#########################################################################################
########### Script for the simulations described in Boulesteix et al (2008) #############
#####################  Anne-Laure Boulesteix, April 5, 2008 #############################
#########################################################################################

library(MAclinical)

#############################
### muZ=0 muX=0 redundant ###
#############################
datalist<-simuldata_list(niter=100,muZ=0,muX=0)
muZ0muX0plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ0muX0plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ0muX0plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ0muX0plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ0muX0rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ0muX0logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ0muX0svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)



###############################
### muZ=0 muX=0.5 redundant ###
###############################
datalist<-simuldata_list(niter=100,muZ=0,muX=0.5)
muZ0muX0.5plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ0muX0.5plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ0muX0.5plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ0muX0.5plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ0muX0.5rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ0muX0.5logistic_z_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ0muX0.5svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


#############################
### muZ=0 muX=1 redundant ###
#############################
datalist<-simuldata_list(niter=100,muZ=0,muX=1)
muZ0muX1plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ0muX1plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ0muX1plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ0muX1plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ0muX1rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ0muX1logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ0muX1svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


#############################
### muZ=1 muX=0 redundant ###
#############################
datalist<-simuldata_list(niter=100,muZ=1,muX=0)
muZ1muX0plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ1muX0plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ1muX0plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ1muX0plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ1muX0rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ1muX0logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ1muX0svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


###############################
### muZ=1 muX=0.5 redundant ###
###############################
datalist<-simuldata_list(niter=100,muZ=1,muX=0.5)
muZ1muX0.5plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ1muX0.5plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ1muX0.5plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ1muX0.5plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ1muX0.5rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ1muX0.5logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ1muX0.5svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


#############################
### muZ=1 muX=1 redundant ###
#############################
datalist<-simuldata_list(niter=100,muZ=1,muX=1)
muZ1muX1plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ1muX1plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ1muX1plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ1muX1plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ1muX1rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ1muX1logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ1muX1svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)




#############################
### muZ=3 muX=0 redundant ###
#############################
datalist<-simuldata_list(niter=100,muZ=3,muX=0)
muZ3muX0plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ3muX0plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ3muX0plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ3muX0plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ3muX0rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ3muX0logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ3muX0svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


###############################
### muZ=3 muX=0.5 redundant ###
###############################
datalist<-simuldata_list(niter=100,muZ=3,muX=0.5)
muZ3muX0.5plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ3muX0.5plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ3muX0.5plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ3muX0.5plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ3muX0.5rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ3muX0.5logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ3muX0.5svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)



#############################
### muZ=3 muX=1 redundant ###
#############################
datalist<-simuldata_list(niter=100,muZ=3,muX=1)
muZ3muX1plsrf_xz_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ3muX1plsrf_xz_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ3muX1plsrf_x_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ3muX1plsrf_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ3muX1rf_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ3muX1logistic_z_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ3muX1svm_x_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)




#######################


#################################
### muZ=0 muX=0 non-redundant ###
#################################
datalist<-simuldatacluster_list(niter=100,muZ=0,muX=0)
muZ0muX0plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ0muX0plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ0muX0plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ0muX0plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ0muX0rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ0muX0logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ0muX0svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)



###################################
### muZ=0 muX=0.5 non-redundant ###
###################################
datalist<-simuldatacluster_list(niter=100,muZ=0,muX=0.5)
muZ0muX0.5plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ0muX0.5plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ0muX0.5plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ0muX0.5plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ0muX0.5rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ0muX0.5logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ0muX0.5svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


#################################
### muZ=0 muX=1 non-redundant ###
#################################
datalist<-simuldatacluster_list(niter=100,muZ=0,muX=1)
muZ0muX1plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ0muX1plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ0muX1plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ0muX1plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ0muX1rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ0muX1logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ0muX1svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


#################################
### muZ=1 muX=0 non-redundant ###
#################################
datalist<-simuldatacluster_list(niter=100,muZ=1,muX=0)
muZ1muX0plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ1muX0plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ1muX0plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ1muX0plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ1muX0rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ1muX0logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ1muX0svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


###################################
### muZ=1 muX=0.5 non-redundant ###
###################################
datalist<-simuldatacluster_list(niter=100,muZ=1,muX=0.5)
muZ1muX0.5plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ1muX0.5plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ1muX0.5plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ1muX0.5plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ1muX0.5rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ1muX0.5logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ1muX0.5svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


#################################
### muZ=1 muX=1 non-redundant ###
#################################
datalist<-simuldatacluster_list(niter=100,muZ=1,muX=1)
muZ1muX1plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ1muX1plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ1muX1plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ1muX1plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ1muX1rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ1muX1logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ1muX1svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)




#################################
### muZ=3 muX=0 non-redundant ###
#################################
datalist<-simuldatacluster_list(niter=100,muZ=3,muX=0)
muZ3muX0plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ3muX0plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ3muX0plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ3muX0plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ3muX0rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ3muX0logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ3muX0svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)


###################################
### muZ=3 muX=0.5 non-redundant ###
###################################
datalist<-simuldatacluster_list(niter=100,muZ=3,muX=0.5)
muZ3muX0.5plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ3muX0.5plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ3muX0.5plsrf_x_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ3muX0.5plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ3muX0.5rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ3muX0.5logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ3muX0.5svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)



#################################
### muZ=3 muX=1 non-redundant ###
#################################
datalist<-simuldatacluster_list(niter=100,muZ=3,muX=1)
muZ3muX1plsrf_xz_pv_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz_pv,ncomp=0:3)
muZ3muX1plsrf_xz_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_xz,ncomp=0:3)
muZ3muX1plsrf_x_cl_pv_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x_pv,ncomp=0:3)
muZ3muX1plsrf_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=plsrf_x,ncomp=0:3)
muZ3muX1rf_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=rf_z,ncomp=0:3)
muZ3muX1logistic_z_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=logistic_z)
muZ3muX1svm_x_cl_opt_cforest<-testclass_simul(datalist=datalist,nlearn=50,classifier=svm_x)








##################################
##### Information extraction #####
##################################

# Information from Tables 1 and 2 are extracted as follows:
c(mean(muZ0muX0plsrf_xz_pv_opt_cforest$error/450),sd(muZ0muX0plsrf_xz_pv_opt_cforest$error/450))

# Information from Table 3 are extracted as follows:
sum(muZ0muX0plsrf_xz_pv_opt_cforest$bestncomp>0)/100


list2matrix<-function(my.list)
{
niter<-length(my.list$bestncomp)
kmax<-length(my.list$OOB[[1]])
OOBmat<-matrix(0,niter,kmax)
for (i in 1:niter)
 {
 OOBmat[i,]<-as.numeric(my.list$OOB[i][[1]])
 }
return(OOBmat)
}

apply(list2matrix(muZ0muX0plsrf_xz_pv_opt_cforest),FUN=mean,MARGIN=2)[1:2]