https://github.com/bozenne/article-netbenefit-inference

Code and software for the article "The asymptotic distribution of the Net Benefit estimator in presence of right-censoring" by Ozenne B, Budtz-Jørgensen E, Péron J. in Statistical Methods in Medical Research. October 2021 (link: https://doi.org/10.1177%2F09622802211037067).

https://github.com/bozenne/article-netbenefit-inference

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Code and software for the article "The asymptotic distribution of the Net Benefit estimator in presence of right-censoring" by Ozenne B, Budtz-Jørgensen E, Péron J. in Statistical Methods in Medical Research. October 2021 (link: https://doi.org/10.1177%2F09622802211037067).

README.org

This directory contains the R code used to generate the results
presented in the article 'The asymptotic distribution of the net 
benefit estimator in presence of right-censoring' by Ozenne B, Budtz-Jørgensen E, Péron J. 
published in Statistical Methods in Medical Research (2021, link: https://doi.org/10.1177%2F09622802211037067). 

It is organized as follows:

- *the SIMULATION files* run the simulation study for the section
  "Studentized vs. standard a permutation test"
  (=SIMULATION-comparisonWithPermutationTest.R=) and for supplementary
  material B.2 (=SIMULATION-SM-comparison-bebu-lachin.R=). The latter
  file imports functions defined in =FCT-Bebu-Lachin.R=.

- *the BATCH_SIMULATION files* define the simulation studies used in
  the sections "Coverage of the asymptotic CIs". Each file was
  excecuted 200 times using a different id and therefore a different
  seed when randomly generating the data. The output of the
  simulations were saved in a =Results= directory, not uploaded on
  Github to save space but available upon request.

- *the SUBM_SIMULATION files* are used to run the batch files via a
  queuing system.

- *the BUILD files* gather the results of the various simulations by
  reading the data in the =Results= directory (=BUILD_results.R=) and
  save key summary statistics in the =Results= folder. Then the file
  =BUILD_graphtable.R= read these results and generate all figures and
  tables and save them in the directories =figures= and =tables= (not
  used in the article). Imports functions defined in =FCT-gg.R=.

- *the FIGURE files* generate the figures displayed in the article and
  save them in the directory =figures-article=. Imports functions
  defined in =FCT-gg.R=.

- *the TABLE files* generate the tables displayed in the article and save them in the directory =tables-article=.

- *the ILLUSTRATION files* contains the code used to generate the
  results for the section "Illustration" as well as the additional
  illustration mentionned in supplementary material G.

#+BEGIN_SRC R  :results output   :exports results  :session *R* :cache yes 
sessionInfo()
#+END_SRC

#+begin_example
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BuyseTest_2.2.7   butils.base_1.2   devtools_2.3.2    usethis_2.0.1    
[5] data.table_1.14.0 Rcpp_1.0.6       

loaded via a namespace (and not attached):
 [1] lattice_0.20-41          prettyunits_1.1.1        ps_1.6.0                
 [4] rprojroot_2.0.2          digest_0.6.27            foreach_1.5.1           
 [7] utf8_1.2.1               R6_2.5.0                 stats4_4.0.5            
[10] ggplot2_3.3.3            pillar_1.5.1             rlang_0.4.10            
[13] rstudioapi_0.13          callr_3.6.0              Matrix_1.3-2            
[16] desc_1.3.0               splines_4.0.5            stringr_1.4.0           
[19] munsell_0.5.0            compiler_4.0.5           xfun_0.22               
[22] pkgconfig_2.0.3          pkgbuild_1.2.0           tidyselect_1.1.0        
[25] tibble_3.1.0             prodlim_2019.11.13       roxygen2_7.1.1          
[28] codetools_0.2-18         fansi_0.4.2              crayon_1.4.1            
[31] dplyr_1.0.5              withr_2.4.1              grid_4.0.5              
[34] gtable_0.3.0             lifecycle_1.0.0          magrittr_2.0.1          
[37] scales_1.1.1             cli_2.4.0                stringi_1.5.3           
[40] cachem_1.0.4             pbapply_1.4-3            fs_1.5.0                
[43] RcppArmadillo_0.10.2.2.0 remotes_2.3.0            doParallel_1.0.16       
[46] testthat_3.0.2           xml2_1.3.2               ellipsis_0.3.1          
[49] generics_0.1.0           vctrs_0.3.7              lava_1.6.9              
[52] iterators_1.0.13         tools_4.0.5              glue_1.4.2              
[55] purrr_0.3.4              processx_3.5.1           pkgload_1.2.0           
[58] parallel_4.0.5           fastmap_1.1.0            survival_3.2-10         
[61] colorspace_2.0-0         sessioninfo_1.1.1        memoise_2.0.0           
[64] knitr_1.31
#+end_example

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