Last updated: 2018-05-15

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Expand here to see past versions:
    File Version Author Date Message
    html 69e0c7d LSun 2018-05-14 Update to 1.0
    html e05bc83 LSun 2018-05-12 Update to 1.0
    rmd cc0ab83 Lei Sun 2018-05-11 update
    html 0f36d99 LSun 2017-12-21 Build site.
    html 7e06347 LSun 2017-11-11 Build site.
    html 2c74856 LSun 2017-11-11 Build site.
    rmd 60487d0 LSun 2017-11-11 wflow_publish(“analysis/seqgendiff.rmd”)

Introduction

In order to perform a large-scale simulation, we explore the seqgendiff::poisthin function developed by David.

library(seqgendiff)
source("../code/count_to_summary.R")
source("../code/gdash_lik.R")
counts <- readRDS("../data/liver.sim.rds")

More flexible effects

Instead of \(g = \pi_0\delta_0 + (1 - \pi_0)N(0, \sigma^2)\), we would like to add effects following \(g = \pi_0\delta_0 + \pi_1N(0, \sigma_1^2) + \pi_2N(0, \sigma_2^2)\).

The data is simulated by Poisson thinning, not by normal mean models.

Expand here to see past versions of plot_pihat0-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2c74856 LSun 2017-11-11

Expand here to see past versions of plot_mse-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2c74856 LSun 2017-11-11

Expand here to see past versions of plot_auc-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2c74856 LSun 2017-11-11

Expand here to see past versions of qvalue calibration plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2c74856 LSun 2017-11-11

Expand here to see past versions of qvalue calibration plotting-2.png:
Version Author Date
0f36d99 LSun 2017-12-21
2c74856 LSun 2017-11-11

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] ashr_2.2-2        Rmosek_8.0.69     PolynomF_1.0-1   
 [4] CVXR_0.95         REBayes_1.2       Matrix_1.2-12    
 [7] SQUAREM_2017.10-1 EQL_1.0-0         ttutils_1.0-1    
[10] seqgendiff_0.1.0 

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

This reproducible R Markdown analysis was created with workflowr 1.0.1