R Under development (unstable) (2024-10-11 r87227 ucrt) -- "Unsuffered Consequences"
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> ## * load packages
> library(testthat)
> library(BuyseTest)
Loading required package: Rcpp
BuyseTest version 3.0.5
>
> library(lava)
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
> library(data.table)
> library(survival)
Attaching package: 'survival'
The following object is masked from 'package:BuyseTest':
brier
> xx <- capture.output(print(veteran))
> library(riskRegression)
riskRegression version 2023.12.21
> library(prodlim)
> library(mvtnorm)
>
> ## * run tests
> ## setwd("~/Documents/GitHub/BuyseTest/tests/")
> ## source("~/Documents/GitHub/BuyseTest/tests/testthat/test-BuyseTest-engine.R")
> test_check("BuyseTest")
Generalized pairwise comparisons with 2 prioritized endpoints and 2 strata
- statistic : win odds (delta: endpoint specific, Delta: global)
- null hypothesis : Delta == 1
- confidence level: 0.95
- inference : H-projection of order 2 after log transformation
- treatment groups: T (treatment) vs. C (control)
- strata weights : 50%, 50%
- neutral pairs : re-analyzed using lower priority endpoints
- results
endpoint threshold strata total(%) favorable(%) unfavorable(%) neutral(%)
eventtime 0.1 global 100.00 37.27 41.73 21.01
0 50.00 16.81 21.75 11.44
1 50.00 20.46 19.97 9.57
score 3 global 21.01 0.56 0.25 20.20
0 11.44 0.35 0.12 10.97
1 9.57 0.21 0.12 9.23
uninf(%) delta Delta CI [2.5% ; 97.5%] p.value
0 0.9146 0.9146 [0.6482;1.2906] 0.61138
0 0.8199
0 1.0197
0 1.0303 0.9204 [0.6521;1.2991] 0.63695
0 1.0403
0 1.0185
Generalized pairwise comparisons with 2 prioritized endpoints and 2 strata
- statistic : net treatment benefit (delta: endpoint specific, Delta: global)
- null hypothesis : Delta == 0
- confidence level: 0.95
- inference : H-projection of order 2 after atanh transformation
- treatment groups: T (treatment) vs. C (control)
- strata weights : 50%, 50%
- neutral pairs : re-analyzed using lower priority endpoints
- results
endpoint threshold strata total(%) favorable(%) unfavorable(%) neutral(%)
eventtime 0.1 global 100.00 37.27 41.73 21.01
0 50.00 16.81 21.75 11.44
1 50.00 20.46 19.97 9.57
score 3 global 21.01 0.56 0.25 20.20
0 11.44 0.35 0.12 10.97
1 9.57 0.21 0.12 9.23
uninf(%) delta Delta CI [2.5% ; 97.5%] p.value
0 -0.0446 -0.0446 [-0.2135;0.1268] 0.61137
0 -0.0990
0 0.0098
0 0.0031 -0.0415 [-0.2106;0.1301] 0.63694
0 0.0045
0 0.0018
[ FAIL 0 | WARN 6 | SKIP 1 | PASS 1166 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-BuyseTest-previousBug.R:553:1'
[ FAIL 0 | WARN 6 | SKIP 1 | PASS 1166 ]
>
> ## * memory check
> ## /data/gannet/ripley/R/packages/tests-clang-SAN/BuyseTest/src/FCT_buyseTest.cpp:894:20
>
> ## ** valgrind
> ## Information: https://kevinushey.github.io/blog/2015/04/05/debugging-with-valgrind/
>
> ## R -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes" --vanilla < testthat.R
> ## R -d "valgrind --dsymutil=yes" -e "Rcpp::sourceCpp('segfault.cpp')"
> ## R -d valgrind
>
> ## ** san
> ## docker run --rm -ti -v $(pwd):/mydir wch1/r-debug
> ## wget -O - https://github.com/bozenne/BuyseTest/tarball/master | tar xz
> ## cd bozenne
> ## cd test/testthat
> ## RDcsan
> ## install.packages(c("Rcpp","RcppArmadillo","devtools","riskRegrssion","cvAUC"))
> ## devtools::install_github("bozenne/BuyseTest")
> ## allFiles <- list.files()
> ## lapply(rev(allFiles), function(x){cat(x,"\n"); source(x)})
> ## gctorture(TRUE)
> ##
>
>
>
>
> proc.time()
user system elapsed
34.57 1.20 35.76