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<title>CASH Simulation, Part 2: Over-dispersion</title>

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<h1 class="title toc-ignore">CASH Simulation, Part 2: Over-dispersion</h1>
<h4 class="author"><em>Lei Sun</em></h4>
<h4 class="date"><em>2017-11-10</em></h4>

</div>


<!-- The file analysis/chunks.R contains chunks that define default settings
shared across the workflowr files. -->
<!-- Update knitr chunk options -->
<!-- Insert the date the file was last updated -->
<p><strong>Last updated:</strong> 2017-12-21</p>
<!-- Insert the code version (Git commit SHA1) if Git repository exists and R
 package git2r is installed -->
<p><strong>Code version:</strong> 6e42447</p>
<!-- Add your analysis here -->
<section id="conditioned-on-over-dispersed-data-sets-only" class="level2">
<h2>Conditioned on over-dispersed data sets only</h2>
<pre class="r"><code>source(&quot;../code/gdash_lik.R&quot;)</code></pre>
<pre class="r"><code>z.mat = readRDS(&quot;../output/z_null_liver_777.rds&quot;)
se.mat = readRDS(&quot;../output/sebetahat_null_liver_777.rds&quot;)</code></pre>
<pre class="r"><code>z.sd &lt;- apply(z.mat, 1, sd)
inflation.index = (z.sd &gt; qchisq(0.9995, ncol(z.mat) - 1) / (ncol(z.mat) - 1))
deflation.index = (z.sd &lt; qchisq(0.0005, ncol(z.mat) - 1) / (ncol(z.mat) - 1))
## Number of inflation data sets
sum(inflation.index)</code></pre>
<pre><code>[1] 299</code></pre>
<pre class="r"><code>## Number of deflation data sets
sum(deflation.index)</code></pre>
<pre><code>[1] 477</code></pre>
<pre class="r"><code>z.mat = z.mat[inflation.index, ]
se.mat = se.mat[inflation.index, ]</code></pre>
<p><img src="figure/cash_sim_2.rmd/plot_pihat0-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><img src="figure/cash_sim_2.rmd/plot_mse-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><img src="figure/cash_sim_2.rmd/plot_auc-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><img src="figure/cash_sim_2.rmd/qvalue%20calibration%20plotting-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/cash_sim_2.rmd/qvalue%20calibration%20plotting-2.png" width="672" style="display: block; margin: auto;" /></p>
</section>
<section id="session-information" class="level2">
<h2>Session information</h2>
<!-- Insert the session information into the document -->
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

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] ashr_2.2-2        Rmosek_8.0.69     PolynomF_1.0-1    CVXR_0.94-4      
[5] REBayes_1.2       Matrix_1.2-12     SQUAREM_2017.10-1 EQL_1.0-0        
[9] ttutils_1.0-1    

loaded via a namespace (and not attached):
 [1] gmp_0.5-13.1      Rcpp_0.12.14      compiler_3.4.3   
 [4] git2r_0.20.0      R.methodsS3_1.7.1 R.utils_2.6.0    
 [7] iterators_1.0.9   tools_3.4.3       digest_0.6.13    
[10] bit_1.1-12        evaluate_0.10.1   lattice_0.20-35  
[13] foreach_1.4.4     yaml_2.1.16       parallel_3.4.3   
[16] Rmpfr_0.6-1       ECOSolveR_0.3-2   stringr_1.2.0    
[19] knitr_1.17        rprojroot_1.3-1   bit64_0.9-7      
[22] grid_3.4.3        R6_2.2.2          rmarkdown_1.8    
[25] magrittr_1.5      MASS_7.3-47       backports_1.1.2  
[28] codetools_0.2-15  htmltools_0.3.6   scs_1.1-1        
[31] stringi_1.1.6     doParallel_1.0.11 pscl_1.5.2       
[34] truncnorm_1.0-7   R.oo_1.21.0      </code></pre>
</section>

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