==28025== Memcheck, a memory error detector ==28025== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==28025== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==28025== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R --vanilla --encoding=UTF-8 ==28025== R Under development (unstable) (2019-10-04 r77256) -- "Unsuffered Consequences" Copyright (C) 2019 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 <- "macs" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('macs') > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("forecast.ctree") > ### * forecast.ctree > > flush(stderr()); flush(stdout()) > > ### Name: forecast.ctree > ### Title: Predict method for RTREE Model Fits > ### Aliases: forecast.ctree > > ### ** Examples > > # load "macs" library > library("macs") > > # construct RTREE model > set.seed(1234) > data <- data.frame(y = sample(1:3, 1000, replace = TRUE), + n = as.factor(sample(1:4, 1000, replace = TRUE, + prob = c(0.1, 0.3, 0.2, 0.4))), + o1 = sample(1:50, 1000, replace = TRUE), + o2 = sample(1:30, 1000, replace = TRUE), + o3 = sample(1:10, 1000, replace = TRUE), + o4 = sample(1:60, 1000, replace = TRUE), + o5 = sample(1:20, 1000, replace = TRUE), + o6 = sample(1:40, 1000, replace = TRUE)) > head(data) y n o1 o2 o3 o4 o5 o6 1 2 2 38 27 7 5 18 2 2 2 2 46 2 9 1 11 1 3 1 3 30 3 3 7 17 29 4 3 4 10 17 3 5 3 9 5 1 4 19 28 5 18 3 10 6 1 2 21 30 1 22 3 4 > result <- rtree(data, method = "entropy", alpha = 0.01, cost = c(1, 1, 1)) > result call: rtree(data = data, method = "entropy", alpha = 0.01, cost = c(1, 1, 1)) nodeclass: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 3 3 2 3 2 2 3 3 3 2 2 1 3 1 2 2 1 3 3 3 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 2 1 2 3 1 3 3 2 2 3 2 3 3 1 2 2 2 3 3 2 41 42 43 44 45 46 47 1 1 2 3 1 2 1 nnd: 47 > > # predictions > forecast(result, data[1:10, 2:8]) 1 2 3 4 5 6 7 8 9 10 2 1 3 1 1 1 3 3 1 3 > > > > cleanEx() > nameEx("forecast.masal") > ### * forecast.masal > > flush(stderr()); flush(stdout()) > > ### Name: forecast.masal > ### Title: Predict method for MASAL Model Fits > ### Aliases: forecast.masal > > ### ** Examples > > > > > cleanEx() > nameEx("forecast.stree") > ### * forecast.stree > > flush(stderr()); flush(stdout()) > > ### Name: forecast.stree > ### Title: Predict method for STREE Model Fits > ### Aliases: forecast.stree > > ### ** Examples > > # load "macs" library > library("macs") > set.seed(1234) > data <- data.frame(r = runif(1000, 1, 10), c = rbinom(1000, 1, 0.5), + n = as.factor(sample(1:4, 1000, replace = TRUE, + prob = c(0.1, 0.3, 0.2, 0.4))), + o1 = sample(1:50, 1000, replace = TRUE), + o2 = sample(1:30, 1000, replace = TRUE), + o3 = sample(1:10, 1000, replace = TRUE), + o4 = sample(1:60, 1000, replace = TRUE), + o5 = sample(1:20, 1000, replace = TRUE), + o6 = sample(1:40, 1000, replace = TRUE)) > head(data) r c n o1 o2 o3 o4 o5 o6 1 2.023331 1 4 47 3 7 24 13 25 2 6.600695 0 4 47 15 6 10 3 40 3 6.483473 0 2 18 26 4 57 4 39 4 6.610415 0 2 14 23 10 13 19 39 5 8.748238 1 4 26 27 5 9 9 25 6 6.762795 0 2 27 21 3 41 16 11 > result <- stree(data, family = "likelihood") ==28025== Invalid write of size 4 ==28025== at 0x1724830C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1133) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== Address 0x11ac0740 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x172471D2: dvector(int) (packages/tests-vg/macs/src/cstree.cpp:2459) ==28025== by 0x1724A666: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:69) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== ==28025== Invalid read of size 4 ==28025== at 0x17240984: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:1005) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0x11ac0740 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x172471D2: dvector(int) (packages/tests-vg/macs/src/cstree.cpp:2459) ==28025== by 0x1724A666: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:69) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== ==28025== Invalid read of size 4 ==28025== at 0x172409EB: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:990) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0x11ac0740 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x172471D2: dvector(int) (packages/tests-vg/macs/src/cstree.cpp:2459) ==28025== by 0x1724A666: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:69) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== ==28025== Invalid read of size 4 ==28025== at 0x172409EF: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:991) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0x11ac1720 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x17247232: ivector(int) (packages/tests-vg/macs/src/cstree.cpp:2474) ==28025== by 0x1724A67E: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:70) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== ==28025== Invalid write of size 4 ==28025== at 0x172409F2: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:992) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0x11ac0740 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x172471D2: dvector(int) (packages/tests-vg/macs/src/cstree.cpp:2459) ==28025== by 0x1724A666: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:69) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== ==28025== Invalid write of size 4 ==28025== at 0x172409FA: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:993) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0x11ac1720 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x17247232: ivector(int) (packages/tests-vg/macs/src/cstree.cpp:2474) ==28025== by 0x1724A67E: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:70) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== > result call: stree(data = data, family = "likelihood") median: 1 2 3 4 5 6 7 8 9 10 11 5.592 5.583 5.608 5.827 5.557 5.224 5.919 5.714 5.827 5.570 4.879 12 13 14 15 16 17 18 19 20 21 22 5.354 4.719 6.932 5.919 4.119 6.173 6.391 5.566 5.481 5.653 5.332 23 24 25 5.375 6.995 6.247 nnd: 25 > > # predictions > forecast(result, data[1:10, 3:9]) 1 2 3 4 5 6 7 8 9 10 5.566 5.375 5.919 4.719 5.332 5.919 5.481 5.566 6.995 5.481 > > > > cleanEx() > nameEx("kmgraph") > ### * kmgraph > > flush(stderr()); flush(stdout()) > > ### Name: kmgraph > ### Title: Kaplan-Meier curves plot > ### Aliases: kmgraph > > ### ** Examples > > test <- data.frame(runif(1000, 1, 10), rbinom(1000, 1, 0.5), + sample(1:4, 1000, replace = TRUE, prob = c(0.1, 0.3, 0.2, 0.4)), + sample(1:50, 1000, replace = TRUE), + sample(1:30, 1000, replace = TRUE), + sample(1:10, 1000, replace = TRUE), + sample(1:60, 1000, replace = TRUE), + sample(1:20, 1000, replace = TRUE), + sample(1:40, 1000, replace = TRUE)) > test[,3] <- as.factor(test[,3]) > object <- stree(test,"likelihood") ==28025== Invalid read of size 4 ==28025== at 0x1724096B: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:1009) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0xfb074d0 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x17247232: ivector(int) (packages/tests-vg/macs/src/cstree.cpp:2474) ==28025== by 0x1724A67E: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:70) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== ==28025== Invalid write of size 4 ==28025== at 0x172409C4: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:1014) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0x16eadc10 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x172471D2: dvector(int) (packages/tests-vg/macs/src/cstree.cpp:2459) ==28025== by 0x1724A666: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:69) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== ==28025== Invalid write of size 4 ==28025== at 0x172409C8: sort2(int, float*, int*) (packages/tests-vg/macs/src/cstree.cpp:1015) ==28025== by 0x1724835C: split_a_node1(int, float**, float**, int***, int**, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1140) ==28025== by 0x17241331: grow_large_tree1(float**, float**, int, int*, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>) (packages/tests-vg/macs/src/cstree.cpp:1109) ==28025== by 0x172474FA: similarity(float**, float**, int, float*, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int*, int**, Rcpp::Vector<13, Rcpp::PreserveStorage>, float**, Rcpp::Vector<14, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:108) ==28025== by 0x1724A815: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:75) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== Address 0xfb074d0 is 0 bytes after a block of size 4,000 alloc'd ==28025== at 0x483880B: malloc (/builddir/build/BUILD/valgrind-3.15.0/coregrind/m_replacemalloc/vg_replace_malloc.c:309) ==28025== by 0x17247232: ivector(int) (packages/tests-vg/macs/src/cstree.cpp:2474) ==28025== by 0x1724A67E: cstree(Rcpp::DataFrame_Impl, Rcpp::Vector<13, Rcpp::PreserveStorage>, int) (packages/tests-vg/macs/src/cstree.cpp:70) ==28025== by 0x17221470: _macs_cstree (packages/tests-vg/macs/src/RcppExports.cpp:48) ==28025== by 0x4D33A5: bcEval (svn/R-devel/src/main/eval.c:7343) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== by 0x4D640C: bcEval (svn/R-devel/src/main/eval.c:6764) ==28025== by 0x4E609F: Rf_eval (svn/R-devel/src/main/eval.c:620) ==28025== by 0x4E7DCE: R_execClosure (svn/R-devel/src/main/eval.c:1780) ==28025== by 0x4E8B14: Rf_applyClosure (svn/R-devel/src/main/eval.c:1706) ==28025== > kmgraph(object) > > > > cleanEx() > nameEx("masal") > ### * masal > > flush(stderr()); flush(stdout()) > > ### Name: masal > ### Title: Recursive partitioning based masal > ### Aliases: masal > > ### ** Examples > > > > > > cleanEx() > nameEx("plot.ctree") > ### * plot.ctree > > flush(stderr()); flush(stdout()) > > ### Name: plot.ctree > ### Title: Plot function for a ctree object > ### Aliases: plot.ctree > > ### ** Examples > > # load "macs" library > library("macs") > > # construct RTREE model > set.seed(1234) > data <- data.frame(y = sample(1:3, 1000, replace = TRUE), + n = as.factor(sample(1:4, 1000, replace = TRUE, + prob = c(0.1, 0.3, 0.2, 0.4))), + o1 = sample(1:50, 1000, replace = TRUE), + o2 = sample(1:30, 1000, replace = TRUE), + o3 = sample(1:10, 1000, replace = TRUE), + o4 = sample(1:60, 1000, replace = TRUE), + o5 = sample(1:20, 1000, replace = TRUE), + o6 = sample(1:40, 1000, replace = TRUE)) > head(data) y n o1 o2 o3 o4 o5 o6 1 2 2 38 27 7 5 18 2 2 2 2 46 2 9 1 11 1 3 1 3 30 3 3 7 17 29 4 3 4 10 17 3 5 3 9 5 1 4 19 28 5 18 3 10 6 1 2 21 30 1 22 3 4 > result <- rtree(data, method = "entropy", alpha = 0.01, cost = c(1, 1, 1)) > result call: rtree(data = data, method = "entropy", alpha = 0.01, cost = c(1, 1, 1)) nodeclass: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 3 3 2 3 2 2 3 3 3 2 2 1 3 1 2 2 1 3 3 3 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 2 1 2 3 1 3 3 2 2 3 2 3 3 1 2 2 2 3 3 2 41 42 43 44 45 46 47 1 1 2 3 1 2 1 nnd: 47 > > # plot result of rtree > plot(result, main = "example of ctree plot") > plot(result, shape = 2) > > > > cleanEx() > nameEx("plot.stree") > ### * plot.stree > > flush(stderr()); flush(stdout()) > > ### Name: plot.stree > ### Title: Plot function for a stree object > ### Aliases: plot.stree > > ### ** Examples > > # load "macs" library > library("macs") > > # construct STREE model > set.seed(1234) > data <- data.frame(r = runif(1000, 1, 10), c = rbinom(1000, 1, 0.5), + n = as.factor(sample(1:4, 1000, replace = TRUE, + prob = c(0.1, 0.3, 0.2, 0.4))), + o1 = sample(1:50, 1000, replace = TRUE), + o2 = sample(1:30, 1000, replace = TRUE), + o3 = sample(1:10, 1000, replace = TRUE), + o4 = sample(1:60, 1000, replace = TRUE), + o5 = sample(1:20, 1000, replace = TRUE), + o6 = sample(1:40, 1000, replace = TRUE)) > head(data) r c n o1 o2 o3 o4 o5 o6 1 2.023331 1 4 47 3 7 24 13 25 2 6.600695 0 4 47 15 6 10 3 40 3 6.483473 0 2 18 26 4 57 4 39 4 6.610415 0 2 14 23 10 13 19 39 5 8.748238 1 4 26 27 5 9 9 25 6 6.762795 0 2 27 21 3 41 16 11 > result <- stree(data, family = "likelihood") > > # plot result of stree > plot(result, main = "example of stree plot") > plot(result, shape = 2) > > > > cleanEx() > nameEx("rtree") > ### * rtree > > flush(stderr()); flush(stdout()) > > ### Name: rtree > ### Title: Tree-based analysis of rare variants to analyze genomic data. > ### Aliases: rtree > > ### ** Examples > > library(macs) > set.seed(1234) > data <- data.frame(y = sample(1:3, 1000, replace = TRUE), + n = sample(1:4, 1000, replace = TRUE, + prob = c(0.1, 0.3, 0.2, 0.4)), + o1 = sample(1:50, 1000, replace = TRUE), + o2 = sample(1:30, 1000, replace = TRUE), + o3 = sample(1:10, 1000, replace = TRUE), + o4 = sample(1:60, 1000, replace = TRUE), + o5 = sample(1:20, 1000, replace = TRUE), + o6 = sample(1:40, 1000, replace = TRUE)) > data[,2] <- as.factor(data[,2]) > result <- rtree(data, method = "entropy", alpha = 0.01, cost = NULL) > plot(result) > > > > cleanEx() > nameEx("stree") > ### * stree > > flush(stderr()); flush(stdout()) > > ### Name: stree > ### Title: Recursive partitioning based survival tree > ### Aliases: stree > > ### ** Examples > > test <- data.frame(runif(1000, 1, 10), rbinom(1000, 1, 0.5), + sample(1:4, 1000, replace = TRUE, prob = c(0.1, 0.3, 0.2, 0.4)), + sample(1:50, 1000, replace = TRUE), + sample(1:30, 1000, replace = TRUE), + sample(1:10, 1000, replace = TRUE), + sample(1:60, 1000, replace = TRUE), + sample(1:20, 1000, replace = TRUE), + sample(1:40, 1000, replace = TRUE)) > test[,3] <- as.factor(test[,3]) > result <- stree(test, "likelihood") > plot(result) > > > > cleanEx() > nameEx("tarv") > ### * tarv > > flush(stderr()); flush(stdout()) > > ### Name: tarv > ### Title: Recursive partitioning based classification trees for risk > ### profile and diagnosis > ### Aliases: tarv > > ### ** Examples > > library(macs) > set.seed(123) > sex <- rbinom(1000, 1, 0.5) > race <- sample(1:3, 1000, replace = TRUE, prob = c(0.4, 0.4, 0.2)) > gg <- replicate(100, rbinom(1000, 1, runif(1, 0.005, 0.05))) > annotation <- paste("gene", rep(1:5, each = 20), sep = "") > causal <- rbinom(40, 1, 0.8) > x1 <- rowSums(gg[, 1:20][, causal[1:20] > 0]) > 0 > x2 <- rowSums(gg[, 21:40][, causal[21:40] > 0]) > 0 > xb <- sex * 0.2 + (race == 2) * 0.2 + x1 * 0.6 + x2 * 0.8 - 0.7 > r <- rbinom(1000, 1, exp(xb)/(1+exp(xb))) > pheno <- data.frame(disease = r, sex = sex, race = as.factor(race)) > geno <- t(gg) > rownames(geno) <- annotation > > result <- tarv(pheno, geno, formula = "disease~sex+race", + method = "entropy", family = "binomial", + direction = "both", alpha = 0.01, cost = c(1, 1)) > plot(result) > > > > ### *