R/tune_parameters_ml.R
In pablogonzalezginestet/stackBagg: Stacked IPCW Bagging
Defines functions
tune_params_ml
Documented in
tune_params_ml
#' Tuning parameter selection
#' @description Tuning parameter selection
#' @param gam_param a vector containing degree of freedom 3 and 4
#' @param lasso_param a grid of values for the shrinkage term
#' @param randomforest_param a two column matrix: first column denotes the num_trees parameter and the second column denotes the mtry parameter.
#' @param knn_param a grid of positive integers values
#' @param svm_param a three column matrix: first column denotes the cost parameter, second column the gamma and third column the kernel. kernel=1 denotes "radial" and kernel=2 denotes "linear".
#' @param nn_param a grid of positive integers values for the neurons
#' @param bart_param a three column matrix: first column denotes the num_tree parameter, second column the k parameter and third column the q parameter.
#' @param folds number of folds
#' @param xnam vector with the names of the covariates to be included in the model
#' @param tao evaluation time point of interest
#' @param data data set that contains at least id, E , ttilde, delta, wts and covariates
#' @param weighting Procedure to compute the inverse probability of censoring weights. Weighting="CoxPH" and weighting="CoxBoost" model the censoring by the Cox model and CoxBoost model respectively.
#' @return a list with the tune parameters selected using the IPCW AUC loss function.
#' @export
tune_params_ml <- function( gam_param,
lasso_param,
randomforest_param,
knn_param,
svm_param,
nn_param,
bart_param,
folds,
xnam,
tao,
data,
weighting) {
xnam.factor <- colnames(data[xnam])[sapply(data[xnam], class)=="factor"]
if(length(xnam.factor)==0){ xnam.factor<- NULL}
xnam.cont <- xnam[!(xnam %in% xnam.factor)]
# continous variables to be applied the smoothing function in the gam must have
# 10 or more unique values or
# have to have four values with more than 5%
xnam.cont.gam <- xnam.cont[apply(data[xnam.cont],2, function(z) length(unique(z))>10 | length(unique(z))<=10 & sum(table(z)/dim(data)[1]>0.05)>=4)]
names(data)[1] <- "ttilde"
names(data)[2] <- "delta"
# create binary outcome,E, was created by dichotomizing the time to failure at tao
# and we create id: unique identifiers of each subject
data<- dplyr::mutate(data,id = 1:length(ttilde),E=as.factor(ifelse(ttilde < tao & delta==1, 1 , ifelse(ttilde < tao & delta==2 | ttilde>tao, 0, NA))),
deltac=ifelse(delta==0,1,0))
#check that there is no rare categories in each factor variable
if(!is.null(xnam.factor)) {
for(s in 1:length(xnam.factor)) {
level_to_drop <- table(data[xnam.factor][,s])/dim(data)[1]<.05
for(q in 1:length(level_to_drop)){
if(level_to_drop[q]==TRUE){
data<- data[!data[xnam.factor][,s]==levels(data[xnam.factor][,s])[q],]
}
}
if(any(level_to_drop==TRUE)){
data[xnam.factor][,s] <- droplevels(data[xnam.factor][,s])
}
}
}
if(weighting=="CoxBoost"){
# CoxBoost Weights
#train data
if(is.null(xnam.factor)){
X.boost <- as.matrix(data[xnam])
fit.cboost <- peperr::fit.CoxBoost(Surv(data$ttilde,data$deltac), x=X.boost,cplx=300)
wts.boost=NULL
for (i in 1:nrow(data) ){
tao_temp <- min(data$ttilde[i],tao)
wts.boost<- c(wts.boost,as.numeric(!is.na(data$E[i])) / peperr::predictProb(fit.cboost, Surv(data$ttilde[i],data$deltac[i]), data[xnam],tao_temp,complexity = 300)[i])
}
}else{
X.boost <- data[xnam.cont]
X.boost <- cbind(X.boost,predict(caret::dummyVars( ~ ., data =data[xnam.factor], fullRank=TRUE), newdata=data[xnam.factor]))
colnames(X.boost)=c(paste("x", 1:(dim(X.boost)[2]), sep=""))
data2=as.data.frame(cbind(ttilde=data$ttilde,deltac=data$deltac,X.boost))
X.boost=as.matrix(data2[,-(1:2)])
fit.cboost <- peperr::fit.CoxBoost(Surv(data2$ttilde,data2$deltac), x=X.boost,cplx=300)
wts.boost=NULL
xnam2 <-names(data2)[-(1:2)]
for (i in 1:nrow(data2) ){
tao_temp <- min(data2$ttilde[i],tao)
wts.boost<- c(wts.boost,as.numeric(!is.na(data$E[i])) / peperr::predictProb(fit.cboost, Surv(data2$ttilde[i],data2$deltac[i]), data2[xnam2],tao_temp,complexity = 300)[i])
}
}
data$wts <- wts.boost
}
if(weighting=="CoxPH"){
#Cox PH weights
fmla.c <- as.formula(paste("Surv(ttilde,deltac) ~ ", paste(xnam, collapse= "+")))
#train data set
cox.C.train<- survival::coxph(fmla.c, data=data)
newdata_zero <- data[1,]
if(is.null(xnam.factor)){
newdata_zero[xnam] <- 0
basel_surv <- survival::survfit(cox.C.train, newdata=newdata_zero[xnam])
beta.cox.train <- cox.C.train$coef
wts.coxph=NULL
for (i in 1:nrow(data)){
newdata <- data[i,]
newdata_cov <- data[i,xnam]
G <- basel_surv$surv ^(exp(sum(newdata_cov * beta.cox.train )))
wts.coxph <- c(wts.coxph, as.numeric(!is.na(newdata$E)) / (G[ max(which(basel_surv$time <= min(newdata$ttilde, tao) ) ) ] ) )
}
}else{
for(s in 1:length(xnam.factor)) {newdata_zero[xnam.factor[s]]=levels(data[xnam.factor][,s])[1]}
newdata_zero[xnam.cont] <- 0
basel_surv <- survival::survfit(cox.C.train, newdata=newdata_zero[xnam])
beta.cox.train <- cox.C.train$coef
dummies.factor.train=as.data.frame(predict(caret::dummyVars( ~ ., data =data[xnam.factor],fullRank = TRUE), newdata=data[xnam.factor]))
beta.cox.train=c(beta.cox.train[xnam.cont],beta.cox.train[!names(beta.cox.train) %in% xnam.cont ])
wts.coxph=NULL
for (i in 1:nrow(data)){
newdata <- data[i,]
newdata_cov = cbind(data[i,xnam.cont],dummies.factor.train[i,])
G <- basel_surv$surv ^(exp(sum(newdata_cov * beta.cox.train )))
wts.coxph <- c(wts.coxph, as.numeric(!is.na(newdata$E)) / (G[ max(which(basel_surv$time <= min(newdata$ttilde, tao) ) ) ] ) )
}
}
data$wts <- wts.coxph
}
data <- data[c("id","E","wts","ttilde","delta",xnam)]
fmla <- as.formula(paste("E ~ ", paste(xnam, collapse= "+")))
pred.test.gam=NULL
pred.test.knn=NULL
pred.test.svm=NULL
pred.test.nn=NULL
pred.test.rf=NULL
pred.test.bart=NULL
pred.test.lasso=NULL
id.set=NULL
test.id_temp=1:nrow(data)
for (k in 1:folds) {
if (k==folds){
test.id=test.id_temp
}else{
test.id=sample(test.id_temp,floor( nrow(data)/folds ), replace=FALSE) # nrow(data)/folds=100
test.id_temp <- setdiff(test.id_temp, test.id) # update the test id candidates
}
train.id <- setdiff(1:nrow(data), test.id)
train.set <- data.frame(data[train.id,])
test.set <- data.frame(data[test.id,])
n_test.set <- nrow(test.set)
train.set=train.set[!is.na(train.set$E),]
pred.gam=ML_list$GAMfun(data=train.set,
testdata=test.set,
fmla,
xnam,
xnam.factor,
xnam.cont,
xnam.cont.gam,
param=gam_param)
pred.test.gam<-rbind(pred.test.gam, pred.gam )
pred.lasso=apply(as.matrix(lasso_param),1,function(x) ML_list$lassofun(data=train.set,
testdata=test.set,
fmla,
xnam,
xnam.factor,
xnam.cont,
param=x) )
pred.test.lasso=rbind(pred.test.lasso, pred.lasso )
pred.rf=apply(as.matrix(randomforest_param),1,function(x) ML_list$rffun(data=train.set,
testdata=test.set,
fmla,
xnam,
xnam.factor,
xnam.cont,
param=x) )
pred.test.rf=rbind(pred.test.rf, pred.rf )
pred.knn=apply(as.matrix(knn_param),1,function(x) ML_list$knnfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.knn<-rbind(pred.test.knn, pred.knn )
pred.svm=apply(as.matrix(svm_param),1,function(x) ML_list$svmfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.svm=rbind(pred.test.svm, pred.svm )
pred.nn=apply(as.matrix(nn_param),1,function(x) ML_list$nnfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.nn=rbind(pred.test.nn, pred.nn )
pred.bart=apply(as.matrix(bart_param),1,function(x) ML_list$bartfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.bart=rbind(pred.test.bart, pred.bart )
id.set=rbind(id.set,as.matrix(test.set$id))
print(k)
}
pred.test.gam=pred.test.gam[order(id.set),]
pred.test.knn=pred.test.knn[order(id.set),]
pred.test.svm=pred.test.svm[order(id.set),]
pred.test.nn=pred.test.nn[order(id.set),]
pred.test.rf=pred.test.rf[order(id.set),]
pred.test.bart=pred.test.bart[order(id.set),]
pred.test.lasso=pred.test.lasso[order(id.set),]
data=data[order(data$id),]
loss.function.gam=apply(pred.test.gam,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.knn=apply(pred.test.knn,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.svm=apply(pred.test.svm,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.nn=apply(pred.test.nn,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.rf=apply(pred.test.rf,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.bart=apply(pred.test.bart,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.lasso=apply(pred.test.lasso,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
tuneparams=list(
gam_param=gam_param[which.max(loss.function.gam)],
knn_param=knn_param[which.max(loss.function.knn)],
svm_param=svm_param[which.max(loss.function.svm),],
nn_param=nn_param[which.max(loss.function.nn)],
randomforest_param=randomforest_param[which.max(loss.function.rf),],
bart_param=bart_param[which.max(loss.function.bart),],
lasso_param=lasso_param[which.max(loss.function.lasso)]
)
names(tuneparams$lasso_param)=c("lambda")
names(tuneparams$knn_param)=c("k")
names(tuneparams$gam_param)=c("df")
names(tuneparams$nn_param)=c("neurons")
names(tuneparams$randomforest_param)=c("num_trees","mtry")
names(tuneparams$svm_param)=c("cost","gamma","kernel")
names(tuneparams$bart_param)=c("num_tree","k","q")
return(tuneparams)
}
pablogonzalezginestet/stackBagg documentation built on Aug. 27, 2023, 10:21 p.m.
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Defines functions tune_params_ml
Documented in tune_params_ml
#' Tuning parameter selection
#' @description Tuning parameter selection
#' @param gam_param a vector containing degree of freedom 3 and 4
#' @param lasso_param a grid of values for the shrinkage term
#' @param randomforest_param a two column matrix: first column denotes the num_trees parameter and the second column denotes the mtry parameter.
#' @param knn_param a grid of positive integers values
#' @param svm_param a three column matrix: first column denotes the cost parameter, second column the gamma and third column the kernel. kernel=1 denotes "radial" and kernel=2 denotes "linear".
#' @param nn_param a grid of positive integers values for the neurons
#' @param bart_param a three column matrix: first column denotes the num_tree parameter, second column the k parameter and third column the q parameter.
#' @param folds number of folds
#' @param xnam vector with the names of the covariates to be included in the model
#' @param tao evaluation time point of interest
#' @param data data set that contains at least id, E , ttilde, delta, wts and covariates
#' @param weighting Procedure to compute the inverse probability of censoring weights. Weighting="CoxPH" and weighting="CoxBoost" model the censoring by the Cox model and CoxBoost model respectively.
#' @return a list with the tune parameters selected using the IPCW AUC loss function.
#' @export
tune_params_ml <- function( gam_param,
lasso_param,
randomforest_param,
knn_param,
svm_param,
nn_param,
bart_param,
folds,
xnam,
tao,
data,
weighting) {
xnam.factor <- colnames(data[xnam])[sapply(data[xnam], class)=="factor"]
if(length(xnam.factor)==0){ xnam.factor<- NULL}
xnam.cont <- xnam[!(xnam %in% xnam.factor)]
# continous variables to be applied the smoothing function in the gam must have
# 10 or more unique values or
# have to have four values with more than 5%
xnam.cont.gam <- xnam.cont[apply(data[xnam.cont],2, function(z) length(unique(z))>10 | length(unique(z))<=10 & sum(table(z)/dim(data)[1]>0.05)>=4)]
names(data)[1] <- "ttilde"
names(data)[2] <- "delta"
# create binary outcome,E, was created by dichotomizing the time to failure at tao
# and we create id: unique identifiers of each subject
data<- dplyr::mutate(data,id = 1:length(ttilde),E=as.factor(ifelse(ttilde < tao & delta==1, 1 , ifelse(ttilde < tao & delta==2 | ttilde>tao, 0, NA))),
deltac=ifelse(delta==0,1,0))
#check that there is no rare categories in each factor variable
if(!is.null(xnam.factor)) {
for(s in 1:length(xnam.factor)) {
level_to_drop <- table(data[xnam.factor][,s])/dim(data)[1]<.05
for(q in 1:length(level_to_drop)){
if(level_to_drop[q]==TRUE){
data<- data[!data[xnam.factor][,s]==levels(data[xnam.factor][,s])[q],]
}
}
if(any(level_to_drop==TRUE)){
data[xnam.factor][,s] <- droplevels(data[xnam.factor][,s])
}
}
}
if(weighting=="CoxBoost"){
# CoxBoost Weights
#train data
if(is.null(xnam.factor)){
X.boost <- as.matrix(data[xnam])
fit.cboost <- peperr::fit.CoxBoost(Surv(data$ttilde,data$deltac), x=X.boost,cplx=300)
wts.boost=NULL
for (i in 1:nrow(data) ){
tao_temp <- min(data$ttilde[i],tao)
wts.boost<- c(wts.boost,as.numeric(!is.na(data$E[i])) / peperr::predictProb(fit.cboost, Surv(data$ttilde[i],data$deltac[i]), data[xnam],tao_temp,complexity = 300)[i])
}
}else{
X.boost <- data[xnam.cont]
X.boost <- cbind(X.boost,predict(caret::dummyVars( ~ ., data =data[xnam.factor], fullRank=TRUE), newdata=data[xnam.factor]))
colnames(X.boost)=c(paste("x", 1:(dim(X.boost)[2]), sep=""))
data2=as.data.frame(cbind(ttilde=data$ttilde,deltac=data$deltac,X.boost))
X.boost=as.matrix(data2[,-(1:2)])
fit.cboost <- peperr::fit.CoxBoost(Surv(data2$ttilde,data2$deltac), x=X.boost,cplx=300)
wts.boost=NULL
xnam2 <-names(data2)[-(1:2)]
for (i in 1:nrow(data2) ){
tao_temp <- min(data2$ttilde[i],tao)
wts.boost<- c(wts.boost,as.numeric(!is.na(data$E[i])) / peperr::predictProb(fit.cboost, Surv(data2$ttilde[i],data2$deltac[i]), data2[xnam2],tao_temp,complexity = 300)[i])
}
}
data$wts <- wts.boost
}
if(weighting=="CoxPH"){
#Cox PH weights
fmla.c <- as.formula(paste("Surv(ttilde,deltac) ~ ", paste(xnam, collapse= "+")))
#train data set
cox.C.train<- survival::coxph(fmla.c, data=data)
newdata_zero <- data[1,]
if(is.null(xnam.factor)){
newdata_zero[xnam] <- 0
basel_surv <- survival::survfit(cox.C.train, newdata=newdata_zero[xnam])
beta.cox.train <- cox.C.train$coef
wts.coxph=NULL
for (i in 1:nrow(data)){
newdata <- data[i,]
newdata_cov <- data[i,xnam]
G <- basel_surv$surv ^(exp(sum(newdata_cov * beta.cox.train )))
wts.coxph <- c(wts.coxph, as.numeric(!is.na(newdata$E)) / (G[ max(which(basel_surv$time <= min(newdata$ttilde, tao) ) ) ] ) )
}
}else{
for(s in 1:length(xnam.factor)) {newdata_zero[xnam.factor[s]]=levels(data[xnam.factor][,s])[1]}
newdata_zero[xnam.cont] <- 0
basel_surv <- survival::survfit(cox.C.train, newdata=newdata_zero[xnam])
beta.cox.train <- cox.C.train$coef
dummies.factor.train=as.data.frame(predict(caret::dummyVars( ~ ., data =data[xnam.factor],fullRank = TRUE), newdata=data[xnam.factor]))
beta.cox.train=c(beta.cox.train[xnam.cont],beta.cox.train[!names(beta.cox.train) %in% xnam.cont ])
wts.coxph=NULL
for (i in 1:nrow(data)){
newdata <- data[i,]
newdata_cov = cbind(data[i,xnam.cont],dummies.factor.train[i,])
G <- basel_surv$surv ^(exp(sum(newdata_cov * beta.cox.train )))
wts.coxph <- c(wts.coxph, as.numeric(!is.na(newdata$E)) / (G[ max(which(basel_surv$time <= min(newdata$ttilde, tao) ) ) ] ) )
}
}
data$wts <- wts.coxph
}
data <- data[c("id","E","wts","ttilde","delta",xnam)]
fmla <- as.formula(paste("E ~ ", paste(xnam, collapse= "+")))
pred.test.gam=NULL
pred.test.knn=NULL
pred.test.svm=NULL
pred.test.nn=NULL
pred.test.rf=NULL
pred.test.bart=NULL
pred.test.lasso=NULL
id.set=NULL
test.id_temp=1:nrow(data)
for (k in 1:folds) {
if (k==folds){
test.id=test.id_temp
}else{
test.id=sample(test.id_temp,floor( nrow(data)/folds ), replace=FALSE) # nrow(data)/folds=100
test.id_temp <- setdiff(test.id_temp, test.id) # update the test id candidates
}
train.id <- setdiff(1:nrow(data), test.id)
train.set <- data.frame(data[train.id,])
test.set <- data.frame(data[test.id,])
n_test.set <- nrow(test.set)
train.set=train.set[!is.na(train.set$E),]
pred.gam=ML_list$GAMfun(data=train.set,
testdata=test.set,
fmla,
xnam,
xnam.factor,
xnam.cont,
xnam.cont.gam,
param=gam_param)
pred.test.gam<-rbind(pred.test.gam, pred.gam )
pred.lasso=apply(as.matrix(lasso_param),1,function(x) ML_list$lassofun(data=train.set,
testdata=test.set,
fmla,
xnam,
xnam.factor,
xnam.cont,
param=x) )
pred.test.lasso=rbind(pred.test.lasso, pred.lasso )
pred.rf=apply(as.matrix(randomforest_param),1,function(x) ML_list$rffun(data=train.set,
testdata=test.set,
fmla,
xnam,
xnam.factor,
xnam.cont,
param=x) )
pred.test.rf=rbind(pred.test.rf, pred.rf )
pred.knn=apply(as.matrix(knn_param),1,function(x) ML_list$knnfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.knn<-rbind(pred.test.knn, pred.knn )
pred.svm=apply(as.matrix(svm_param),1,function(x) ML_list$svmfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.svm=rbind(pred.test.svm, pred.svm )
pred.nn=apply(as.matrix(nn_param),1,function(x) ML_list$nnfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.nn=rbind(pred.test.nn, pred.nn )
pred.bart=apply(as.matrix(bart_param),1,function(x) ML_list$bartfun(data=train.set,
testdata=test.set,
xnam,
xnam.factor,
xnam.cont,
param=x)
)
pred.test.bart=rbind(pred.test.bart, pred.bart )
id.set=rbind(id.set,as.matrix(test.set$id))
print(k)
}
pred.test.gam=pred.test.gam[order(id.set),]
pred.test.knn=pred.test.knn[order(id.set),]
pred.test.svm=pred.test.svm[order(id.set),]
pred.test.nn=pred.test.nn[order(id.set),]
pred.test.rf=pred.test.rf[order(id.set),]
pred.test.bart=pred.test.bart[order(id.set),]
pred.test.lasso=pred.test.lasso[order(id.set),]
data=data[order(data$id),]
loss.function.gam=apply(pred.test.gam,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.knn=apply(pred.test.knn,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.svm=apply(pred.test.svm,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.nn=apply(pred.test.nn,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.rf=apply(pred.test.rf,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.bart=apply(pred.test.bart,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
loss.function.lasso=apply(pred.test.lasso,2,function(x) ipcw_auc(T=data$ttilde,delta=data$delta,marker=crossprod(t(x),1),cause=1,wts=data$wts,tao))
tuneparams=list(
gam_param=gam_param[which.max(loss.function.gam)],
knn_param=knn_param[which.max(loss.function.knn)],
svm_param=svm_param[which.max(loss.function.svm),],
nn_param=nn_param[which.max(loss.function.nn)],
randomforest_param=randomforest_param[which.max(loss.function.rf),],
bart_param=bart_param[which.max(loss.function.bart),],
lasso_param=lasso_param[which.max(loss.function.lasso)]
)
names(tuneparams$lasso_param)=c("lambda")
names(tuneparams$knn_param)=c("k")
names(tuneparams$gam_param)=c("df")
names(tuneparams$nn_param)=c("neurons")
names(tuneparams$randomforest_param)=c("num_trees","mtry")
names(tuneparams$svm_param)=c("cost","gamma","kernel")
names(tuneparams$bart_param)=c("num_tree","k","q")
return(tuneparams)
}
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