DSC query

Last updated: 2019-01-17

• ✔ R Markdown file: up-to-date

  Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

• ✔ Environment: empty

  Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

• ✔ Seed: set.seed(20190115)

  The command set.seed(20190115) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

• ✔ Session information: recorded

  Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

• ✔ Repository version: 2b216ae

  Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
  
  Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

  
  Ignored files:
      Ignored:    .Rhistory
      Ignored:    .Rproj.user/
      Ignored:    .sos/
      Ignored:    data/.DS_Store
  
  Untracked files:
      Untracked:  .gitattributes
      Untracked:  analysis/SusieZConverge.Rmd
      Untracked:  data/sim_gaussian_475.rds
      Untracked:  data/sim_gaussian_75.rds
      Untracked:  output/dscout_gaussian_init.rds
      Untracked:  output/dscout_gaussian_null.rds
      Untracked:  output/dscout_gaussian_z.rds
  
  Unstaged changes:
      Modified:   README.md
  
  

  Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

library(dscrutils)
dscout_null = dscquery(dsc.outdir='output/susie_z_gaussian_benchmark', targets='sim_gaussian_null susie_z score susie_z.avg_purity susie_z.niter score.hit score.signal_num score.cs_medianSize score.top_hit')
saveRDS(dscout_null, 'output/susie_z_gaussian_benchmark/dscout_gaussian_null.rds')

dscout_gaussian_z = dscquery(dsc.outdir='output/susie_z_gaussian_benchmark', targets='sim_gaussian susie_z score sim_gaussian.effect_num sim_gaussian.pve sim_gaussian.sigma sim_gaussian.mean_corX susie_z.avg_purity susie_z.niter susie_z.L score.hit score.signal_num score.cs_medianSize score.top_hit')
saveRDS(dscout_gaussian_z, 'output/susie_z_gaussian_benchmark/dscout_gaussian_z.rds')

dscout_gaussian_init = dscquery(dsc.outdir='output/susie_z_gaussian_benchmark', targets='sim_gaussian susie_z_init score sim_gaussian.effect_num sim_gaussian.pve sim_gaussian.sigma sim_gaussian.mean_corX susie_z_init.avg_purity susie_z_init.niter score.hit score.signal_num score.cs_medianSize score.top_hit')
saveRDS(dscout_gaussian_init, 'output/susie_z_gaussian_benchmark/dscout_gaussian_init.rds')

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.2

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_1.0.0        digest_0.6.18    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.3  
 [7] git2r_0.24.0      magrittr_1.5      evaluate_0.12    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.11    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20       

This reproducible R Markdown analysis was created with workflowr 1.1.1