library(hyperion)
#>
#>
#> ── pharos configuration ────────────────────────────────────────────────────────
#> ✔ pharos.toml found: /data/user-homes/tariq/projects/prism-pkgdocs-build/installed-pkgs/2026-03-02/hyperion_0.3.2/vignettes/pharos.toml
#> ── hyperion options ────────────────────────────────────────────────────────────
#> ✔ hyperion.significant_number_display : 4
#> ── hyperion nonmem object options ──────────────────────────────────────────────
#> ✔ hyperion.nonmem_model.show_included_columns : FALSE
#> ✔ hyperion.nonmem_summary.rse_threshold : 50
#> ✔ hyperion.nonmem_summary.shrinkage_threshold : 30
test_data_dir <- system.file("extdata", package = "hyperion")
get_eta_shrinkage(file.path(test_data_dir, "shk", "3068.shk"))
#> method subpop eta_number etabar etabar_se etabar_pval shrinkage_sd
#> 1 FOCE 1 1 0.0000000 0.0000000 -1 0.00000e+00
#> 2 FOCE 1 2 0.0237710 0.0913935 -1 4.31620e+00
#> 3 FOCE 1 3 -0.0796227 0.0581043 -1 2.54950e+01
#> 4 FOCE 1 4 0.0000000 0.0000000 -1 0.00000e+00
#> 5 FOCE 2 1 0.0000000 0.0000000 -1 0.00000e+00
#> 6 FOCE 2 2 0.0160635 0.0612727 -1 2.01072e+00
#> 7 FOCE 2 3 0.0336938 0.0544894 -1 1.00000e-10
#> 8 FOCE 2 4 0.0000000 0.0000000 -1 0.00000e+00
#> shrinkage_vr rel_info ebv_shrinkage_sd ebv_shrinkage_vr n_individuals
#> 1 0.00000e+00 0.0000 0.0000000 0.000000 15
#> 2 8.44611e+00 99.8320 0.0840177 0.167965 15
#> 3 4.44901e+01 98.9961 0.5031960 1.003860 15
#> 4 0.00000e+00 0.0000 0.0000000 0.000000 15
#> 5 0.00000e+00 0.0000 0.0000000 0.000000 35
#> 6 3.98102e+00 99.8591 0.0703129 0.140576 35
#> 7 1.00000e-10 99.5060 0.2471630 0.493716 35
#> 8 0.00000e+00 0.0000 0.0000000 0.000000 35
get_eps_shrinkage(file.path(test_data_dir, "shk", "3068.shk"))
#> method subpop eps_number shrinkage_sd shrinkage_vr n_individuals
#> 1 FOCE 1 1 0.690562 1.37636 15
#> 2 FOCE 1 2 100.000000 100.00000 15
#> 3 FOCE 2 1 2.182010 4.31641 35
#> 4 FOCE 2 2 100.000000 100.00000 35
get_eta_shrinkage(file.path(test_data_dir, "shk", "bql.shk"))
#> method subpop eta_number etabar etabar_se etabar_pval shrinkage_sd
#> 1 FOCE 1 1 0.000801602 0.02268020 0.971806 0.666197
#> 2 FOCE 1 2 -0.000218944 0.01334130 0.986906 2.317320
#> 3 FOCE 1 3 -0.000308648 0.00618609 0.960207 18.695000
#> shrinkage_vr rel_info ebv_shrinkage_sd ebv_shrinkage_vr n_individuals
#> 1 1.32796 98.9891 0.492543 0.98266 193
#> 2 4.58094 94.3077 2.148600 4.25104 193
#> 3 33.89500 65.0838 18.702700 33.90750 193
get_eps_shrinkage(file.path(test_data_dir, "shk", "bql.shk"))
#> method subpop eps_number shrinkage_sd shrinkage_vr n_individuals
#> 1 FOCE 1 1 9.70268 18.4639 193
get_eta_shrinkage(file.path(test_data_dir, "shk", "itsimp.shk"))
#> method subpop eta_number etabar etabar_se etabar_pval shrinkage_sd
#> 1 ITS 1 1 -4.25284e-08 0.00471323 0.999993 6.91515
#> 2 ITS 1 2 -5.31037e-08 0.00298829 0.999986 32.91140
#> 3 ITS 1 3 -9.87707e-08 0.00294211 0.999973 41.05200
#> 4 ITS 1 4 -8.86959e-08 0.00369138 0.999981 25.07310
#> 5 IMP 1 1 -1.73309e-04 0.00472073 0.970714 6.96378
#> 6 IMP 1 2 1.85832e-04 0.00297941 0.950266 33.25240
#> 7 IMP 1 3 -1.82834e-04 0.00288863 0.949532 41.55920
#> 8 IMP 1 4 -2.16587e-04 0.00370010 0.953322 24.87670
#> shrinkage_vr rel_info ebv_shrinkage_sd ebv_shrinkage_vr n_individuals
#> 1 13.3521 NA 6.91507 13.3520 400
#> 2 54.9912 NA 32.91120 54.9910 400
#> 3 65.2513 NA 41.05040 65.2494 400
#> 4 43.8596 NA 25.07240 43.8586 400
#> 5 13.4426 NA 6.95439 13.4251 400
#> 6 55.4475 NA 33.01970 55.1364 400
#> 7 65.8467 NA 41.41680 65.6801 400
#> 8 43.5649 NA 25.12010 43.9300 400
get_eps_shrinkage(file.path(test_data_dir, "shk", "itsimp.shk"))
#> method subpop eps_number shrinkage_sd shrinkage_vr n_individuals
#> 1 ITS 1 1 26.1873 45.5168 400
#> 2 IMP 1 1 26.3813 45.8028 400