R Under development (unstable) (2026-02-27 r89498 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(AgeTopicModels) > > test_check("AgeTopicModels") remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0.1 GB Disease code that have less than 5 entries will be removed. CVB inference number: 1 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Interation: 2 Interation: 3 Interation: 4 Interation: 5 Current Lower bound -13487.0771356173 at iteration: 5 Interation: 6 Interation: 7 Interation: 8 Interation: 9 Interation: 10 Current Lower bound -13478.616858373 at iteration: 10 Interation: 11 Interation: 12 Interation: 13 Interation: 14 Interation: 15 Current Lower bound -13465.1349637596 at iteration: 15 Interation: 16 Interation: 17 Interation: 18 Interation: 19 Interation: 20 Current Lower bound -13456.2805125173 at iteration: 20 Interation: 21 Interation: 22 Interation: 23 Interation: 24 Interation: 25 Current Lower bound -13449.6494457043 at iteration: 25 Interation: 26 Interation: 27 Interation: 28 Interation: 29 Interation: 30 Current Lower bound -13445.9937195142 at iteration: 30 Interation: 31 Interation: 32 Interation: 33 Interation: 34 Interation: 35 Current Lower bound -13444.0113783726 at iteration: 35 Interation: 36 Interation: 37 Interation: 38 Interation: 39 Interation: 40 Current Lower bound -13445.4489335913 at iteration: 40 Optimization converged at step 40 Number of diseases selected: 7 Disease code that have less than 5 entries will be removed. 0 cases still have out of range age, they will be removed. If age is missing, we set these records to age_diag as 50 (which is the median of diagnosis age for most data sets). Disease code that have less than 5 entries will be removed. CVB inference number: 1 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Interation: 2 Interation: 3 Interation: 4 Interation: 5 Current Lower bound -13475.283724255 at iteration: 5 Interation: 6 Interation: 7 Interation: 8 Interation: 9 Interation: 10 Current Lower bound -13465.5954902026 at iteration: 10 Interation: 11 Interation: 12 Interation: 13 Interation: 14 Interation: 15 Current Lower bound -13451.0340595842 at iteration: 15 Interation: 16 Interation: 17 Interation: 18 Interation: 19 Interation: 20 Current Lower bound -13441.4748473172 at iteration: 20 Interation: 21 Interation: 22 Interation: 23 Interation: 24 Interation: 25 Current Lower bound -13434.806144468 at iteration: 25 Interation: 26 Interation: 27 Interation: 28 Interation: 29 Interation: 30 Current Lower bound -13430.8030102758 at iteration: 30 Interation: 31 Interation: 32 Interation: 33 Interation: 34 Interation: 35 Current Lower bound -13431.1500860593 at iteration: 35 Optimization converged at step 35 Disease code that have less than 5 entries will be removed. 0 cases still have out of range age, they will be removed. If age is missing, we set these records to age_diag as 50 (which is the median of diagnosis age for most data sets). Disease code that have less than 5 entries will be removed. CVB inference number: 1 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Interation: 2 Interation: 3 Interation: 4 Interation: 5 Current Lower bound -13540.745894224 at iteration: 5 Interation: 6 Interation: 7 Interation: 8 Interation: 9 Interation: 10 Current Lower bound -13535.2178526821 at iteration: 10 Interation: 11 Interation: 12 Interation: 13 Interation: 14 Interation: 15 Current Lower bound -13525.0230596491 at iteration: 15 Interation: 16 Interation: 17 Interation: 18 Interation: 19 Interation: 20 Current Lower bound -13516.9068566313 at iteration: 20 Interation: 21 Interation: 22 Interation: 23 Interation: 24 Interation: 25 Current Lower bound -13512.4992431724 at iteration: 25 Interation: 26 Interation: 27 Interation: 28 Interation: 29 Interation: 30 Current Lower bound -13509.5416883483 at iteration: 30 Interation: 31 Interation: 32 Interation: 33 Interation: 34 Interation: 35 Current Lower bound -13508.5568572437 at iteration: 35 Interation: 36 Interation: 37 Interation: 38 Interation: 39 Interation: 40 Current Lower bound -13509.8759195643 at iteration: 40 Optimization converged at step 40 The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 100 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -16318.4629306698 at iteration: 1 Interation: 2 Current Lower bound -16310.7903486478 at iteration: 2 Interation: 3 Current Lower bound -16310.7600745035 at iteration: 3 Interation: 4 Current Lower bound -16310.7596368631 at iteration: 4 Optimization converged at step 4 The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. LFA RAM occupation: 745336384GBSI remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0.1 GB remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -9864.7276881296 at iteration: 1 Interation: 2 Current Lower bound -9864.7276881296 at iteration: 2 Optimization converged at step 2 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -20151.6506850227 at iteration: 1 Interation: 2 Current Lower bound -20128.4764949683 at iteration: 2 Interation: 3 Current Lower bound -20128.4661132994 at iteration: 3 Optimization converged at step 3 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -30630.000420423 at iteration: 1 Interation: 2 Current Lower bound -30566.3144373346 at iteration: 2 Interation: 3 Current Lower bound -30565.7551901598 at iteration: 3 Interation: 4 Current Lower bound -30565.6945486182 at iteration: 4 Interation: 5 Current Lower bound -30565.687203868 at iteration: 5 Optimization converged at step 5 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -28322.1031237011 at iteration: 1 Interation: 2 Current Lower bound -28233.5421998583 at iteration: 2 Interation: 3 Current Lower bound -28232.2007215704 at iteration: 3 Interation: 4 Current Lower bound -28232.0515208274 at iteration: 4 Interation: 5 Current Lower bound -28232.0285530562 at iteration: 5 Optimization converged at step 5 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -9864.7276881296 at iteration: 1 Interation: 2 Current Lower bound -9864.7276881296 at iteration: 2 Optimization converged at step 2 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -20151.4181778552 at iteration: 1 Interation: 2 Current Lower bound -20128.4783874051 at iteration: 2 Interation: 3 Current Lower bound -20128.4665986619 at iteration: 3 Interation: 4 Current Lower bound -20128.4671702924 at iteration: 4 Optimization converged at step 4 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -30630.2323923344 at iteration: 1 Interation: 2 Current Lower bound -30566.3340525611 at iteration: 2 Interation: 3 Current Lower bound -30565.7549102086 at iteration: 3 Interation: 4 Current Lower bound -30565.6946738848 at iteration: 4 Interation: 5 Current Lower bound -30565.6871592029 at iteration: 5 Interation: 6 Current Lower bound -30565.6842563717 at iteration: 6 Optimization converged at step 6 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -28324.7160712776 at iteration: 1 Interation: 2 Current Lower bound -28233.4768310566 at iteration: 2 Interation: 3 Current Lower bound -28232.1934093736 at iteration: 3 Interation: 4 Current Lower bound -28232.0504837129 at iteration: 4 Interation: 5 Current Lower bound -28232.028202613 at iteration: 5 Interation: 6 Current Lower bound -28232.0213512272 at iteration: 6 Interation: 7 Current Lower bound -28232.0194442413 at iteration: 7 Optimization converged at step 7 remove duplicated diagnoses; keep the earliest age-at-diagnosis when mulitple diagnoses are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -10133.4932144057 at iteration: 1 Interation: 2 Current Lower bound -10133.4932144057 at iteration: 2 Optimization converged at step 2 remove duplicated diagnoses; keep the earliest age-at-diagnosis when mulitple diagnoses are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -20751.3174990189 at iteration: 1 Interation: 2 Current Lower bound -20727.3680590765 at iteration: 2 Interation: 3 Current Lower bound -20727.3200927066 at iteration: 3 Interation: 4 Current Lower bound -20727.3162233627 at iteration: 4 Optimization converged at step 4 remove duplicated diagnoses; keep the earliest age-at-diagnosis when mulitple diagnoses are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -31670.2099740131 at iteration: 1 Interation: 2 Current Lower bound -31604.4459381168 at iteration: 2 Interation: 3 Current Lower bound -31603.8719918598 at iteration: 3 Interation: 4 Current Lower bound -31603.8039528376 at iteration: 4 Interation: 5 Current Lower bound -31603.7956093156 at iteration: 5 Optimization converged at step 5 remove duplicated diagnoses; keep the earliest age-at-diagnosis when mulitple diagnoses are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -29363.3637504602 at iteration: 1 Interation: 2 Current Lower bound -29272.5879084505 at iteration: 2 Interation: 3 Current Lower bound -29271.4302377905 at iteration: 3 Interation: 4 Current Lower bound -29271.3074942653 at iteration: 4 Interation: 5 Current Lower bound -29271.2903540363 at iteration: 5 Optimization converged at step 5 remove duplicated diagnoses; keep the earliest age-at-diagnosis when mulitple diagnoses are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -10133.4932144057 at iteration: 1 Interation: 2 Current Lower bound -10133.4932144057 at iteration: 2 Optimization converged at step 2 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -20749.8871559674 at iteration: 1 Interation: 2 Current Lower bound -20727.3597285453 at iteration: 2 Interation: 3 Current Lower bound -20727.3221921249 at iteration: 3 Interation: 4 Current Lower bound -20727.3162456883 at iteration: 4 Interation: 5 Current Lower bound -20727.3169813521 at iteration: 5 Optimization converged at step 5 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -31662.8270730815 at iteration: 1 Interation: 2 Current Lower bound -31604.3965696992 at iteration: 2 Interation: 3 Current Lower bound -31603.8704391303 at iteration: 3 Interation: 4 Current Lower bound -31603.8038781156 at iteration: 4 Interation: 5 Current Lower bound -31603.7956141803 at iteration: 5 Interation: 6 Current Lower bound -31603.7924733758 at iteration: 6 Optimization converged at step 6 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB The age profiles contain 10 disease topics of 349 diseases up to age 81. 0 records are not in the ds_list, if this number is high it means many of the records is not covered by the comorbidity profiles. 0 records have age outside the disease range, they will be thrown away, considering using the age_imputation function. remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Current Lower bound -29353.7169124565 at iteration: 1 Interation: 2 Current Lower bound -29272.4162171462 at iteration: 2 Interation: 3 Current Lower bound -29271.4154096942 at iteration: 3 Interation: 4 Current Lower bound -29271.3049840975 at iteration: 4 Interation: 5 Current Lower bound -29271.2895974974 at iteration: 5 Interation: 6 Current Lower bound -29271.2846649911 at iteration: 6 Interation: 7 Current Lower bound -29271.2834148343 at iteration: 7 Optimization converged at step 7 simulated alpha: 0.932253900914568simulated alpha: 0.942741103711874simulated alpha: 0.884801254743395 Disease code that have less than 5 entries will be removed. CVB inference number: 1 remove duplicated diagnosis; keep the earliest age-at-diagnosis when mulitple diagnosis are presented. Rough RAM needed: 0 GB Interation: 1 Interation: 2 Interation: 3 Interation: 4 Interation: 5 Current Lower bound -13553.6597845903 at iteration: 5 Interation: 6 Interation: 7 Interation: 8 Interation: 9 Interation: 10 Current Lower bound -13257.9705966935 at iteration: 10 Interation: 11 Interation: 12 Interation: 13 Interation: 14 Interation: 15 Current Lower bound -12966.9849371933 at iteration: 15 Interation: 16 Interation: 17 Interation: 18 Interation: 19 Interation: 20 Current Lower bound -12853.2921923117 at iteration: 20 Interation: 21 Interation: 22 Interation: 23 Interation: 24 Interation: 25 Current Lower bound -12828.4814604522 at iteration: 25 Interation: 26 Interation: 27 Interation: 28 Interation: 29 Interation: 30 Current Lower bound -12821.447449765 at iteration: 30 Interation: 31 Interation: 32 Interation: 33 Interation: 34 Interation: 35 Current Lower bound -12818.5568976578 at iteration: 35 Interation: 36 Interation: 37 Interation: 38 Interation: 39 Interation: 40 Current Lower bound -12817.2602700648 at iteration: 40 Interation: 41 Interation: 42 Interation: 43 Interation: 44 Interation: 45 Current Lower bound -12816.6080539805 at iteration: 45 Interation: 46 Interation: 47 Interation: 48 Interation: 49 Interation: 50 Current Lower bound -12816.0842569838 at iteration: 50 Interation: 51 Interation: 52 Interation: 53 Interation: 54 Interation: 55 Current Lower bound -12815.9165935753 at iteration: 55 Interation: 56 Interation: 57 Interation: 58 Interation: 59 Interation: 60 Current Lower bound -12815.8551166018 at iteration: 60 Interation: 61 Interation: 62 Interation: 63 Interation: 64 Interation: 65 Current Lower bound -12815.7849010412 at iteration: 65 Interation: 66 Interation: 67 Interation: 68 Interation: 69 Interation: 70 Current Lower bound -12815.6285942864 at iteration: 70 Interation: 71 Interation: 72 Interation: 73 Interation: 74 Interation: 75 Current Lower bound -12815.5560449493 at iteration: 75 Interation: 76 Interation: 77 Interation: 78 Interation: 79 Interation: 80 Current Lower bound -12815.5388230507 at iteration: 80 Interation: 81 Interation: 82 Interation: 83 Interation: 84 Interation: 85 Current Lower bound -12815.4908567539 at iteration: 85 Interation: 86 Interation: 87 Interation: 88 Interation: 89 Interation: 90 Current Lower bound -12815.4919426133 at iteration: 90 Optimization converged at step 90 [ FAIL 0 | WARN 7 | SKIP 1 | PASS 21 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-lfa.R:18:1' [ FAIL 0 | WARN 7 | SKIP 1 | PASS 21 ] > > proc.time() user system elapsed 247.45 10.51 258.28