Last updated: 2018-05-26

workflowr checks: (Click a bullet for more information)

✔ R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
✔ Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
✔ Seed: set.seed(20180501)

The command set.seed(20180501) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
✔ Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
✔ Repository version: 6fdb0c7
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
```
Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    log/

Untracked files:
    Untracked:  analysis/binom.Rmd
    Untracked:  analysis/glm.Rmd
    Untracked:  analysis/glmcovariate.Rmd
    Untracked:  analysis/overdis.Rmd
    Untracked:  analysis/smashtutorial.Rmd
    Untracked:  analysis/test.Rmd
    Untracked:  data/treas_bill.csv
    Untracked:  docs/figure/poiwavelog.Rmd/
    Untracked:  docs/figure/smashtutorial.Rmd/
    Untracked:  docs/figure/test.Rmd/

Unstaged changes:
    Modified:   analysis/ashpmean.Rmd
    Modified:   analysis/nugget.Rmd
```
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	6fdb0c7	Dongyue	2018-05-26	log scale

Compare smash and smashgen on estimating \(\mu\) and \(\log\mu\). \(T=256\), 100 runs.

Step Function

Mean function Range:(1,50)

mu=c(rep(1,64), rep(20, 64), rep(50, 64), rep(1, 64))
result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Mean function Range:(50,100)

mu=c(rep(50,64), rep(70, 64), rep(100, 64), rep(50, 64))
result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

HeaviSine

Range: (1,31)

mu=DJ.EX(256,signal = 9)$heavi
mu=mu-min(mu)+1
result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Range: (50,100)

mu=DJ.EX(256,signal = 15)$heavi
mu=mu-min(mu)+50
result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Doppler

Rnage: (1,32)

mu=DJ.EX(256,signal = 9)$doppler
mu=mu-min(mu)+1
result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Rnage: (50,100)

mu=DJ.EX(256,signal = 15)$doppler
mu=mu-min(mu)+50
result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Parabola

Range: (1,31)

r=function(x,c){return((x-c)^2*(x>c)*(x<=1))}
f=function(x){return(0.8 − 30*r(x,0.1) + 60*r(x, 0.2) − 30*r(x, 0.3) +
500*r(x, 0.35) − 1000*r(x, 0.37) + 1000*r(x, 0.41) − 500*r(x, 0.43) +
7.5*r(x, 0.5) − 15*r(x, 0.7) + 7.5*r(x, 0.9))}
mu=f(1:256/256)
mu=mu*50-9

result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Range: (50,100)

mu=f(1:256/256)
mu=mu*65+47

result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Wave

Range: (1,30)

f=function(x){return(0.5 + 0.2*cos(4*pi*x) + 0.1*cos(24*pi*x))}
mu=f(1:256/256)
mu=mu*50-10

result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Range: (50,96)

mu=f(1:256/256)
mu=mu*80+32

result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Bumps

Range: (1,33)

m=seq(0,1,length.out = 256)
h = c(4, 5, 3, 4, 5, 4.2, 2.1, 4.3, 3.1, 5.1, 4.2)
w = c(0.005, 0.005, 0.006, 0.01, 0.01, 0.03, 0.01, 0.01, 0.005,0.008,0.005)
t=c(.1,.13,.15,.23,.25,.4,.44,.65,.76,.78,.81)
f = c()
for(i in 1:length(m)){
  f[i]=sum(h*(1+((m[i]-t)/w)^4)^(-1))
}
mu=f*6+1

result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Range: (50,104)

mu=f*10+50

result=simu_study_scale(mu,nsimu=100)
ggplot(df2gg(result$err.logmu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('log mu')

ggplot(df2gg(result$err.mu),aes(x=method,y=MSE))+geom_boxplot(aes(fill=method))+labs(x='')+ggtitle('mu')

ggplot(result$est.mu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=mu,colour='mu'))+ggtitle('mu')+labs(x='',y='')+geom_point(aes(y=y),color='gray70',shape=1)+scale_colour_manual(values=c('black',"red", "green",'blue'))

ggplot(result$est.logmu,aes(1:256))+geom_line(aes(y=smash,colour='smash'))+geom_line(aes(y=smashgen.haar,colour='smashgen.haar'))+geom_line(aes(y=smashgen.sym,colour='smashgen.symm8'))+geom_line(aes(y=log(mu),colour='log mu'))+ggtitle('log mu')+labs(x='',y='')+scale_colour_manual(values=c('black',"red", "green",'blue'))

Session information

sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

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] ggplot2_2.2.1    smashrgen_0.1.0  wavethresh_4.6.8 MASS_7.3-47     
[5] caTools_1.17.1   ashr_2.2-7       smashr_1.1-5    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16        plyr_1.8.4          compiler_3.4.0     
 [4] git2r_0.21.0        workflowr_1.0.1     R.methodsS3_1.7.1  
 [7] R.utils_2.6.0       bitops_1.0-6        iterators_1.0.8    
[10] tools_3.4.0         digest_0.6.13       tibble_1.3.3       
[13] evaluate_0.10       gtable_0.2.0        lattice_0.20-35    
[16] rlang_0.1.2         Matrix_1.2-9        foreach_1.4.3      
[19] yaml_2.1.19         parallel_3.4.0      stringr_1.3.0      
[22] knitr_1.20          REBayes_1.3         rprojroot_1.3-2    
[25] grid_3.4.0          data.table_1.10.4-3 rmarkdown_1.8      
[28] magrittr_1.5        whisker_0.3-2       backports_1.0.5    
[31] scales_0.4.1        codetools_0.2-15    htmltools_0.3.5    
[34] assertthat_0.2.0    colorspace_1.3-2    labeling_0.3       
[37] stringi_1.1.6       Rmosek_8.0.69       lazyeval_0.2.1     
[40] munsell_0.4.3       doParallel_1.0.11   pscl_1.4.9         
[43] truncnorm_1.0-7     SQUAREM_2017.10-1   R.oo_1.21.0

This reproducible R Markdown analysis was created with workflowr 1.0.1

Poisson wave, wavelet basis and scale of mu

Dongyue Xie

May 25, 2018

Step Function

Mean function Range:(1,50)

Mean function Range:(50,100)

HeaviSine

Range: (1,31)

Range: (50,100)

Doppler

Rnage: (1,32)

Rnage: (50,100)

Parabola

Range: (1,31)

Range: (50,100)

Wave

Range: (1,30)

Range: (50,96)

Bumps

Range: (1,33)

Range: (50,104)

Session information