Last updated: 2024-06-12

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Knit directory: ~/dynamicHRpaper/

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Ignored files:
    Ignored:    data/amit_df.rds
    Ignored:    data/amit_df_with_pc_correction.rds
    Ignored:    data/baseline_withPCS.rds
    Ignored:    data/fh_full.rds
    Ignored:    data/fh_prs.rds
    Ignored:    data/fhs_prs_with_pc_corrrection.rds
    Ignored:    data/followupdates.rds
    Ignored:    data/genotype_data_nodup.eigenvec
    Ignored:    output/amit_df_with_pc_correction.rds
    Ignored:    output/fhs_prs_with_pc_corrrection
    Ignored:    output/fhs_prs_with_pc_corrrection.rds
    Ignored:    output/h1hs_withPC.rds
    Ignored:    output/hall_withPC.rds
    Ignored:    output/hallpce.rds
    Ignored:    output/hazards_fh_EQ_withPC_corrections.rds
    Ignored:    output/hazards_fh_EQ_withPC_corrections_sex0.rds
    Ignored:    output/hazards_fh_EQ_withPC_corrections_sex1.rds
    Ignored:    output/hazards_rate_UKB_amit_EQ_withPCcorrection.rds
    Ignored:    output/hazards_rate_lowerbound_amit_EQ_withPCcorrection.rds
    Ignored:    output/hazards_rate_lowerbound_fh_EQ_withPC_corrections.rds
    Ignored:    output/hazards_rate_lowerbound_fh_EQ_withPC_corrections_sex0.rds
    Ignored:    output/hazards_rate_lowerbound_fh_EQ_withPC_corrections_sex1.rds
    Ignored:    output/hazards_rate_upperbound_amit_EQ_withPCcorrection.rds
    Ignored:    output/hazards_rate_upperbound_fh_EQ_withPC_corrections.rds
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    Ignored:    output/hrindex_fhs_eq_with_pc.csv
    Ignored:    output/hrindex_ukb_eq.csv
    Ignored:    output/r2_withPC.rds
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    Ignored:    output/r2index_fhs_eq_with_pc.csv
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    Ignored:    output/r2pce.rds
    Ignored:    output/zph_all.rds
    Ignored:    output/zph_amit_EQ.rds

Untracked files:
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    Untracked:  analysis/.DS_Store
    Untracked:  analysis/Fig1.Rmd
    Untracked:  analysis/Fig1_pcesd.Rmd
    Untracked:  analysis/Fig1b.Rmd
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Unstaged changes:
    Modified:   .DS_Store
    Modified:   .gitignore
    Modified:   analysis/about.Rmd
    Modified:   docs/about.html

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.

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Plot median by age for all 500K with SCORE normalized by ALl

without PC

Density plots

Scaling using whole poulation

NOw we do it without the PC scaling

Finally, we can do qqplots showing scaling overall:

And wihtout PCS:


R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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] ggsci_3.1.0       ggridges_0.5.6    tidyr_1.3.1       ggplot2_3.5.1    
[5] dplyr_1.1.4       data.table_1.15.4

loaded via a namespace (and not attached):
 [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    stringi_1.8.4    
 [5] digest_0.6.35     magrittr_2.0.3    evaluate_0.23     grid_4.4.0       
 [9] fastmap_1.2.0     rprojroot_2.0.4   workflowr_1.7.1   plyr_1.8.9       
[13] jsonlite_1.8.8    promises_1.3.0    purrr_1.0.2       fansi_1.0.6      
[17] scales_1.3.0      jquerylib_0.1.4   cli_3.6.2         rlang_1.1.4      
[21] munsell_0.5.1     withr_3.0.0       cachem_1.1.0      yaml_2.3.8       
[25] tools_4.4.0       reshape2_1.4.4    colorspace_2.1-0  httpuv_1.6.15    
[29] vctrs_0.6.5       R6_2.5.1          lifecycle_1.0.4   git2r_0.33.0     
[33] stringr_1.5.1     fs_1.6.4          pkgconfig_2.0.3   pillar_1.9.0     
[37] bslib_0.7.0       later_1.3.2       gtable_0.3.5      glue_1.7.0       
[41] Rcpp_1.0.12       xfun_0.44         tibble_3.2.1      tidyselect_1.2.1 
[45] highr_0.10        rstudioapi_0.16.0 knitr_1.46        farver_2.1.2     
[49] htmltools_0.5.8.1 rmarkdown_2.26    labeling_0.4.3    compiler_4.4.0