==45321== Memcheck, a memory error detector
==45321== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==45321== Using Valgrind-3.14.0 and LibVEX; rerun with -h for copyright info
==45321== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R --vanilla
==45321== 

R Under development (unstable) (2019-03-05 r76199) -- "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 <- "treatSens"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('treatSens')
Loading required package: Rcpp
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("sensPlot")
> ### * sensPlot
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: sensPlot
> ### Title: Create a contour plot sumamrizing the result of the sensitivity
> ###   analysis
> ### Aliases: sensPlot
> 
> ### ** Examples
> 
> #See the manual for treatSens.
> 
> 
> 
> cleanEx()
> nameEx("summary")
> ### * summary
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: summary.sensitivity.default
> ### Title: Summarizing sensitivity analysis results
> ### Aliases: summary.sensitivity summary.sensitivity.default
> 
> ### ** Examples
> 
> #See treatSens documentation
> 
> 
> 
> cleanEx()
> nameEx("treatSens")
> ### * treatSens
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: treatSens
> ### Title: Performing Dual-Parameter Sensitivity Analysis
> ### Aliases: treatSens
> 
> ### ** Examples
> 
> N = 250          #number of observations
> 
> zetay = .5             #coefficient on U in the outcome model
> zetaz = .5             #coefficient on U in the treatment model
> betaz = c(.75,-.5,.25) #coefficients of X in the treatment model
> betay = c(.5,1,-1.5)   #coefficients of X in the outcome model
> tau = .25              #treatment effect
> 
> X = matrix(rnorm(3*N),N,3)           #covariates
> 
> ###################################
> # Example with continuous treatment
> set.seed(836)
> U = rnorm(N, 0, 1)         #unmeasured confounder
> Z = rnorm(N,X %*% betaz + zetaz*U,1)         #treatment variable
> Y = rnorm(N,X %*% betay + zetay*U + tau*Z,2) #outcome variable
> 
> # sensitivity analysis
> # small grid.dim and nsim just for example purposes
> out.cont <- treatSens(Y~Z+X, grid.dim = c(3,2), nsim = 5,
+                      standardize = FALSE, verbose = TRUE, zero.loc = "full")
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Gaussian family with identity link function is assumed in the treatment model.
Gaussian family with identity link function is assumed in the response model.
Normally distributed continous U is assumed.
Fitting null models...
Computing final grid...
Completed  1  of  6  cells.
Completed  2  of  6  cells.
Completed  3  of  6  cells.
Completed  4  of  6  cells.
Completed  5  of  6  cells.
Completed  6  of  6  cells.
> 
> sensPlot(out.cont) # draw contour plot
Note: Predictors with negative coefficients for the response surface have been transformed through multiplication by -1 and are displayed as inverted triangles. 
> # You can see when zetay=zetaz=.5, tau is about .25.
> 
> ###############################
> # Example with binary treatment
> set.seed(725)
> U = rbinom(N,1,.5)                   #unmeasured confounder
> ps = pnorm(X%*%betaz + zetaz*(U-.5)) #propensity score
> Z = rbinom(N,1,ps)                   #treatment variable
> epsilon = rnorm(N,0,2)               #error term
> Y0 = X%*%betay + zetay*(U-.5) + epsilon       #potential outcome(Z=0)
> Y1 = X%*%betay + zetay*(U-.5) + tau + epsilon #potential outcome(Z=1)
> Y = Y0*(1-Z) + Y1*Z                  #realization of potential outcome
> 
> # sensitivity analysis
> out.bin <- treatSens(Y~Z+X, trt.family = binomial(link="probit"), nsim = 3, 
+                       spy.range = c(0,4), spz.range = c(-2,2),grid.dim = c(5,3),
+                       standardize = FALSE, verbose = TRUE)
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Binomial family with probit link function is assumed in the treatment model.
Gaussian family with identity link function is assumed in the response model.
Binary U with binomial distribution is assumed.
Fitting null models...
Warning in calc.range.coef(grid.dim, zetaz.range, zetay.range, buffer, U.model,  :
  Sensitivity parameter range for Y inconsistent with possible values given data.  Range restricted.
Computing final grid...
Completed  1  of  15  cells.
Completed  2  of  15  cells.
Completed  3  of  15  cells.
Completed  4  of  15  cells.
Completed  5  of  15  cells.
Completed  6  of  15  cells.
Completed  7  of  15  cells.
Completed  8  of  15  cells.
Completed  9  of  15  cells.
Completed  10  of  15  cells.
Completed  11  of  15  cells.
Completed  12  of  15  cells.
Completed  13  of  15  cells.
Completed  14  of  15  cells.
Completed  15  of  15  cells.
> 
> sensPlot(out.bin) # draw contour plot
Note: Predictors with negative coefficients for the response surface have been transformed through multiplication by -1 and are displayed as inverted triangles. 
> 
> 
> 
> 
> cleanEx()
> nameEx("treatSensBART")
> ### * treatSensBART
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: treatSens.BART
> ### Title: Dual-Parameter Sensitivity Analysis Using BART
> ### Aliases: treatSens.BART
> 
> ### ** Examples
> 
> N <- 250                      # number of observations
> 
> zetay <- 0.5                  # coefficient on U in the outcome model
> zetaz <- 0.5                  # coefficient on U in the treatment model
> betaz <- c(0.75, -0.5,  0.25) # coefficients of X in the treatment model
> betay <- c(0.5,   1.0, -1.5)  # coefficients of X in the outcome model
> tau   <- 0.25                 # treatment effect
> 
> set.seed(725)
> X <- matrix(rnorm(3 * N), N)  # covariates
> 
> U  <- rbinom(N, 1, 0.5)                        # unmeasured confounder
> ps <- pnorm(X %*% betaz + zetaz * (U - 0.5)) # propensity score
> Z  <- rbinom(N, 1, ps)                         # treatment variable
> epsilon <- rnorm(N, 0.0, 2.0)                  # error term
> 
> Y0 <- X %*% betay + zetay * (U - 0.5) + epsilon       # potential outcome(Z=0)
> Y1 <- X %*% betay + zetay * (U - 0.5) + tau + epsilon # potential outcome(Z=1)
> Y  <- Y0 * (1 - Z) + Y1 * Z                             # realization of potential outcome
> 
> # sensitivity analysis
> out.bin <- treatSens.BART(Y ~ Z + X, nsim = 3, nthin = 2, nburn = 0,
+                           spy.range = c(0, 4), spz.range = c(-2 , 2), grid.dim = c(5, 3),
+                           standardize = FALSE, verbose = TRUE)
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Binary U with binomial distribution is assumed.
"ATE" option is selected. Sensitivity analysis is performed with the default Weights for the average treatment effect.
Weight trimming is applied.  The maximum size of weights is set to 25 , which is 10 % of the size of the inferential group.
Computing final grid...
==45321== Thread 3:
==45321== Invalid read of size 4
==45321==    at 0x1937E1E4: ext_rng_simulateContinuousUniform (packages/tests-vg/treatSens/src/external/randomBase.c:632)
==45321==    by 0x19372F50: (anonymous namespace)::sampleConfounders((anonymous namespace)::Data const&, (anonymous namespace)::Scratch&) [clone .isra.1] (packages/tests-vg/treatSens/src/sensitivityAnalysis.cpp:512)
==45321==    by 0x193733DB: sensitivityAnalysisTask (packages/tests-vg/treatSens/src/sensitivityAnalysis.cpp:357)
==45321==    by 0x193801CA: threadLoop (packages/tests-vg/treatSens/src/external/thread.c:276)
==45321==    by 0x793A593: start_thread (in /usr/lib64/libpthread-2.27.so)
==45321==    by 0x7C4BE6E: clone (in /usr/lib64/libc-2.27.so)
==45321==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
==45321== 

 *** caught segfault ***

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: treatSens:::cibart(c(-0.287105525077626, -3.70603922044676, 2.496600707264, -4.01750932507933, -2.92570861620553, 3.17501260162248, 1.85234290423963, 2.19534764723042, -1.65837895712157, -2.31578201611595, -2.67851481006858, 0.109860646635892, -1.49935084035548, -0.899450178491997, 3.13722765961788, 0.532635979587116, 2.23869523242292, -2.05371895798485, -3.20763044409215, 1.9168764031243, -1.07652067490374, 0.12063225676724, 1.63954885114794, -1.87783060216948, -5.99959929551615, -0.795470749734402, -3.93378900034891, -0.287565804713476, 2.15663912971916, -0.138129916228105, -5.783036170259, -0.104239699227465, 0.213613950001719, -1.53094952901838, 0.0326262954858827, 0.102654676000026, -3.21053663377968, -0.788000743967875, -1.4013439017232, 0.439792794174101, -3.47086264204734, -2.5195459114019, 2.03909719703329, -1.25931032566604, -4.25482420869461, -1.61503236585148, 1.94090886323951, -2.65306498344254, -2.52591930710055, 1.05824498718806, 1.79703724196605, 1.0996660499214, 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1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0), c(0, 2, 4), c(-2, -0.333333333333333, 0, 0.333333333333333, 2), 0.5, "ATE", list(maxIter = 30L), list(n.sim = 3L, n.burn.init = 0L,     n.burn.cell = 0L, n.thin = 2L, n.thread = 16L), TRUE)
 2: eval(cibartCall, parent.frame(1))
 3: eval(cibartCall, parent.frame(1))
 4: treatSens.BART(Y ~ Z + X, nsim = 3, nthin = 2, nburn = 0, spy.range = c(0,     4), spz.range = c(-2, 2), grid.dim = c(5, 3), standardize = FALSE,     verbose = TRUE)
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: treatSens:::cibart(c(-0.287105525077626, -3.70603922044676, 2.496600707264, -4.01750932507933, -2.92570861620553, 3.17501260162248, 1.85234290423963, 2.19534764723042, -1.65837895712157, -2.31578201611595, -2.67851481006858, 0.109860646635892, -1.49935084035548, -0.899450178491997, 3.13722765961788, 0.532635979587116, 2.23869523242292, -2.05371895798485, -3.20763044409215, 1.9168764031243, -1.07652067490374, 0.12063225676724, 1.63954885114794, ==45321== 
==45321== Process terminating with default action of signal 11 (SIGSEGV): dumping core
==45321==    at 0x7944E29: raise (in /usr/lib64/libpthread-2.27.so)
==45321==    by 0x504D0F: sigactionSegv (svn/R-devel/src/main/main.c:634)
==45321==    by 0x7944FAF: ??? (in /usr/lib64/libpthread-2.27.so)
==45321==    by 0x1937E1E3: ext_rng_simulateContinuousUniform (packages/tests-vg/treatSens/src/external/randomBase.c:627)
==45321== 
==45321== HEAP SUMMARY:
==45321==     in use at exit: 100,317,863 bytes in 18,599 blocks
==45321==   total heap usage: 3,921,596 allocs, 3,902,997 frees, 1,745,988,830 bytes allocated
==45321== 
==45321== Thread 1:
==45321== 5,040 bytes in 15 blocks are possibly lost in loss record 336 of 2,524
==45321==    at 0x4C3114A: calloc (/builddir/build/BUILD/valgrind-3.14.0/coregrind/m_replacemalloc/vg_replace_malloc.c:762)
==45321==    by 0x4011981: allocate_dtv (in /usr/lib64/ld-2.27.so)
==45321==    by 0x40122FD: _dl_allocate_tls (in /usr/lib64/ld-2.27.so)
==45321==    by 0x793B1A5: pthread_create@@GLIBC_2.2.5 (in /usr/lib64/libpthread-2.27.so)
==45321==    by 0x19380A6B: ext_mt_create (packages/tests-vg/treatSens/src/external/thread.c:93)
==45321==    by 0x19373F45: cibart::fitSensitivityAnalysis(double const*, double const*, double const*, unsigned long, unsigned long, double const*, unsigned long, double const*, double const*, unsigned long, unsigned long, double, cibart::EstimandType, cibart::TreatmentModel&, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, double*, double*, bool) (packages/tests-vg/treatSens/src/sensitivityAnalysis.cpp:258)
==45321==    by 0x19370824: (anonymous namespace)::fitSensitivityAnalysis(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) (packages/tests-vg/treatSens/src/R_interface.cpp:300)
==45321==    by 0x49571D: R_doDotCall (svn/R-devel/src/main/dotcode.c:617)
==45321==    by 0x495CE3: do_dotcall (svn/R-devel/src/main/dotcode.c:1252)
==45321==    by 0x4CE9B6: bcEval (svn/R-devel/src/main/eval.c:7289)
==45321==    by 0x4D896F: Rf_eval (svn/R-devel/src/main/eval.c:620)
==45321==    by 0x4DA51E: R_execClosure (svn/R-devel/src/main/eval.c:1780)
==45321== 
==45321== LEAK SUMMARY:
==45321==    definitely lost: 0 bytes in 0 blocks
==45321==    indirectly lost: 0 bytes in 0 blocks
==45321==      possibly lost: 5,040 bytes in 15 blocks
==45321==    still reachable: 100,312,823 bytes in 18,584 blocks
==45321==         suppressed: 0 bytes in 0 blocks
==45321== Reachable blocks (those to which a pointer was found) are not shown.
==45321== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==45321== 
==45321== For counts of detected and suppressed errors, rerun with: -v
==45321== ERROR SUMMARY: 16 errors from 2 contexts (suppressed: 0 from 0)