---
title: "reproducibility - application"
output: rmarkdown::html_vignette
editor_options: 
  chunk_output_type: console
vignette: >
  %\VignetteIndexEntry{application}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
---

This script requires that the working directory includes the folders "data", "results", and "manuscript", with the files "PPMI_Baseline_Data_02Jul2018.csv", "PPMI_Year_1-3_Data_02Jul2018.csv" and "PPMI_Data_Dictionary_for_Baseline_Dataset_Jul2018.csv" in the folder "data". We obtained our results using R 4.3.0 (2023-04-21) with cornet 0.0.8 (2023-06-01) on a local machine (aarch64-apple-darwin20, macOS Ventura 13.4).

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo=TRUE,eval=FALSE)
#setwd("~/Desktop/cornet")
#utils::install.packages(pkgs=c("devtools","missRanger","xtable","randomForest","MLmetrics"))
#devtools::install_github("rauschenberger/cornet")
```

# Processing

```{r process}
# features
X <- read.csv("data/PPMI_Baseline_Data_02Jul2018.csv",row.names="PATNO",na.strings=c(".",""))
X <- X[X$APPRDX==1,] # Parkinson's disease
X[c("SITE","APPRDX","EVENT_ID","symptom5_comment")] <- NULL
100*mean(is.na(X)) # proportion missingness
#x <- mice::complete(data=mice::mice(X,m=10,maxit=5,method="pmm",seed=1),action="all") # low-dimensional
x <- lapply(seq_len(10),function(x) missRanger::missRanger(data=X,pmm.k=3,
        num.trees=100,verbose=0,seed=1)) # high-dimensional
x <- lapply(x,function(x) model.matrix(~.-1,data=x))

# outcome
Y <- read.csv("data/PPMI_Year_1-3_Data_02Jul2018.csv",na.strings=".")
Y <- Y[Y$APPRDX==1 & Y$EVENT_ID %in% c("V04","V06","V08"),]
Y <- Y[,c("EVENT_ID","PATNO","moca")]
Y <- reshape(Y,idvar="PATNO",timevar="EVENT_ID",direction="wide")
rownames(Y) <- Y$PATNO; Y$PATNO <- NULL

# overlap
names <- intersect(rownames(X),rownames(Y))
Y <- Y[names,]; x <- lapply(x,function(x) x[names,])
save(Y,x,file="data/processed_data.RData")
writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
        sessioninfo::session_info()),con="data/info_data.txt")

# dictionary
rm(list=ls())
info <- read.csv("data/PPMI_Data_Dictionary_for_Baseline_Dataset_Jul2018.csv",nrows=238)
info <- info[!info$Variable %in% c("","PATNO","SITE","APPRDX","EVENT_ID","symptom5_comment"),]
info <- paste(paste0("\\item \\textit{",info$Variable,"}: ",info$Description),collapse=" ")
info <- gsub(pattern=" \\(OFF\\)",replacement="",x=info)
info <- gsub(pattern="_",replacement="\\_",x=info,fixed=TRUE)
info <- gsub(pattern="&",replacement="\\\\&",x=info)
cat(info)
```

# Analysis

```{r analyse}
load("data/processed_data.RData",verbose=TRUE)

colSums(!is.na(Y)) # sample size
round(100*colMeans(Y<25.5,na.rm=TRUE),1) # proportion impairment

# --- Cross-validating models. ---
names <- paste0(rep(c("lasso","ridge"),each=3),seq_len(3)) # change to 3!
loss <- fit <- p.log <- p.lin <- list()
for(i in seq_along(x)){
  loss[[i]] <- fit[[i]] <- p.log[[i]] <- p.lin[[i]] <- list()
    cat("i =",i,"\n")
    for(j in seq_along(names)){
      cat("j =",j," ")
      alpha <- 1*(substr(names[j],start=1,stop=5)=="lasso")
      index <- as.numeric(substr(names[j],start=6,stop=6))
      y <- Y[,index]
      cond <- !is.na(y)
      set.seed(i)
      loss[[i]][[names[j]]] <- cornet::cv.cornet(y=y[cond],cutoff=25.5,
                                  X=x[[i]][cond,],alpha=alpha,rf=(alpha==1),xgboost=(alpha==1))
      set.seed(i)
      fit[[i]][[names[j]]] <- cornet::cornet(y=y[cond],cutoff=25.5,
                                  X=x[[i]][cond,],alpha=alpha)
      set.seed(i)
      temp <- replicate(n=50,expr=cornet:::.test(y=y[cond],cutoff=25.5,X=x[[i]][cond,],alpha=alpha))
      p.log[[i]][[names[j]]] <- median(unlist(temp["log",]))
      p.lin[[i]][[names[j]]] <- median(unlist(temp["lin",]))
    }
    cat("\n")
}

save(loss,fit,p.log,p.lin,file="results/application.RData")
writeLines(text=capture.output(utils::sessionInfo(),cat("\n"),
        sessioninfo::session_info()),con="results/info_app.txt")
```

# Results

```{r table_test}
load("results/application.RData",verbose=TRUE)

k <- "binomial" # compare: k <- "gaussian

names <- c(paste0("lasso",1:3),paste0("ridge",1:3))
frame <- data.frame(row.names=names)
for(i in names){

  # deviance
  dev <- as.data.frame(t(sapply(loss,function(x) x[[i]]$deviance)))
  dec <- (dev$combined-dev[[k]])/dev[[k]]
  # change in percent
  frame[i,"dev.min"] <- round(100*min(dec),digits=1)
  frame[i,"dev.max"] <- round(100*max(dec),digits=1)
  
  # proportion with improvement
  frame[i,"dev.num"] <- sum(dev$combined < dev[[k]])

  # significance based on multi-split
  if(k=="binomial"){
    pvalue <- sapply(p.log,function(x) x[[i]])
  }
  if(k=="gaussian"){
    pvalue <- sapply(p.lin,function(x) x[[i]])
  }
  frame[i,"pval.min"] <- round(min(pvalue),digits=3)
  frame[i,"pval.max"] <- round(max(pvalue),digits=3)

  # quantiles weight parameter
  q <- round(quantile(sapply(fit,function(x) x[[i]]$pi.min),probs=c(0,0.5,1)),digits=2)
  frame[i,"pi.min"] <- q[1]
  frame[i,"pi.med"] <- q[2]
  frame[i,"pi.max"] <- q[3]
  
  # quantiles scale parameter
  q <- round(quantile(sapply(fit,function(x) x[[i]]$sigma.min),probs=c(0,0.5,1)),digits=2)
  frame[i,"sd.min"] <- q[1]
  frame[i,"sd.med"] <- q[2]
  frame[i,"sd.max"] <- q[3]
}

# presentation
frame <- format(frame)
rownames(frame) <- paste0(substr(x=rownames(frame),start=1,stop=5)," ",
                          substr(x=rownames(frame),start=6,stop=6))
colnames(frame) <- gsub(pattern="dev.",replacement="\\\\delta_{\\\\text{",x=colnames(frame))
colnames(frame) <- gsub(pattern="pval.",replacement="p_{\\\\text{",x=colnames(frame))
colnames(frame) <- gsub(pattern="pi.",replacement="\\\\pi_{\\\\text{",x=colnames(frame))
colnames(frame) <- gsub(pattern="sd.",replacement="\\\\sigma_{\\\\text{",x=colnames(frame))
colnames(frame) <- paste0("$",colnames(frame),"}}$")

xtable <- xtable::xtable(frame,align="r|rrc|cc|ccc|ccc")
xtable::print.xtable(xtable,include.rownames=TRUE,sanitize.text.function=function(x) x,comment=FALSE)
```


```{r table_change}
load("results/application.RData",verbose=TRUE)

names <- c(paste0("lasso",1:3),paste0("ridge",1:3))
type <- c("deviance","class","mse","mae","auc","prauc")

k <- "binomial"

frame <- matrix(NA,nrow=length(names),ncol=length(type),dimnames=list(names,type))

for(i in names){
  for(j in type){
    value <- as.data.frame(t(sapply(loss,function(x) x[[i]][[j]])))
    change <- 100*(value$combined-value[[k]])/value[[k]]
    frame[i,j] <- median(change)
  }
}

frame <- format(round(frame,digits=1))
frame <- gsub(pattern=" ",replacement="+",x=frame)
colnames(frame) <- sapply(colnames(frame),function(x) switch(x,class="\\textsc{mcr}",mse="\\textsc{mse}",mae="\\textsc{mae}",auc="\\textsc{roc-auc}",prauc="\\textsc{pr-auc}",x))
colnames(frame) <- paste0("$\\Delta$",colnames(frame))
rownames(frame) <- paste0(substr(x=rownames(frame),start=1,stop=5)," ",
                          substr(x=rownames(frame),start=6,stop=6))
xtable <- xtable::xtable(frame,align="r|cccccc")
xtable::print.xtable(xtable,include.rownames=TRUE,sanitize.text.function=function(x) x,comment=FALSE)
```

```{r table_other}
load("results/application.RData",verbose=TRUE)

table <- numeric()
for(i in 1:3){
  lasso <- apply(sapply(loss,function(x) x[[paste0("lasso",i)]]$deviance),1,median)
  names(lasso)[names(lasso)=="binomial"] <- "logistic lasso regression"
  names(lasso)[names(lasso)=="combined"] <- "combined lasso regression"
  ridge <- apply(sapply(loss,function(x) x[[paste0("ridge",i)]]$deviance),1,median)
  names(ridge)[names(ridge)=="binomial"] <- "logistic ridge regression"
  names(ridge)[names(ridge)=="combined"] <- "combined ridge regression"
  table <- cbind(table,c(lasso[c("logistic lasso regression","combined lasso regression")],ridge[c("logistic ridge regression","combined ridge regression")],lasso["rf"],lasso["xgboost"])) 
  rownames(table)[rownames(table)=="rf"] <- "\\texttt{randomForest}"
  rownames(table)[rownames(table)=="xgboost"] <- "\\texttt{xgboost}"
}
colnames(table) <- paste("year",1:3)
rownames(table) <- paste("\\footnotesize",rownames(table))
xtable <- xtable::xtable(table)
xtable::print.xtable(xtable,comment=FALSE,hline.after=c(0,2,4),sanitize.text.function=identity)

```


# Figures

```{r figure_MAP}
load("results/application.RData",verbose=TRUE)
sum <- fit[[1]]$lasso1
sum$cvm <- Reduce("+",lapply(fit,function(x) x$lasso1$cvm))
sum$sigma.min <- sapply(fit,function(x) x$lasso1$sigma.min)
sum$pi.min <- sapply(fit,function(x) x$lasso1$pi.min)

grDevices::pdf("manuscript/figure_MAP.pdf",width=4,height=3)

graphics::par(mar=c(4,4,0.5,0.5))
cornet:::plot.cornet(sum)

grDevices::dev.off()
```

```{r figure_TFN}
rm(list=ls())

sigma <- c(1,2,3); cutoff <- 25.5
x <- seq(from=20,to=30,length.out=100)

grDevices::pdf("manuscript/figure_TFN.pdf",width=4,height=3)

graphics::par(mar=c(4,4,0.5,0.5))
graphics::plot.new()
graphics::plot.window(xlim=range(x),ylim=c(0,1))
graphics::box()
graphics::axis(side=1)
graphics::axis(side=2)
graphics::title(xlab=expression(hat(y)),ylab=expression(Phi(hat(y),mu,sigma^2)),line=2.5)
graphics::abline(h=0.5,lty=2,col="grey")
graphics::abline(v=cutoff,lty=2,col="grey")

lty <- c(2,1,3); lwd <- c(1,1,2)
lty <- c("dashed","solid","dotted")
for(i in seq_along(sigma)){
  p <- stats::pnorm(q=x,mean=cutoff,sd=sigma[i])
  graphics::lines(x=x,y=p,lty=lty[i],lwd=lwd[i])
}

graphics::text(x=cutoff,y=0.40,labels=bquote(mu==.(cutoff)),pos=4)
legend <- sapply(sigma,function(x) as.expression(bquote(sigma == .(x))))
graphics::legend(x="topleft",legend=legend,lty=lty,bty="n",lwd=lwd)

grDevices::dev.off()
```

<!--
# ordinal regression

It is possible to compare combined regression with ordinal regression by slightly modifying the function cv.cornet. Add the argument "ordinal = TRUE/FALSE" and two code chunks (see below). Such a comparison does not make much sense for ordinal response variables with many categories.

```{r ordinal,eval=FALSE}
cv.cornet <- function (y, cutoff, X, alpha = 1, nfolds.ext = 5, nfolds.int = 10, foldid.ext = NULL, foldid.int = NULL, type.measure = "deviance", ordinal = FALSE,...) {
    z <- 1 * (y > cutoff)
    if (is.null(foldid.ext)) {
        foldid.ext <- palasso:::.folds(y = z, nfolds = nfolds.ext)
    } else {
        nfolds.ext <- length(unique(foldid.ext))
    }
    cols <- c("intercept", "binomial", "combined")
    ### trial start ###
    if(ordinal){cols <- c(cols,"ordinal")}
    ### trial end ###
    pred <- matrix(data = NA, nrow = length(y), ncol = length(cols), 
        dimnames = list(NULL, cols))
    for (i in seq_len(nfolds.ext)) {
        y0 <- y[foldid.ext != i]
        z0 <- z[foldid.ext != i]
        X0 <- X[foldid.ext != i, ]
        X1 <- X[foldid.ext == i, ]
        if (is.null(foldid.int)) {
            foldid <- palasso:::.folds(y = z0, nfolds = nfolds.int)
        } else {
            foldid <- foldid.int[foldid.ext != i]
        }
        fit <- cornet::cornet(y = y0, cutoff = cutoff, X = X0, 
            alpha = alpha, type.measure = type.measure, foldid = foldid, 
            ...)
        tryCatch(expr = plot.cornet(fit), error = function(x) NULL)
        temp <- predict.cornet(fit, newx = X1)
        if (any(temp < 0 | temp > 1)) {
            stop("Outside unit interval.", call. = FALSE)
        }
        model <- colnames(temp)
        for (j in seq_along(model)) {
            pred[foldid.ext == i, model[j]] <- temp[[model[j]]]
        }
        if(ordinal){
          ### trial start ###
          #browser()
          y0_ord <- as.factor(y0)
          fit <- ordinalNet::ordinalNet(x=X0,y=y0_ord,alpha=alpha)
          pred_ord <- predict(fit,newx=X1)
          above <- as.numeric(levels(y0_ord))>cutoff
          pred[foldid.ext ==i,"ordinal"] <- rowSums(pred_ord[,above])
        } ### trial end ###
    }
    type <- c("deviance", "class", "mse", "mae", "auc")
    loss <- lapply(X = type, FUN = function(x) palasso:::.loss(y = z, 
        fit = pred, family = "binomial", type.measure = x, 
        foldid = foldid.ext)[[1]])
    names(loss) <- type
    loss <- lapply(loss, function(x) signif(x, digits = 6))
    return(loss)
}
predict.cornet <- cornet:::predict.cornet

loss <- list()
for(i in seq_along(Y)){
  load("data/processed_data.RData",verbose=TRUE)
  cond <- !is.na(Y[[i]])
  loss[[i]] <- cv.cornet(y=Y[[i]][cond],X=x[[1]][cond,],cutoff=25.5,ordinal=TRUE)
}
sapply(loss,function(x) x$deviance)


### Ordinal regression with two different packages.
#
# load("data/processed_data.RData",verbose=TRUE)
# cond <- !is.na(Y$moca.V04)
# y <- as.factor(x=Y$moca.V04[cond])
# x <- x[[1]][cond,]
#
# # ordinalNet
# model <- ordinalNet::ordinalNet(x=x,y=y)
# y_hat <- predict(model)
# below <- as.numeric(levels(y))<=25.5
# above <- as.numeric(levels(y))>25.5
# b1 <- rowSums(y_hat[,below])
# a1 <- rowSums(y_hat[,above])
# 
# # glmnetcr
# model <- glmnetcr::glmnetcr(x=x,y=y)
# s <- glmnetcr::select.glmnetcr(model)
# y_hat <- predict(model)$probs[,,s]
# below <- as.numeric(colnames(y_hat))<=25.5
# above <- as.numeric(colnames(y_hat))>25.5
# b2 <- rowSums(y_hat[,below])
# a2 <- rowSums(y_hat[,above])
# 
# cor(a1,a2)
# cor(b1,b2)
```
-->
