Last updated: 2018-05-05

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Examine the performance of smash-gen(known \(\sigma\)) under different simulation settings.

Algorithm

Let \(X_t\) be a Poisson observation, \(t=1,2,\dots,T\).

  1. Input \(\sigma\) and initialize \(m_t^{(0)}=\frac{\Sigma_{t=1}^T X_t}{T}\), \(Y_t^{(0)}=\log(m_t^{(0)})+\frac{X_t-m_t^{(0)}}{m_t^{(0)}}\) and \(s_t^{2(0)}=\frac{1}{m_t^{(0)}}\) for \(t=1,2,\dots,T\).
  2. For \(i=1,2,...\), iterate until convergence:
  1. Fit \(Y_t=\mu_t+N(0,\sigma^2)+N(0,s_t^2)\) using smash.gaus and obtain \(\hat\mu_t\).
  2. Update \(m_t^{(i)}=\exp(\hat\mu_t)\), \(Y_t^{(i)}=\log(m_t^{(i)})+\frac{X_t-m_t^{(i)}}{m_t^{(i)}}\), and \(s_t^{2(i)}=\frac{1}{m_t^{(i)}}\)

Convergence criteria: \(||\mu_t^{(i)}-\mu_t^{(i-1)}||_2\leq \epsilon\).

#' smash generaliation function

#' This function is for $Y_t=\mu_t+N(0,s_t^2)+N(0,\sigma^2)$ with known $s_t^2$ and $\sigma^2$.

#' @param x: a vector of observations
#' @param sigma: standard deviations, scalar.
#' @param family: choice of wavelet basis to be used, as in wavethresh.
#' @param niter: number of iterations for IRLS
#' @param tol: criterion to stop the iterations

smash.gen=function(x,sigma,family='DaubExPhase',niter=100,tol=1e-2){
  mu=c()
  s=c()
  mu=rbind(mu,rep(mean(x),length(x)))
  s=rbind(s,rep(1/mu[1],length(x)))
  y=log(mean(x))+(x-mean(x))/mean(x)
  for(i in 1:niter){
    mu.hat=smash.gaus(y,sigma=sigma+s[i,])
    mu=rbind(mu,mu.hat)
    #update m and s_t
    s=rbind(s,1/mu.hat)
    #update y
    mt=exp(mu.hat)
    y=log(mt)+(x-mt)/mt
    #y=log(mu.hat)+(x-mu.hat)/mu.hat
    if(norm(mu.hat-mu[i,],'2')<tol){
      break
    }
  }
  return(list(mu.hat=mu.hat,mu=mu,s=s))
}

Data generation by Poisson glm:

\(\lambda_t=\exp(m_t+\epsilon_t)\), where \(\epsilon_t\sim N(0,\sigma^2)\).

\(X_t\sim Poi(\lambda_t)\).

#' Simulation study comparing smash and smashgen

simu_study=function(m,sigma,seed=1234,
                    niter=100,family='DaubExPhase',tol=1e-2,
                    reflect=FALSE){
  set.seed(seed)
  lamda=exp(m+rnorm(length(m),0,sigma))
  x=rpois(length(m),lamda)
  #fit data
  smash.out=smash.poiss(x,reflect=FALSE)
  smash.gen.out=smash.gen(x,sigma=sigma,niter=niter,family = family,tol=tol)
  return(list(smash.out=smash.out,smash.gen.out=exp(smash.gen.out$mu.hat),smash.gen.est=smash.gen.out,x=x))
}

Simulation 1: Constant trend Poisson nugget

\(\sigma=0.01\)

library(smashr)
m=rep(3,256)
simu.out=simu_study(m,0.01)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", # places a legend at the appropriate place
       c("truth","smash-gen"), # puts text in the legend
       lty=c(1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=0.1\)

simu.out=simu_study(m,0.1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=0.5\)

simu.out=simu_study(m,0.5)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m),col='gray80')
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m),col='gray80')
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=1\)

simu.out=simu_study(m,1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m),col='black')
legend("topleft", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m),col='black')
legend("topleft", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

Simulation 2: Step trend

\(\sigma=0.01\)

m=c(rep(3,128), rep(5, 128), rep(6, 128), rep(4, 128))
simu.out=simu_study(m,0.01)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=0.1\)

simu.out=simu_study(m,0.1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=0.5\)

simu.out=simu_study(m,0.5)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=1\)

simu.out=simu_study(m,1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topleft", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topleft", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

Simulation 3: Oscillating Poisson nugget

Low Oscillating Poisson nugget

\(\sigma=0.01\)

m=c()
for(k in 1:8){
    m=c(m, rep(1,16), rep(5, 16))
}
simu.out=simu_study(m,0.01)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

\(\sigma=0.1\)

simu.out=simu_study(m,0.1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

\(\sigma=0.5\)

simu.out=simu_study(m,0.5)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

\(\sigma=1\)

simu.out=simu_study(m,1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

Fast Oscillating Poisson nugget

\(\sigma=0.01\)

m=c()
for(k in 1:32){
    m=c(m, c(1,5))
}
simu.out=simu_study(m,0.01)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

\(\sigma=0.1\)

simu.out=simu_study(m,0.1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

\(\sigma=0.5\)

simu.out=simu_study(m,0.5)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

\(\sigma=1\)

simu.out=simu_study(m,1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash-gen')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))

plot(simu.out$x,col = "gray80" ,ylab = '',main='smash')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))

Simulation 4: Polynomial curve Poisson nugget

\(\sigma=0.01\)

m = seq(-1,1,length.out = 256)
m = m^3-2*m+1
simu.out=simu_study(m,0.01)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=0.1\)

m = seq(-1,1,length.out = 256)
m = m^3-2*m+1
simu.out=simu_study(m,0.1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=0.5\)

m = seq(-1,1,length.out = 256)
m = m^3-2*m+1
simu.out=simu_study(m,0.5)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

\(\sigma=1\)

m = seq(-1,1,length.out = 256)
m = m^3-2*m+1
simu.out=simu_study(m,1)

#par(mfrow = c(1,2))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.gen.out, col = "red", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth","smash-gen"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black","red", "blue"))

plot(simu.out$x,col = "gray80" ,ylab = '')
lines(simu.out$smash.out, col = "blue", lwd = 2)
lines(exp(m))
legend("topright", 
       c("truth", "smash"), 
       lty=c(1,1), 
       lwd=c(1,1),
       cex = 1,
       col=c("black", "blue"))

Summary

  1. Generally, smash-gen gives more smooth fit under large nugget effect. But sometimes it seems that the iterative algorithm does not converge.
  2. When the nugget effect is small, smash-gen may not perform well especially under oscillating Poisson nugget and polynomial curve.

Session information

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] smashr_1.1-1    workflowr_1.0.1 rmarkdown_1.8  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16        compiler_3.4.0      git2r_0.21.0       
 [4] R.methodsS3_1.7.1   R.utils_2.6.0       bitops_1.0-6       
 [7] iterators_1.0.8     tools_3.4.0         digest_0.6.13      
[10] evaluate_0.10       lattice_0.20-35     Matrix_1.2-9       
[13] foreach_1.4.3       rstudioapi_0.7      yaml_2.1.19        
[16] parallel_3.4.0      stringr_1.3.0       knitr_1.20         
[19] REBayes_1.3         caTools_1.17.1      rprojroot_1.3-2    
[22] grid_3.4.0          glue_1.2.0          data.table_1.10.4-3
[25] R6_2.2.2            ashr_2.2-7          magrittr_1.5       
[28] whisker_0.3-2       backports_1.0.5     codetools_0.2-15   
[31] htmltools_0.3.5     MASS_7.3-47         assertthat_0.2.0   
[34] wavethresh_4.6.8    stringi_1.1.6       Rmosek_8.0.69      
[37] doParallel_1.0.11   pscl_1.4.9          truncnorm_1.0-7    
[40] SQUAREM_2017.10-1   crayon_1.3.4        R.oo_1.21.0

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