## ----eval=FALSE---------------------------------------------------------------
#  library(ggplot2)
#  library(kko)
#  library(knockoff)
#  set.seed(12345)
#  
#  ### generate regression coefficent
#  p=20 # number of predictors
#  sig_mag=10 # signal strength
#  s=5  # sparsity, number of nonzero component functions
#  reg_coef=c(rep(1,s),rep(0,p-s))  # regression coefficient
#  reg_coef=reg_coef*(2*(rnorm(p)>0)-1)*sig_mag
#  
#  ### generate response and design
#  model="poly"
#  n= 600 # sample size
#  X=matrix(rnorm(n*p),n,p)   # generate design
#  X_k = create.second_order(X) # generate knockoff
#  y=generate_data(X,reg_coef,model) # response

## ----eval=FALSE---------------------------------------------------------------
#  rkernel="laplacian" # kernel choice
#  rk_scale=1  # scaling paramtere of kernel
#  rfn_range=c(2,3,4)  # number of random features
#  cv_folds=15  # folds of cross-validation in group lasso
#  n_stb=200 # number of subsampling for importance scores
#  n_stb_tune=100 # number of subsampling for tuning random feature number
#  frac_stb=1/2 # fraction of subsample
#  nCores_para=2 # number of cores for parallelization
#  
#  ### KKO selection
#  kko_fit=kko(X,y,X_k,rfn_range,n_stb_tune,n_stb,cv_folds,frac_stb,nCores_para,rkernel,rk_scale)

## ----echo=FALSE---------------------------------------------------------------
library(kko)
library(knockoff)
library(ggplot2)
load("demo.Rdata")
p=length(kko_fit$importance_score)

## ----fig.width=6,fig.height=4-------------------------------------------------
reg_coef  # true regression coefficient 

W=kko_fit$importance_score # knockoff importance scores generated by KKO 
W 

mydata=data.frame(W=W,var_group=ifelse(reg_coef!=0,"Active","NUll"))
myplot = ggplot(mydata, aes(W, fill = var_group)) +  
  geom_histogram(color = "gray2",binwidth=1/p) + theme_bw()+
  xlab("Importance scores")+ylab("Number of variables")+
  xlim(-1,1)

print(myplot)

## -----------------------------------------------------------------------------
fdr=0.2 #FDR control level 
thres = knockoff.threshold(W, fdr=fdr) # thresholding on scores by knockoff filter
selected = which(W >= thres) 
selected  # indices of selected variables