added relevant output such as html reports and sessionInfo call to the repository

.gitignore

@@ -9,6 +9,4 @@
 *.log
 *.pdfsync
 *.gz
-*.txt
 data
-*.html

CLL/figures_results.Rmd

 ---
 title: "CLL example: predicting drug responses using 3 omics (drug/mRNA/meth) on original scales"
 author: "Britta Velten"
-date: "12/07/2018"
+date: "11/05/2019"
 output:
   BiocStyle::html_document:
     toc: true

CLL_std/figures_results.Rmd

 ---
-title: "CLL example: predicting drug responses using 3 omics (drug/mRNA/meth)"
+title: "CLL example: predicting drug responses using 3 omics (drug/mRNA/meth) after standardization"
 author: "Britta Velten"
-date: "12/07/2018"
+date: "11/05/2019"
 output:
   BiocStyle::html_document:
     toc: true

GTEX/figures_results.Rmd

 ---
 title: "GTEx example: predicting age using gene expression data from 5 tissues"
 author: "Britta Velten"
-date: "13/07/2018"
+date: "11/05/2019"
 output:
   BiocStyle::html_document:
     toc: true
@@ -74,8 +74,8 @@ ggRMSE <- ggplot(df_RMSE, aes(x=method, y=RMSE, fill=method)) +
 ggRMSE
 ```
 
-## Penalty Factors (in graper and related methods)
-```{r hyperparameters_all, fig.width=12, fig.height=12}
+## Penalty Factors
+```{r hyperparameters_all, fig.width=12, fig.height=12, eval = FALSE, echo = FALSE}
 methods4comp <- c("graper","graper_SS","graper_FF", "IPFLasso", "GRridge")
 df_pf <- melt(lapply(resultList, function(l) {
   nms <- rownames(l$pf_mat)
@@ -130,14 +130,14 @@ ggPF <- plot_grid(gg1,gg2, rel_widths = c(1,1.25), nrow=1, align = "hv", axis =
 ggPF
 ```
 
-# Joint plot
+## Joint plot
 ```{r joint, fig.widht=8, fig.height=9}
 plot_grid(ggRMSE, ggPF, ncol=1, labels = letters[1:2],
           label_size = 18, rel_heights = c(2,1))
 ```
 
 
-## Runtime
+# Runtime
 ```{r time}
 time_mat <- sapply(resultList, function(l) l$runtime)
 df_time <- melt(time_mat,
@@ -160,7 +160,7 @@ ggplot(df_time, aes(x=method, y=time, col=method)) +
 df_time %>% group_by(method) %>% dplyr::summarize(mean(time))
 ```
 
-SessionInfo
+# SessionInfo
 ```{r}
 sessionInfo()
 ```

run_time/grid_figures.Rmd

 ---
-title: "Figures for results from grid simulation"
+title: "Figures for results from grid simulation evaluating scalability"
 author: "Britta Velten"
-date: "13/07/2018"
+date: "11/05/2019"
 output: BiocStyle::html_document
 ---
 

session_info.txt

+R version 3.5.1 (2018-07-02)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: CentOS Linux 7 (Core)
+
+Matrix products: default
+BLAS/LAPACK: /g/easybuild/x86_64/CentOS/7/haswell/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_haswellp-r0.2.20.so
+
+locale:
+ [1] LC_CTYPE=en_IE.UTF-8       LC_NUMERIC=C              
+ [3] LC_TIME=en_IE.UTF-8        LC_COLLATE=en_IE.UTF-8    
+ [5] LC_MONETARY=en_IE.UTF-8    LC_MESSAGES=en_IE.UTF-8   
+ [7] LC_PAPER=en_IE.UTF-8       LC_NAME=C                 
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C            
+[11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C       
+
+attached base packages:
+[1] parallel  stats     graphics  grDevices utils     datasets  methods  
+[8] base     
+
+other attached packages:
+ [1] dplyr_0.7.7         reshape2_1.4.3      cowplot_0.9.3      
+ [4] ggplot2_3.1.0       randomForest_4.6-14 grpreg_3.2-0       
+ [7] GRridge_1.5.3       mvtnorm_1.0-8       graph_1.59.2       
+[10] BiocGenerics_0.27.1 Iso_0.0-17          penalized_0.9-51   
+[13] ipflasso_0.1        survival_2.42-3     SGL_1.1            
+[16] glmnet_2.0-16       foreach_1.4.4       varbvs_2.4-0       
+[19] Matrix_1.2-14       grpRR_0.99.0        stringr_1.3.1      
+
+loaded via a namespace (and not attached):
+ [1] Rcpp_0.12.19        pillar_1.3.0        compiler_3.5.1     
+ [4] RColorBrewer_1.1-2  plyr_1.8.4          bindr_0.1.1        
+ [7] iterators_1.0.10    tools_3.5.1         tibble_1.4.2       
+[10] gtable_0.2.0        lattice_0.20-35     pkgconfig_2.0.2    
+[13] rlang_0.3.0.1       bindrcpp_0.2.2      withr_2.1.2        
+[16] stats4_3.5.1        grid_3.5.1          tidyselect_0.2.5   
+[19] glue_1.3.0          R6_2.3.0            latticeExtra_0.6-28
+[22] purrr_0.2.5         magrittr_1.5        splines_3.5.1      
+[25] scales_1.0.0        codetools_0.2-15    assertthat_0.2.0   
+[28] colorspace_1.3-2    stringi_1.2.3       lazyeval_0.2.1     
+[31] munsell_0.5.0       crayon_1.3.4      
\ No newline at end of file

simulation/grid_figures.Rmd

 ---
-title: "Figures for results from grid simulation"
+title: "Figures for results from grid simulation evaluating prediction performance and hyperparameter recovery"
 author: "Britta Velten"
-date: "13/07/2018"
+date: "11/05/2019"
 output: BiocStyle::html_document
 ---