── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.5.0     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Loading required package: magrittr

Attaching package: ‘magrittr’

The following object is masked from ‘package:purrr’:

    set_names

The following object is masked from ‘package:tidyr’:

    extract


Attaching package: ‘cowplot’

The following object is masked from ‘package:lubridate’:

    stamp


TIMING STUDY...


Timing different prior families.
  n ranges from 100 to 10000.

  n: 100 
  n: 316.2278 
  n: 1000 
  n: 3162.278 
  n: 10000 
There were 21 warnings (use warnings() to see them)
  Done. Time elapsed: 5.3 minutes.
`summarise()` has grouped output by 'n'. You can override using the `.groups` argument.

SIMULATION STUDY...

  Sim function: normal 
    trial 1 
    trial 2 
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  Sim function: point_t 
    trial 1 
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  Sim function: asymm_tophat 
    trial 1 
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    trial 8 
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    trial 10 
Warning messages:
1: In stats::nlm(f = loglik, p = aStart, gradtol = 1e-10, ...) :
  NA/Inf replaced by maximum positive value
2: In stats::nlm(f = loglik, p = aStart, gradtol = 1e-10, ...) :
  NA/Inf replaced by maximum positive value
3: In stats::nlm(f = loglik, p = aStart, gradtol = 1e-10, ...) :
  NA/Inf replaced by maximum positive value
4: In stats::nlm(f = loglik, p = aStart, gradtol = 1e-10, ...) :
  NA/Inf replaced by maximum positive value
5: In stats::nlm(f = loglik, p = aStart, gradtol = 1e-10, ...) :
  NA/Inf replaced by maximum positive value
Warning messages:
1: Since gt v0.9.0, the `colors` argument has been deprecated.
• Please use the `fn` argument instead.
This warning is displayed once every 8 hours. 
2: Some values were outside the color scale and will be treated as NA 
3: Some values were outside the color scale and will be treated as NA 
4: Some values were outside the color scale and will be treated as NA 
5: Some values were outside the color scale and will be treated as NA 
6: Some values were outside the color scale and will be treated as NA 
7: Some values were outside the color scale and will be treated as NA 
8: Some values were outside the color scale and will be treated as NA 
9: Some values were outside the color scale and will be treated as NA 
10: Some values were outside the color scale and will be treated as NA 

EXAMPLES...

[1] 688
  FanGraphsID           Name Team  PA     x     s
1       19952     Khalil Lee  NYM   2 1.036 0.733
2       16953 Chadwick Tromp  ATL   4 0.852 0.258
3       19608     Otto Lopez  TOR  10 0.599 0.162
4       24770   James Outman  LAD  16 0.584 0.151
5        8090 Matt Carpenter  NYY 154 0.472 0.054
6       15640    Aaron Judge  NYY 696 0.458 0.024
                mean     sd
Khalil Lee     0.303 0.0287
Chadwick Tromp 0.308 0.0286
Otto Lopez     0.310 0.0283
James Outman   0.311 0.0282
Matt Carpenter 0.339 0.0254
Aaron Judge    0.394 0.0184
                PA     x mean_n   sd_n mean_u   sd_u
Khalil Lee       2 1.036  0.303 0.0287  0.302 0.0277
Chadwick Tromp   4 0.852  0.308 0.0286  0.307 0.0306
Otto Lopez      10 0.599  0.310 0.0283  0.310 0.0315
James Outman    16 0.584  0.311 0.0282  0.311 0.0318
Matt Carpenter 154 0.472  0.339 0.0254  0.355 0.0430
Aaron Judge    696 0.458  0.394 0.0184  0.439 0.0155
Warning message:
Removed 729 rows containing missing values or values outside the scale range (`geom_line()`). 
Warning message:
Removed 729 rows containing missing values or values outside the scale range (`geom_line()`). 
'log Lik.' 992.6578 (df=40)
'log Lik.' 994.193 (df=94)
               CI.lower CI.upper
Khalil Lee        0.265    0.309
Chadwick Tromp    0.276    0.342
Otto Lopez        0.276    0.342
James Outman      0.276    0.342
Matt Carpenter    0.309    0.419
Aaron Judge       0.430    0.430
               CI.lower CI.upper
Khalil Lee        0.000    1.600
Chadwick Tromp    0.563    1.127
Otto Lopez        0.442    0.796
James Outman      0.412    0.742
Matt Carpenter    0.413    0.531
Aaron Judge       0.406    0.459
[1] 1000
[1] 44
                                      Adipose_Subcutaneous
ENSG00000099977.9_22_24266954_A_C_b37             8.099352
ENSG00000233868.1_2_222475922_A_G_b37             1.079264
                                      Adipose_Visceral_Omentum
ENSG00000099977.9_22_24266954_A_C_b37                6.4129683
ENSG00000233868.1_2_222475922_A_G_b37               -0.7760486
Adding factor 1 to flash object...
Adding factor 2 to flash object...
Adding factor 3 to flash object...
Adding factor 4 to flash object...
Adding factor 5 to flash object...
Adding factor 6 to flash object...
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Adding factor 12 to flash object...
Adding factor 13 to flash object...
Adding factor 14 to flash object...
Adding factor 15 to flash object...
Factor doesn't significantly increase objective and won't be added.
Wrapping up...
Done.
Backfitting 14 factors (tolerance: 6.56e-04)...
  Difference between iterations is within 1.0e+02...
  Difference between iterations is within 1.0e+01...
  Difference between iterations is within 1.0e+00...
  Difference between iterations is within 1.0e-01...
  Difference between iterations is within 1.0e-02...
Wrapping up...
Done.
Nullchecking 14 factors...
Done.
elapsed 
  0.786 
Adding factor 1 to flash object...
Adding factor 2 to flash object...
Adding factor 3 to flash object...
Adding factor 4 to flash object...
Adding factor 5 to flash object...
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Adding factor 10 to flash object...
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Adding factor 12 to flash object...
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Adding factor 14 to flash object...
Adding factor 15 to flash object...
Adding factor 16 to flash object...
Adding factor 17 to flash object...
Adding factor 18 to flash object...
Adding factor 19 to flash object...
Adding factor 20 to flash object...
Adding factor 21 to flash object...
Adding factor 22 to flash object...
Factor doesn't significantly increase objective and won't be added.
Wrapping up...
Done.
Backfitting 21 factors (tolerance: 6.56e-04)...
  Difference between iterations is within 1.0e+02...
  Difference between iterations is within 1.0e+01...
  Difference between iterations is within 1.0e+00...
  Difference between iterations is within 1.0e-01...
  Difference between iterations is within 1.0e-02...
  Difference between iterations is within 1.0e-03...
Wrapping up...
Done.
Nullchecking 21 factors...
Done.
elapsed 
   4.38 


R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.3

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] ggrepel_0.9.5   Rtsne_0.17      cowplot_1.1.3   gt_0.10.1      
 [5] flashier_1.0.7  magrittr_2.0.3  ebnm_1.1-25     lubridate_1.9.3
 [9] forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2    
[13] readr_2.1.5     tidyr_1.3.0     tibble_3.2.1    ggplot2_3.5.0  
[17] tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] gtable_0.3.4          softImpute_1.4-1      lattice_0.21-9       
 [4] tzdb_0.4.0            vctrs_0.6.5           tools_4.3.2          
 [7] generics_0.1.3        parallel_4.3.2        fansi_1.0.6          
[10] pkgconfig_2.0.3       Matrix_1.6-1.1        SQUAREM_2021.1       
[13] RColorBrewer_1.1-3    lifecycle_1.0.4       truncnorm_1.0-9      
[16] compiler_4.3.2        farver_2.1.1          textshaping_0.3.7    
[19] microbenchmark_1.4.10 munsell_0.5.0         sass_0.4.8           
[22] htmltools_0.5.7       pillar_1.9.0          trust_0.1-8          
[25] tidyselect_1.2.1      digest_0.6.34         stringi_1.8.3        
[28] ashr_2.2-63           labeling_0.4.3        splines_4.3.2        
[31] fastmap_1.1.1         grid_4.3.2            colorspace_2.1-0     
[34] cli_3.6.2             invgamma_1.1          utf8_1.2.4           
[37] withr_3.0.0           scales_1.3.0          horseshoe_0.2.0      
[40] timechange_0.2.0      deconvolveR_1.2-1     ragg_1.2.7           
[43] hms_1.1.3             irlba_2.3.5.1         rlang_1.1.3          
[46] Rcpp_1.0.12           mixsqp_0.3-54         glue_1.7.0           
[49] xml2_1.3.6            rstudioapi_0.15.0     R6_2.5.1             
[52] systemfonts_1.0.5     fs_1.6.3             
