reproducibility - simulation"

This script requires that the working directory includes the folders "data", "results", and "manuscript". We obtained our results using R 4.0.0 (2020-04-24) with cornet 0.0.4 (2020-03-18) on a local machine (x86_64-w64-mingw32/x64, Windows 10 x64). Floating point errors might lead to slightly different results on other platforms.

knitr::opts_chunk$set(echo=TRUE,eval=FALSE)
#setwd("C:/Users/armin.rauschenberger/Desktop/cornet") # local drive
#setwd("Z:/Rauschenberger/cornet") # shared drive
#devtools::install_github("rauschenberger/cornet")

Analysis

iter <- 1000
set.seed(1)
frame <- data.frame(cor=runif(n=iter,min=0,max=0.9),
                    n=round(runif(n=iter,min=100,max=200)),
                    prob=runif(n=iter,min=0.01,max=0.1),
                    sd=runif(n=iter,min=1,max=2),
                    exp=runif(n=iter,min=0.1,max=2),
                    frac=runif(n=iter,min=0.5,max=0.9))

ridge <- lasso <- list()
pb <- utils::txtProgressBar(min=0,max=nrow(frame),width=20,style=3)
for(i in seq_len(nrow(frame))){
    utils::setTxtProgressBar(pb=pb,value=i)
    set.seed(i)
    data <- do.call(what=cornet:::.simulate,args=cbind(frame[i,],p=500))
    set.seed(i)
    ridge[[i]] <- do.call(what=cornet:::cv.cornet,args=c(data,alpha=0))
    set.seed(i)
    lasso[[i]] <- do.call(what=cornet:::cv.cornet,args=c(data,alpha=1))
}
names(lasso) <- names(ridge) <- paste0("set",seq_len(nrow(frame)))
save(lasso,ridge,frame,file="results/simulation.RData")

writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
        sessioninfo::session_info()),con="results/info_sim.txt")

Figures

#--- boxplot of different metrics ---
load("results/simulation.RData",verbose=TRUE)

fuse0 <- fuse1 <- list()
for(i in c("deviance","class","mse","mae","auc")){
  fuse0[[i]] <- sapply(ridge,function(x) (x[[i]]["combined"]-x[[i]]["binomial"]))
  fuse1[[i]] <- sapply(lasso,function(x) (x[[i]]["combined"]-x[[i]]["binomial"]))
  #if(i=="auc"){fuse0[[i]] <- -fuse0[[i]]; fuse1[[i]] <- -fuse1[[i]]}
}

grDevices::pdf("manuscript/figure_BOX.pdf",width=6,height=4)
graphics::par(mar=c(1.9,1.9,0.1,0.1))
graphics::plot.new()
ylim <- range(unlist(fuse0),unlist(fuse1))
at <- seq(from=1,to=9,by=2)
graphics::plot.window(xlim=c(min(at)-0.6,max(at)+0.6),ylim=ylim)
graphics::axis(side=2)
graphics::abline(h=0,col="grey",lty=2)
graphics::abline(v=at+1,col="grey",lty=2)
graphics::box()
graphics::boxplot(fuse1,at=at-0.5,add=TRUE,axes=FALSE,col="white",border="black")
graphics::boxplot(fuse0,at=at+0.5,add=TRUE,axes=FALSE,col="white",border="darkgrey")
labels <- names(fuse1)
labels <- ifelse(labels=="class","mcr",labels)
labels <- ifelse(labels %in% c("mcr","mse","mae","auc"),toupper(labels),labels)
graphics::axis(side=1,at=at,labels=labels)
grDevices::dev.off()

# decrease
sapply(fuse1,function(x) mean(x<0)) # lasso
sapply(fuse0,function(x) mean(x<0)) # ridge

# constant
sapply(fuse1,function(x) mean(x==0)) # lasso
sapply(fuse0,function(x) mean(x==0)) # ridge

# increase
sapply(fuse1,function(x) mean(x>0)) # lasso
sapply(fuse0,function(x) mean(x>0)) # ridge
#--- plot of percentage changes ---
load("results/simulation.RData",verbose=TRUE)

loss <- list()
loss$ridge <- as.data.frame(t(sapply(ridge,function(x) x$deviance)))
loss$lasso <- as.data.frame(t(sapply(lasso,function(x) x$deviance)))

data <- list()
for(i in c("ridge","lasso")){
  data[[i]] <- data.frame(row.names=rownames(frame))
  data[[i]]$"(1)" <- 100*(loss[[i]]$binomial-loss[[i]]$intercept)/loss[[i]]$intercept
  data[[i]]$"(2)" <- 100*(loss[[i]]$combined-loss[[i]]$intercept)/loss[[i]]$intercept
  data[[i]]$"(3)" <- 100*(loss[[i]]$combined-loss[[i]]$binomial)/loss[[i]]$binomial
}

row <- colnames(data$lasso)
col <- colnames(frame)
txt <- expression(rho,n,s,sigma,t,q)

for(k in c("ridge","lasso")){
  grDevices::pdf(paste0("manuscript/figure_",k,".pdf"),width=6.5,height=4)
  graphics::par(mfrow=c(length(row),length(col)),
              mar=c(0.2,0.2,0.2,0.2),oma=c(4,4,0,0))
  for(i in seq_along(row)){
    for(j in seq_along(col)){
      y <- data[[k]][[row[i]]]
      x <- frame[[col[j]]]
      graphics::plot.new()
      graphics::plot.window(xlim=range(x),ylim=range(y),xaxs="i")
      graphics::box()
      graphics::abline(h=0,lty=1,col="grey")
      graphics::points(y=y,x=x,cex=0.5,pch=16,col=ifelse(y>0,"black","grey"))
      line <- stats::loess.smooth(y=y,x=x,evaluation=200)
      graphics::lines(x=line$x,y=line$y,col="black",lty=2,lwd=1)
      if(j==1){
        graphics::mtext(text=row[i],side=2,line=2.5,las=2)
        graphics::axis(side=2)
      }
      if(i==length(row)){
        graphics::mtext(text=txt[j],side=1,line=2.5)
        graphics::axis(side=1)
      }
    }
  }
  grDevices::dev.off()
}

cbind(col,as.character(txt)) # verify


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cornet documentation built on April 19, 2021, 9:07 a.m.