837: R_ReplConsole (svn/R-devel/src/main/main.c:314) ==572179== by 0x5218C4: run_Rmainloop (svn/R-devel/src/main/main.c:1117) ==572179== by 0x52190D: Rf_mainloop (svn/R-devel/src/main/main.c:1124) ==572179== Uninitialised value was created by a stack allocation ==572179== at 0x173A838A: estepmggm(arma::Mat, arma::Mat, arma::Cube, arma::Col) (packages/tests-vg/mixggm/src/estepmggm.cpp:14) ==572179== > plot(mod1, what = "graph") > plot(mod1, what = "classification") > > > ## Not run: > ##D > ##D # a simple simulated data example > ##D library(MASS) > ##D N <- 200 > ##D tau <- c(0.3, 0.7) > ##D Nk <- rowSums( rmultinom(N, 1, tau) ) > ##D class <- rep(1:2, Nk) > ##D sigma1 <- diag(2) # independent variables > ##D sigma2 <- matrix( c(1,0.9,0.9,1), 2,2 ) # correlated variables > ##D mu1 <- c(0, 0) > ##D mu2 <- c(2, 3) > ##D x <- rbind( MASS::mvrnorm(Nk[1], mu1, sigma1), > ##D MASS::mvrnorm(Nk[2], mu2, sigma2) > ##D ) > ##D mod2 <- mixGGM(x) > ##D plot(mod2) > ##D plot(mod2, what = "classification") > ##D > ##D # fit a mixture of covariance graph models > ##D data(wine, package = "gclus") > ##D mod3 <- mixGGM(wine[,-1], K = 1:4, model = "covariance", > ##D penalty = "erdos", beta = 0.01) > ##D plot(mod3, what = "graph") > ##D plot(mod3, what = "classification", dimens = 1:4) > ##D > ##D > ##D # complex simulated data example > ##D N <- 500 > ##D V <- 20 > ##D tau <- c(0.3, 0.7) > ##D Nk <- rowSums( rmultinom(N, 1, tau) ) > ##D class <- rep(1:2, Nk) > ##D sigma1 <- rWishart(1, V+1, diag(V))[,,1] > ##D mu1 <- rep(0, V) > ##D mu2 <- rnorm(V, 0.5, 2) > ##D x1 <- MASS::mvrnorm(Nk[1], mu1, sigma1) > ##D x2 <- matrix(NA, Nk[2], V) > ##D x2[,1] <- rnorm(Nk[2]) > ##D for ( j in 2:V ) x2[,j] <- x2[,j-1] + rnorm(Nk[2], mu2[j], sd = 0.5) > ##D x <- rbind(x1, x2) > ##D # > ##D mod4 <- mixGGM(x, K = 1:4, model = "concentration", > ##D penalty = "ebic", beta = 0.5) > ##D plot(mod4, what = "classification", dimens = c(1,5,10,15,20) ) > ##D plot(mod4, what = "graph") > ##D plot(mod4, what = "adjacency") > ##D table(class, mod4$classification) > ##D # > ##D mc <- mclust::Mclust(x, G = 1:4) > ##D mc$bic > ##D mod4$bic > ##D > ## End(Not run) > > > > > cleanEx() > nameEx("penalty") > ### * penalty > > flush(stderr()); flush(stdout()) > > ### Name: penalty > ### Title: Penalty functions for graph structure search > ### Aliases: penalty > > ### ** Examples > > > # fit concentration graph model with power law penalty > data(ability.cov) > N <- ability.cov$n.obs > mod1 <- searchGGM(S = ability.cov$cov, N = ability.cov$n.obs, + model = "concentration", penalty = "power", beta = 2*log(N)) > mod1 Gaussian concentration graph model for conditional independence ======================================= N. dependence parameters: 5 Log-likelihood: -1408.95 Penalized log-likelihood: -1462.39 Penalty: power Search: step-forw > plot(mod1) > > > ## Not run: > ##D > ##D # two disconnected blocks of correlated variables > ##D library(MASS) > ##D V <- 10 > ##D N <- 500 > ##D mu <- rep(0, V) > ##D sigma <- matrix(0.9, V,V) > ##D diag(sigma) <- 1 > ##D x <- cbind( MASS::mvrnorm(N, mu, sigma), > ##D MASS::mvrnorm(N, mu, sigma) ) > ##D # > ##D # fit a covariance graph with erdos penalty > ##D mod2 <- searchGGM(x, model = "covariance", > ##D penalty = "erdos") > ##D plot(mod2, "adjacency") > ##D > ##D > ##D # user defined penalty function > ##D data(iris) > ##D x <- iris[,-5] > ##D N <- nrow(x) > ##D V <- ncol(x) > ##D ref <- matrix(0, V, V) > ##D # > ##D # penalize graphs different from a reference graph structure > ##D myPenalty <- function(graph, beta) > ##D { > ##D beta * sum( abs(graph - ref) ) > ##D } > ##D # > ##D mod3 <- mixGGM(x, K = 3, model = "covariance", > ##D penalty = myPenalty, beta = 2*V*log(N)) > ##D plot(mod3) > ##D > ## End(Not run) > > > > > cleanEx() > nameEx("plotting-functionalities") > ### * plotting-functionalities > > flush(stderr()); flush(stdout()) > > ### Name: plotting-functionalities > ### Title: Plotting functionalities for Gaussian covariance and > ### concentration graph models and their mixture > ### Aliases: plot.fitGGM plot.mixGGM > > ### ** Examples > > > # covariance graph > data(mtcars) > x <- mtcars[,c(1,3:7)] > R <- cor(x) > graph <- ( abs(R) < 0.5 )*1 > diag(graph) <- 0 > fit1 <- fitGGM(data = x, graph = graph) > plot(fit1) > plot(fit1, what = "adjacency") > > > # concentration graph > data(swiss) > V <- ncol(swiss) > graph <- matrix( c(0,1,0,1,1,1, + 1,0,1,1,0,0, + 0,1,0,1,1,0, + 1,1,1,0,1,0, + 1,0,1,1,0,0, + 1,0,0,0,0,0), V,V, byrow = TRUE ) > fit2 <- fitGGM(swiss, graph = graph, model = "concentration") > plot(fit2) > plot(fit2, layout = "random") > plot(fit2, what = "adjacency") > > > ## Not run: > ##D > ##D # mixture of Gaussian concentration graph models > ##D data(banknote, package = "mclust") > ##D mod3 <- mixGGM(banknote[,-1], model = "concentration", K = 2) > ##D plot(mod3, what = "graph") > ##D plot(mod3, what = "adjacency") > ##D plot(mod3, what = "classification") > ##D plot(mod3, what = "classification", dimens = c(1,4,5)) > ##D plot(mod3, what = "common") > ##D > ##D > ##D # mixture of Gaussian covariance graph models > ##D data(wine, package = "gclus") > ##D mod4 <- mixGGM(wine[,-1], model = "covariance", K = 3) > ##D clb <- c("#999999", "#E69F00", "#56B4E9") # colorblind friendly palette > ##D plot(mod4, what = "graph", colors = clb) > ##D plot(mod4, what = "adjacency", colors = clb) > ##D plot(mod4, what = "classification", colors = clb, dimens = c(1,7,8,12)) > ##D plot(mod4, what = "common") > ##D > ## End(Not run) > > > > > cleanEx() > nameEx("searchGGM") > ### * searchGGM > > flush(stderr()); flush(stdout()) > > ### Name: searchGGM > ### Title: Structure search and estimation for Gaussian graphical models > ### Aliases: searchGGM > > ### ** Examples > > > # fit covariance graph model with default forward-stepwise search > data(mtcars) > x <- mtcars[,c(1,3:7)] > mod1 <- searchGGM(x, model = "covariance") > mod1 Gaussian covariance graph model for marginal independence ==================================== N. dependence parameters: 13 Log-likelihood: -335.44 Penalized log-likelihood: -357.97 Penalty: bic Search: step-forw > plot(mod1) > # > # prefer a sparser model > mod2 <- searchGGM(x, model = "covariance", penalty = "ebic") > mod2 Gaussian covariance graph model for marginal independence ==================================== N. dependence parameters: 8 Log-likelihood: -353.24 Penalized log-likelihood: -395.77 Penalty: ebic Search: step-forw > plot(mod2) > > > # fit concentration graph model with backward-stepwise structure search > # with a covariance matrix in input > data(ability.cov) > mod3 <- searchGGM(S = ability.cov$cov, N = ability.cov$n.obs, + model = "concentration", search = "step-back") > mod3 Gaussian concentration graph model for conditional independence ======================================= N. dependence parameters: 6 Log-likelihood: -1406.17 Penalized log-likelihood: -1420.32 Penalty: bic Search: step-back > mod3$graph [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 1 1 0 1 0 [2,] 1 0 1 0 0 0 [3,] 1 1 0 1 0 0 [4,] 0 0 1 0 0 0 [5,] 1 0 0 0 0 1 [6,] 0 0 0 0 1 0 > mod3$omega general picture blocks maze reading vocab general 0.08115994 -0.02581133 -0.01049276 0.00000000 -0.02377784 0.00000000 picture -0.02581133 0.23330570 -0.02235247 0.00000000 0.00000000 0.00000000 blocks -0.01049276 -0.02235247 0.01338466 -0.01271862 0.00000000 0.00000000 maze 0.00000000 0.00000000 -0.01271862 0.09810766 0.00000000 0.00000000 reading -0.02377784 0.00000000 0.00000000 0.00000000 0.06033143 -0.02510099 vocab 0.00000000 0.00000000 0.00000000 0.00000000 -0.02510099 0.01977790 > plot(mod3) > > ## Not run: > ##D > ##D # generate data from a Markov model > ##D N <- 1000 > ##D V <- 20 > ##D dat <- matrix(NA, N, V) > ##D dat[,1] <- rnorm(N) > ##D for ( j in 2:V ) dat[,j] <- dat[,j-1] + rnorm(N, sd = 0.5) > ##D mod4 <- searchGGM(data = dat, model = "concentration") # recover the model > ##D plot(mod4, what = "adjacency") > ##D > ## End(Not run) > > > > ### *