pois_mode

Last updated: 2019-10-04

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Rmd	f8b387d	Matthew Stephens	2019-10-04	workflowr::wflow_publish(“pois_mode_est.Rmd”)
html	54f8701	Matthew Stephens	2019-10-04	Build site.
Rmd	7c2b5a6	Matthew Stephens	2019-10-04	workflowr::wflow_publish(“pois_mode_est.Rmd”)

library(ashr)

Introduction

Here I am going to look at an example from Abhishek Sarkar where the Poisson mode estimation in ash did not work well.

Here I read in the data and run ash, plotting the fitted cdf and grid. After fixing the ashr code a bit the grid has improved….

d = readRDS("../data/pois-mode-est.Rds")
hist(d$x)

Version	Author	Date
54f8701	Matthew Stephens	2019-10-04

summary(d$s)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1e+05   1e+05   1e+05   1e+05   1e+05   1e+05

res.ash = ash_pois(d$x,d$s,link="identity")
res.ash$fitted_g

$pi
 [1] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
 [7] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[13] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[19] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[25] 0.00000000 0.02470817 0.95242467 0.00000000 0.02286716 0.00000000
[31] 0.00000000 0.00000000 0.00000000

$a
 [1] 4.201626e-05 4.201333e-05 4.201211e-05 4.201039e-05 4.200796e-05
 [6] 4.200452e-05 4.199966e-05 4.199279e-05 4.198307e-05 4.196932e-05
[11] 4.194987e-05 4.192237e-05 4.188348e-05 4.182848e-05 4.175070e-05
[16] 4.164070e-05 4.148514e-05 4.126514e-05 4.095402e-05 4.051402e-05
[21] 3.989177e-05 3.901178e-05 3.776728e-05 3.600730e-05 3.351830e-05
[26] 2.999833e-05 2.502035e-05 1.798041e-05 8.024432e-06 0.000000e+00
[31] 0.000000e+00 0.000000e+00 0.000000e+00

$b
 [1] 4.201626e-05 4.201920e-05 4.202041e-05 4.202213e-05 4.202456e-05
 [6] 4.202800e-05 4.203286e-05 4.203973e-05 4.204946e-05 4.206321e-05
[11] 4.208265e-05 4.211015e-05 4.214904e-05 4.220404e-05 4.228182e-05
[16] 4.239182e-05 4.254738e-05 4.276738e-05 4.307851e-05 4.351850e-05
[21] 4.414075e-05 4.502074e-05 4.626524e-05 4.802522e-05 5.051422e-05
[26] 5.403419e-05 5.901218e-05 6.605211e-05 7.600809e-05 9.008797e-05
[31] 1.099999e-04 1.381597e-04 1.779836e-04

attr(,"class")
[1] "unimix"
attr(,"row.names")
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
[24] 24 25 26 27 28 29 30 31 32 33

plot(res.ash,xmin=0,xmax=1e-4)
abline(v=res.ash$fitted_g$a,col=1)
abline(v=res.ash$fitted_g$b,col=2)

Version	Author	Date
54f8701	Matthew Stephens	2019-10-04

res.ash$loglik

[1] -2086.446

try ebpm:

res.ebpm = ebpm::ebpm_point_gamma(d$x,d$s)

Warning in log(par[1]): NaNs produced

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
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Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(pi * c + d): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in dnbinom(x, a, b/(b + s), log = F): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Warning in log(par[1]): NaNs produced

Warning in nlm(pg_nlm_fn, transform_param(init_par), x, s): NA/Inf replaced
by maximum positive value

Error in nlm(pg_nlm_fn, transform_param(init_par), x, s): non-finite value supplied by 'nlm'

sessionInfo()

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] ashr_2.2-38

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        knitr_1.23        whisker_0.3-2    
 [4] magrittr_1.5      workflowr_1.4.0   MASS_7.3-51.4    
 [7] pscl_1.5.2        doParallel_1.0.14 ebpm_0.0.0.9000  
[10] SQUAREM_2017.10-1 lattice_0.20-38   foreach_1.4.7    
[13] stringr_1.4.0     tools_3.6.0       parallel_3.6.0   
[16] grid_3.6.0        xfun_0.8          git2r_0.26.1     
[19] htmltools_0.3.6   iterators_1.0.12  yaml_2.2.0       
[22] rprojroot_1.3-2   digest_0.6.20     mixsqp_0.1-97    
[25] Matrix_1.2-17     fs_1.3.1          codetools_0.2-16 
[28] glue_1.3.1        evaluate_0.14     rmarkdown_1.14   
[31] stringi_1.4.3     compiler_3.6.0    backports_1.1.4  
[34] truncnorm_1.0-8

pois_mode_est

Matthew Stephens

2019-09-30

Introduction