Last updated: 2018-05-12

workflowr checks: (Click a bullet for more information)
  • 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(12345)

    The command set.seed(12345) 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: ddf9062

    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:    .DS_Store
        Ignored:    .Rhistory
        Ignored:    .Rproj.user/
        Ignored:    analysis/.DS_Store
        Ignored:    analysis/BH_robustness_cache/
        Ignored:    analysis/FDR_Null_cache/
        Ignored:    analysis/FDR_null_betahat_cache/
        Ignored:    analysis/Rmosek_cache/
        Ignored:    analysis/StepDown_cache/
        Ignored:    analysis/alternative2_cache/
        Ignored:    analysis/alternative_cache/
        Ignored:    analysis/ash_gd_cache/
        Ignored:    analysis/average_cor_gtex_2_cache/
        Ignored:    analysis/average_cor_gtex_cache/
        Ignored:    analysis/brca_cache/
        Ignored:    analysis/cash_deconv_cache/
        Ignored:    analysis/cash_fdr_1_cache/
        Ignored:    analysis/cash_fdr_2_cache/
        Ignored:    analysis/cash_fdr_3_cache/
        Ignored:    analysis/cash_fdr_4_cache/
        Ignored:    analysis/cash_fdr_5_cache/
        Ignored:    analysis/cash_fdr_6_cache/
        Ignored:    analysis/cash_plots_cache/
        Ignored:    analysis/cash_sim_1_cache/
        Ignored:    analysis/cash_sim_2_cache/
        Ignored:    analysis/cash_sim_3_cache/
        Ignored:    analysis/cash_sim_4_cache/
        Ignored:    analysis/cash_sim_5_cache/
        Ignored:    analysis/cash_sim_6_cache/
        Ignored:    analysis/cash_sim_7_cache/
        Ignored:    analysis/correlated_z_2_cache/
        Ignored:    analysis/correlated_z_3_cache/
        Ignored:    analysis/correlated_z_cache/
        Ignored:    analysis/create_null_cache/
        Ignored:    analysis/cutoff_null_cache/
        Ignored:    analysis/design_matrix_2_cache/
        Ignored:    analysis/design_matrix_cache/
        Ignored:    analysis/diagnostic_ash_cache/
        Ignored:    analysis/diagnostic_correlated_z_2_cache/
        Ignored:    analysis/diagnostic_correlated_z_3_cache/
        Ignored:    analysis/diagnostic_correlated_z_cache/
        Ignored:    analysis/diagnostic_plot_2_cache/
        Ignored:    analysis/diagnostic_plot_cache/
        Ignored:    analysis/efron_leukemia_cache/
        Ignored:    analysis/fitting_normal_cache/
        Ignored:    analysis/gaussian_derivatives_2_cache/
        Ignored:    analysis/gaussian_derivatives_3_cache/
        Ignored:    analysis/gaussian_derivatives_4_cache/
        Ignored:    analysis/gaussian_derivatives_5_cache/
        Ignored:    analysis/gaussian_derivatives_cache/
        Ignored:    analysis/gd-ash_cache/
        Ignored:    analysis/gd_delta_cache/
        Ignored:    analysis/gd_lik_2_cache/
        Ignored:    analysis/gd_lik_cache/
        Ignored:    analysis/gd_w_cache/
        Ignored:    analysis/knockoff_10_cache/
        Ignored:    analysis/knockoff_2_cache/
        Ignored:    analysis/knockoff_3_cache/
        Ignored:    analysis/knockoff_4_cache/
        Ignored:    analysis/knockoff_5_cache/
        Ignored:    analysis/knockoff_6_cache/
        Ignored:    analysis/knockoff_7_cache/
        Ignored:    analysis/knockoff_8_cache/
        Ignored:    analysis/knockoff_9_cache/
        Ignored:    analysis/knockoff_cache/
        Ignored:    analysis/knockoff_var_cache/
        Ignored:    analysis/marginal_z_alternative_cache/
        Ignored:    analysis/marginal_z_cache/
        Ignored:    analysis/mosek_reg_2_cache/
        Ignored:    analysis/mosek_reg_4_cache/
        Ignored:    analysis/mosek_reg_5_cache/
        Ignored:    analysis/mosek_reg_6_cache/
        Ignored:    analysis/mosek_reg_cache/
        Ignored:    analysis/pihat0_null_cache/
        Ignored:    analysis/plot_diagnostic_cache/
        Ignored:    analysis/poster_obayes17_cache/
        Ignored:    analysis/real_data_simulation_2_cache/
        Ignored:    analysis/real_data_simulation_3_cache/
        Ignored:    analysis/real_data_simulation_4_cache/
        Ignored:    analysis/real_data_simulation_5_cache/
        Ignored:    analysis/real_data_simulation_cache/
        Ignored:    analysis/rmosek_primal_dual_2_cache/
        Ignored:    analysis/rmosek_primal_dual_cache/
        Ignored:    analysis/seqgendiff_cache/
        Ignored:    analysis/simulated_correlated_null_2_cache/
        Ignored:    analysis/simulated_correlated_null_3_cache/
        Ignored:    analysis/simulated_correlated_null_cache/
        Ignored:    analysis/simulation_real_se_2_cache/
        Ignored:    analysis/simulation_real_se_cache/
        Ignored:    analysis/smemo_2_cache/
        Ignored:    data/LSI/
        Ignored:    docs/.DS_Store
        Ignored:    docs/figure/.DS_Store
        Ignored:    output/fig/
    
    Unstaged changes:
        Deleted:    analysis/cash_plots_fdp.Rmd
    
    
    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.
Expand here to see past versions:
    File Version Author Date Message
    rmd cc0ab83 Lei Sun 2018-05-11 update
    html 4491358 LSun 2018-01-30 linear regression
    rmd c17f67c LSun 2018-01-30 wflow_publish(c(“analysis/index.rmd”, “analysis/knockoff.rmd”, “analysis/knockoff_2.rmd”, “analysis/knockoff_3.rmd”))

Introduction

Similar to previous simulation, only that the design matrix \(X\) is simulated such that the columns in \(X\) have high collinearity.

Each row of \(X\) is independently drawn from a \(N(0, \Sigma_X)\) distribution, where \(\Sigma_X = B_{p \times d} \cdot B_{p \times d}^T + I\), where \(B_{i, j} \stackrel{\text{iid}}{\sim} N(0, 1)\). Then transform \(\Sigma_X\) to a correlation matrix.

\(d = 5\), the sparsity \(\eta \in \{0.5, 0.6, 0.7, 0.8, 0.9\}\)

Overall across all sparsity

Expand here to see past versions of avg-1.png:
Version Author Date
4491358 LSun 2018-01-30

Expand here to see past versions of avg-2.png:
Version Author Date
4491358 LSun 2018-01-30

Low sparsity: \(50\%\) true signal

No id variables; using all as measure variables

Expand here to see past versions of 500-1.png:
Version Author Date
4491358 LSun 2018-01-30
No id variables; using all as measure variables

Expand here to see past versions of 500-2.png:
Version Author Date
4491358 LSun 2018-01-30
Warning in bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z
$group == : Outlier (-Inf) in boxplot 1 is not drawn

Expand here to see past versions of 500-3.png:
Version Author Date
4491358 LSun 2018-01-30

High sparsity: \(10\%\) true signal

No id variables; using all as measure variables

Expand here to see past versions of 100-1.png:
Version Author Date
4491358 LSun 2018-01-30
No id variables; using all as measure variables

Expand here to see past versions of 100-2.png:
Version Author Date
4491358 LSun 2018-01-30
Warning in bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z
$group == : Outlier (-Inf) in boxplot 1 is not drawn

Expand here to see past versions of 100-3.png:
Version Author Date
4491358 LSun 2018-01-30

Session information

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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     

other attached packages:
 [1] ggplot2_2.2.1     reshape2_1.4.3    ashr_2.2-2       
 [4] Rmosek_8.0.69     PolynomF_1.0-1    CVXR_0.95        
 [7] REBayes_1.2       Matrix_1.2-12     SQUAREM_2017.10-1
[10] EQL_1.0-0         ttutils_1.0-1     knockoff_0.3.0   

loaded via a namespace (and not attached):
 [1] gmp_0.5-13.1      Rcpp_0.12.16      pillar_1.0.1     
 [4] plyr_1.8.4        compiler_3.4.3    git2r_0.21.0     
 [7] workflowr_1.0.1   R.methodsS3_1.7.1 R.utils_2.6.0    
[10] iterators_1.0.9   tools_3.4.3       digest_0.6.15    
[13] bit_1.1-12        tibble_1.4.1      gtable_0.2.0     
[16] evaluate_0.10.1   lattice_0.20-35   rlang_0.1.6      
[19] foreach_1.4.4     parallel_3.4.3    yaml_2.1.18      
[22] Rmpfr_0.6-1       ECOSolveR_0.4     stringr_1.3.0    
[25] knitr_1.20        rprojroot_1.3-2   bit64_0.9-7      
[28] grid_3.4.3        R6_2.2.2          rmarkdown_1.9    
[31] magrittr_1.5      whisker_0.3-2     scales_0.5.0     
[34] MASS_7.3-47       codetools_0.2-15  backports_1.1.2  
[37] htmltools_0.3.6   scs_1.1-1         colorspace_1.3-2 
[40] labeling_0.3      stringi_1.1.6     lazyeval_0.2.1   
[43] munsell_0.4.3     pscl_1.5.2        doParallel_1.0.11
[46] truncnorm_1.0-7   R.oo_1.21.0      



This reproducible R Markdown analysis was created with workflowr 1.0.1