automation

R/pkgname.R

@@ -51,7 +51,7 @@
 #' # vector "beta": slopes
 #' 
 #' #--- model comparison ---
-#' \dontrun{
+#' \donttest{
 #' loss <- cv.starnet(y=y,X=X)}
 #' # cross-validated loss for different alpha,
 #' # and for tuning and stacking

cran-comments.md

 
-Thanks for the explanation. As requested, we replaced dontrun not by a hashtag but by donttest.
+Thanks. The vignette does not save files any more.
\ No newline at end of file

docs/pkgdown.yml

@@ -5,5 +5,5 @@ articles:
   article: article.html
   script: script.html
   starnet: starnet.html
-last_built: 2020-06-03T06:38Z
+last_built: 2020-06-03T16:19Z
 

docs/reference/starnet-package.html

@@ -177,10 +177,11 @@ doi: <a href='https://doi.org/10.1093/bioinformatics/btaa535'>10.1093/bioinforma
 <span class='co'># vector "beta": slopes</span>
 
 <span class='co'>#--- model comparison ---</span>
-<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
-<span class='no'>loss</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='cv.starnet.html'>cv.starnet</a></span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)}
-<span class='co'># cross-validated loss for different alpha,</span>
-<span class='co'># and for tuning and stacking</span></div></pre>
+<span class='co'># \donttest{</span>
+<span class='no'>loss</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='cv.starnet.html'>cv.starnet</a></span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)<span class='co'># }</span></div><div class='img'><img src='starnet-package-1.png' alt='' width='700' height='433' /></div><div class='input'># cross-validated loss for different alpha,
+# and for tuning and stacking
+
+</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">

man/starnet-package.Rd

@@ -42,7 +42,7 @@ coef <- coef(object)
 # vector "beta": slopes
 
 #--- model comparison ---
-\dontrun{
+\donttest{
 loss <- cv.starnet(y=y,X=X)}
 # cross-validated loss for different alpha,
 # and for tuning and stacking

vignettes/.Rhistory

+tempdir()
+grDevices::dev.off()
+grDevices::dev.off()

vignettes/script.Rmd

@@ -9,7 +9,7 @@ vignette: >
 ---
 
 This script requires that the working directory includes the folders
-"results" and "manuscript". For each simulation and application, the first chunk performs the computationally intensive analysis, and the other chunks summarise the results. We pre-processed the TCGA data with R 3.6.3 (2020-02-29) on a local machine (x86_64-w64-mingw32/x64, Windows 10 x64), and analysed the data with R 3.6.1 (2019-07-05) on a virtual machine (x86_64-pc-linux-gnu, Ubuntu 16.04.6 LTS).
+"results" and "manuscript". Consider uncommenting the lines for saving results and figures. For each simulation and application, the first chunk performs the computationally intensive analysis, and the other chunks summarise the results. We pre-processed the TCGA data with R 3.6.3 (2020-02-29) on a local machine (x86_64-w64-mingw32/x64, Windows 10 x64), and analysed the data with R 3.6.1 (2019-07-05) on a virtual machine (x86_64-pc-linux-gnu, Ubuntu 16.04.6 LTS).
 
 ```{r start,include=FALSE}
 knitr::opts_chunk$set(echo=TRUE,eval=FALSE)
@@ -65,7 +65,7 @@ pos$beta[1] <- pos$beta[1] - 0.3
 pos$beta[3] <- pos$beta[3] + 0.3
  
 a <- b <- 0.3
-grDevices::pdf(file="manuscript/figure_NET.pdf",width=5,height=3)
+#grDevices::pdf(file="manuscript/figure_NET.pdf",width=5,height=3)
 graphics::plot.new()
 graphics::par(mar=c(0,0,0,0),mfrow=c(1,1))
 graphics::plot.window(xlim=c(0.4,7.6),ylim=c(0.8,5.2))
@@ -85,7 +85,7 @@ text(x=c(4,6.5),y=1,labels=txt$dots,cex=1.2)
 ellipse(x=pos$alpha,y=3,text=txt$alpha,a=a+0.1,b=b,cex=1.2)
 text(x=c(4,6),y=3,labels=txt$dots,cex=1.2)
 ellipse(x=pos$y,y=5,text=txt$y,a=a,b=b,cex=1.2)
-grDevices::dev.off()
+#grDevices::dev.off()
 ```
 
 # Simulation 1
@@ -107,11 +107,11 @@ for(id in c(1,NA,0)){
     set.seed(i)
     loss[[i]] <- tryCatch(cv.starnet(y=data$y,X=data$X,family=family,foldid.ext=fold,alpha.meta=id,nzero=nzero),error=function(x) NULL)
   }
-  save(loss,mode,file=paste0("results/sim_prediction_",id,".RData"))
+  #save(loss,mode,file=paste0("results/sim_prediction_",id,".RData"))
 }
 
-writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
-        sessioninfo::session_info()),con="results/sim_prediction.txt")
+#writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
+#        sessioninfo::session_info()),con="results/sim_prediction.txt")
 ```
 
 ```{r pre_boxplot,fig.height=2}
@@ -120,7 +120,7 @@ load("results/sim_prediction_1.RData")
 cond <- sapply(loss,is.null)
 loss <- loss[!cond]; mode <- mode[!cond]
 
-grDevices::pdf(file="manuscript/figure_BOX.pdf",width=5,height=2)
+#grDevices::pdf(file="manuscript/figure_BOX.pdf",width=5,height=2)
 graphics::par(mfrow=c(1,3),mar=c(2.1,2,0.5,0.5),oma=c(0,2,0,0))
 meta <- sapply(loss,function(x) x$meta)
 base <- sapply(loss,function(x) x$base[c("alpha0.05","alpha0.95")])
@@ -171,7 +171,7 @@ for(i in modes){
   
 }
 graphics::title(ylab=paste0(paste0(rep(" ",times=12),collapse=""),"mean squared error"),outer=TRUE,line=1)
-grDevices::dev.off()
+#grDevices::dev.off()
 
 round(median,digits=2)
 round(winner,digits=2)
@@ -184,7 +184,7 @@ load("results/sim_prediction_1.RData")
 cond <- sapply(loss,is.null)
 loss <- loss[!cond]; mode <- mode[!cond]
 
-grDevices::pdf(file="manuscript/figure_PHS.pdf",width=5,height=2)
+#grDevices::pdf(file="manuscript/figure_PHS.pdf",width=5,height=2)
 graphics::par(mfrow=c(1,3),mar=c(3.3,2,0.5,0.5),oma=c(0,2,0,0))
 for(i in c("sparse","dense","mixed")){
   x <- as.numeric(colnames(loss[mode==i][[1]]$extra))
@@ -207,7 +207,7 @@ for(i in c("sparse","dense","mixed")){
   graphics::title(xlab="nzero",line=2.5)
 }
 graphics::title(ylab=paste0(paste0(rep(" ",times=12),collapse=""),"mean squared error"),outer=TRUE,line=1)
-grDevices::dev.off()
+#grDevices::dev.off()
 ```
 
 # Simulation 2
@@ -280,11 +280,11 @@ for(id in c(1,NA,0)){
     }
     
   }
-  save(mode,mae0,mae1,mse0,mse1,sel0,sel1,TP,FP,TN,FN,loss,file=paste0("results/sim_estimation_",id,".RData"))
+  #save(mode,mae0,mae1,mse0,mse1,sel0,sel1,TP,FP,TN,FN,loss,file=paste0("results/sim_estimation_",id,".RData"))
 }
 
-writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
-        sessioninfo::session_info()),con="results/sim_estimation.txt")
+#writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
+#        sessioninfo::session_info()),con="results/sim_estimation.txt")
 ```
 
 ```{r est_results}
@@ -359,11 +359,11 @@ for(id in c(1,NA,0)){
       loss[[k]][[seed]] <- tryCatch(cv.starnet(y=y[[k]],X=X[[k]],family="binomial",nzero=nzero,alpha.meta=id),error=function(x) NULL)
     }
   }
-  save(loss,n0,n1,file=paste0("results/app_standard_",id,".RData"))
+  #save(loss,n0,n1,file=paste0("results/app_standard_",id,".RData"))
 }
 
-writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
-        sessioninfo::session_info()),con="results/app_standard.txt")
+#writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
+#        sessioninfo::session_info()),con="results/app_standard.txt")
 ```
 
 ```{r sta_table,echo=TRUE}
@@ -376,18 +376,15 @@ for(i in names(loss)){
   for(j in c("meta","base")){
     median[[i]][[j]] <- apply(sapply(loss[[i]],function(x) x[[j]]),1,median)
   }
-  #median[[i]]$ph <- median(sapply(loss[[i]],function(x) x$extra["stack","Inf"]))
   list <- lapply(loss[[i]],function(x) x$extra)
   array <- array(data=unlist(list),dim=c(3,11,10),dimnames=list(rownames(list[[1]]),colnames(list[[1]]),seq_len(10)))
   median[[i]]$extra <- apply(X=array,MARGIN=1:2,FUN=median)
 }
 
 meta <- t(sapply(median,function(x) x$meta[c("ridge","lasso","tune","stack")]))
-#post <- sapply(median,function(x) x$ph)
 post <- sapply(median,function(x) x$extra["stack","Inf"])
 
 table <- cbind("\\#0"=n0,"\\#1"=n1,format(meta,digits=1,nsmall=2)," "=format(post,digits=1,nsmall=2))
-#index <- cbind(seq_len(nrow(meta)),ifelse(meta[,"stack"]<meta[,"tune"],6,5))
 index <- cbind(seq_len(nrow(meta)),apply(meta,1,which.min)+2)
 table[index] <- paste0("\\underline{",table[index],"}") 
 colnames(table) <- paste0("\\text{",colnames(table),"}")
@@ -402,7 +399,7 @@ xtable::print.xtable(xtable,sanitize.text.function=function(x) x)
 ```{r sta_figure,fig.height=2}
 #<<start>>
 #<<sta_table>>
-grDevices::pdf(file="manuscript/figure_STA.pdf",width=5,height=2)
+#grDevices::pdf(file="manuscript/figure_STA.pdf",width=5,height=2)
 graphics::par(mfrow=c(1,3),mar=c(3.3,2,0.5,0.5),oma=c(0,2,0,0))
 median$SRBCT <- list()
 median$SRBCT$meta <- rowMeans(sapply(median[paste0("SRBCT",1:4)],
@@ -428,7 +425,7 @@ for(i in c("colon","leukaemia","SRBCT")){
 
 }
 graphics::title(ylab=paste0(paste0(rep(" ",times=16),collapse=""),"logistic deviance"),outer=TRUE,line=1)
-grDevices::dev.off()
+#grDevices::dev.off()
 
 sapply(median,function(x) names(which.min(x$base)))
 ```
@@ -455,10 +452,10 @@ for(i in seq_along(type)){
   y[[i]] <- Y; x[[i]] <- X
 }
 print(object.size(x),units="Mb")
-save(y,x,type,file=paste0("results/tcga_data.RData"))
+#save(y,x,type,file=paste0("results/tcga_data.RData"))
 
-writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
-        sessioninfo::session_info()),con="results/app_processing.txt")
+#writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
+#        sessioninfo::session_info()),con="results/app_processing.txt")
 
 # cross-validation
 
@@ -472,13 +469,12 @@ for(id in c(1,NA,0)){
     if(sum(y[[i]]==0)<5|sum(y[[i]]==1)<5){next}
     set.seed(1)
     loss[[i]] <- tryCatch(cv.starnet(y=y[[i]],X=x[[i]],family="binomial",alpha.meta=id,nzero=nzero),error=function(x) NA)
-    #graphics::title(main=type[i])
   }
-  save(loss,file=paste0("results/app_extension_",id,".RData"))
+  #save(loss,file=paste0("results/app_extension_",id,".RData"))
 }
 
-writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
-        sessioninfo::session_info()),con="results/app_extension.txt")
+#writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
+#        sessioninfo::session_info()),con="results/app_extension.txt")
 ```
 
 ```{r ext_table}
@@ -493,7 +489,6 @@ meta <- t(sapply(loss[cond],function(x) x$meta[c("ridge","lasso","tune","stack")
 
 post <- sapply(loss[cond],function(x) x$extra["stack","Inf"])
 table <- cbind("\\#0"=n0[cond],"\\#1"=n1[cond],format(meta,digits=1,nsmall=3)," "=format(post,digits=1,nsmall=3))
-#index <- cbind(seq_len(nrow(meta)),ifelse(meta[,"stack"]<meta[,"tune"],6,5))
 index <- cbind(seq_len(nrow(meta)),apply(meta,1,which.min)+2)
 table[index] <- paste0("\\underline{",table[index],"}") 
 colnames(table) <- paste0("\\text{",colnames(table),"}")