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paper2023

This is the repository for Randy's Biometric paper in 2023 We have verified that re-running the supplement’s code on the supplement’s data according to the instructions in the included README file. We have revised, cleaned up and documented the code files in this supplement to make sure that they follow commonly accepted standards for scientific computing. The code and data supplement contains all code and data needed to reproduce all figures, tables and other results in the article and its supplementary material.

  • The main codes of functions and objects are stored under paper2023/R folder

    • Please load this the 00_fucntions.R first before running the .Rmd files

    • The working dataset is stored in train_test.rda file

  • The analytic and simulated results are stored under paper2023/results folder

    • result_alphas_2023-08-23
    • result_anchors_2023-08-23
    • result_ss500_simulation
    • result_ss900_simulation

  • All the figures and latex tables are stored under paper2023/figure folder

    • all the figures and tables are automatically saved as Rmd_file_nameresults_nameSystem.date
    • certain figures and tables are adjusted with the names or contents in the paper
    • there are several versions for each figure, including merged files
    • some of the intermediate result datasets are saved in this folder too

  • The .Rmd files are listed below for all the tables and figure (there are several files reused for multiple figures are commented within)

    • "0- table- demographic.Rmd"
    • "02_table2_plmlmm_code.R"
    • "02_table2_plmlmm.Rmd"
    • "03_table3_multiple-alpha_code.R"
    • "03_table3_multiple-alpha.Rmd"
    • "04_figure- flowchart.Rmd"
    • "05_figure2_individual_plot.Rmd"
    • "06_figure3_small_simulation.Rmd"
    • "07_figure4_large_simulation.Rmd"
    • "08_supp_figure_chi_square.Rmd"
    • "09_supp_figure_merged.Rmd"
    • "10_supp_figure_lmm_aic.Rmd"
    • "11_myapp"

  • An under-development shiny app is saved in folder

    • _myapp