R version 4.6.0 alpha (2026-04-02 r89777 ucrt)
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(HealthMarkers)
> 
> test_check("HealthMarkers")
adipo_is(): column map: G0 -> 'G0', I0 -> 'I0', TG -> 'TG', HDL_c -> 'HDL_c', FFA -> 'FFA', waist -> 'waist', bmi -> 'bmi'
adipo_is(): results: Revised_QUICKI 1/1, VAI_Men_inv 1/1, VAI_Women_inv 1/1, TG_HDL_C_inv 1/1, TyG_inv 1/1, LAP_Men_inv 1/1, LAP_Women_inv 1/1, McAuley_index 1/1, Adipo_inv 1/1, Belfiore_inv_FFA 1/1
adipo_is(): preparing inputs
adipo_is(): results: Revised_QUICKI 1/1, VAI_Men_inv 1/1, VAI_Women_inv 1/1, TG_HDL_C_inv 1/1, TyG_inv 1/1, LAP_Men_inv 1/1, LAP_Women_inv 1/1, McAuley_index 1/1, Adipo_inv 1/1, Belfiore_inv_FFA 1/1
adipo_is(): preparing inputs
adipo_is(): column map: G0 -> 'G0', I0 -> 'I0', TG -> 'TG', HDL_c -> 'HDL_c', FFA -> 'FFA', waist -> 'waist', bmi -> 'bmi'
adiposity_sds(): preparing inputs (1 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 1/1, waist_SDS 1/1
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds(): preparing inputs (3 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 3/3, waist_SDS 3/3
adiposity_sds(): preparing inputs (3 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds(): preparing inputs (3 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/3, waist_SDS 3/3
adiposity_sds(): preparing inputs (3 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds(): preparing inputs (3 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 1/2, waist_SDS 1/2
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds(): preparing inputs (2 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds(): results: BMI_SDS 1/1, waist_SDS 1/1
adiposity_sds(): preparing inputs (1 rows, 2 vars)
adiposity_sds(): results: BMI_SDS 1/1, waist_SDS 1/1
adiposity_sds(): preparing inputs (1 rows, 2 vars)
adiposity_sds(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): preparing inputs (2 vars, 3 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): results: BMI_SDS 3/3, waist_SDS 3/3
adiposity_sds_strat(): preparing inputs (1 vars, 2 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI_col'
adiposity_sds_strat(): results: BMI_SDS 2/2
adiposity_sds_strat(): preparing inputs (2 vars, 3 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): results: BMI_SDS 2/3, waist_SDS 3/3
adiposity_sds_strat(): preparing inputs (2 vars, 3 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds_strat(): preparing inputs (2 vars, 3 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): skipping 1 ref vars absent in data: waist
adiposity_sds_strat(): preparing inputs (1 vars, 2 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI'
adiposity_sds_strat(): results: BMI_SDS 2/2
adiposity_sds_strat(): preparing inputs (2 vars, 2 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): results: BMI_SDS 2/2, waist_SDS 2/2
adiposity_sds_strat(): preparing inputs (1 vars, 2 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI'
adiposity_sds_strat(): results: x_BMI_SDS 2/2
adiposity_sds_strat(): preparing inputs (2 vars, 3 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): results: BMI_SDS 3/3, waist_SDS 3/3
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
adiposity_sds_strat(): results: BMI_SDS 1/1, waist_SDS 1/1
adiposity_sds_strat(): preparing inputs (2 vars, 1 rows)
adiposity_sds_strat(): results: BMI_SDS 1/1, waist_SDS 1/1
adiposity_sds_strat(): preparing inputs (2 vars, 1 rows)
adiposity_sds_strat(): column map: BMI -> 'BMI', waist -> 'waist'
allostatic_load(): column map: A -> 'A', B -> 'B'
allostatic_load(): results: AllostaticLoad 2/2
allostatic_load(): preparing inputs
allostatic_load(): results: AllostaticLoad 2/2
allostatic_load(): preparing inputs
allostatic_load(): column map: A -> 'A', B -> 'B'
alm_bmi_index(): column map: alm -> 'ALM_kg', bmi -> 'BMI', sex -> 'Sex'
alm_bmi_index(): results: alm_bmi_ratio 1/1, low_muscle_mass 1/1
alm_bmi_index(): preparing inputs
alm_bmi_index(): results: alm_bmi_ratio 1/1, low_muscle_mass 1/1
alm_bmi_index(): preparing inputs
alm_bmi_index(): column map: alm -> 'ALM_kg', bmi -> 'BMI', sex -> 'Sex'
atherogenic_indices(): preparing inputs
atherogenic_indices(): column map: TG -> 'TG', HDL_c -> 'HDL_c'
atherogenic_indices(): column map: TG -> 'TG', HDL_c -> 'HDL_c', TC -> 'TC', LDL_c -> 'LDL_c'
atherogenic_indices(): results: AIP 1/1, CRI_I 1/1, CRI_II 1/1
atherogenic_indices(): preparing inputs
atherogenic_indices(): results: AIP 1/1, CRI_I 1/1, CRI_II 1/1
atherogenic_indices(): preparing inputs
atherogenic_indices(): column map: TG -> 'TG', HDL_c -> 'HDL_c', TC -> 'TC', LDL_c -> 'LDL_c'
bode_index(): column map: fev1_pct -> 'FEV1pct', sixmwd -> 'Walk_m', mmrc -> 'mMRC', bmi -> 'BMI'
bode_index(): results: bode_index 1/1, fev1_pct 1/1, fev1_score 1/1, walk_score 1/1, mmrc_score 1/1, bmi_score 1/1
bode_index(): preparing inputs
bode_index(): results: bode_index 1/1, fev1_pct 1/1, fev1_score 1/1, walk_score 1/1, mmrc_score 1/1, bmi_score 1/1
bode_index(): preparing inputs
bode_index(): column map: fev1_pct -> 'FEV1pct', sixmwd -> 'Walk_m', mmrc -> 'mMRC', bmi -> 'BMI'
bone_markers(): completed
bone_markers(): results: OSTA 2/2, ALMI 2/2, FMI 2/2, BMD_Tscore 2/2, TBS 2/2, HSA 2/2, PINP 2/2, CTX 2/2, BSAP 2/2, Osteocalcin 2/2
bone_markers(): completed
bone_markers(): results: OSTA 2/2, ALMI 2/2, FMI 2/2, BMD_Tscore 2/2, TBS 2/2, HSA 2/2, PINP 2/2, CTX 2/2, BSAP 2/2, Osteocalcin 2/2
bone_markers(): column map: age -> 'age', weight -> 'weight', height -> 'height', ALM -> 'ALM', FM -> 'FM', BMD -> 'BMD', BMD_ref_mean -> 'BMD_ref_mean', BMD_ref_sd -> 'BMD_ref_sd'
bone_markers(): completed
calc_sds(): column map: bmi -> 'bmi', sbp -> 'sbp'
Computing SDS for 2 variable(s)...
calc_sds: completed
calc_sds(): results: bmi_sds 6/6, sbp_sds 6/6
calc_sds: starting on 6 row(s), 2 variable(s)
Computing SDS for 2 variable(s)...
calc_sds: completed
calc_sds(): results: bmi_sds 6/6, sbp_sds 6/6
calc_sds: starting on 6 row(s), 2 variable(s)
calc_sds(): column map: bmi -> 'bmi', sbp -> 'sbp'
Computing SDS for 2 variable(s)...
calc_sds: completed
charlson_index(): column map: mi -> 'mi', chf -> 'chf', pvd -> 'pvd', stroke -> 'stroke', dementia -> 'dementia', copd -> 'copd', rheum -> 'rheum', ulcer -> 'ulcer', mild_liver -> 'mild_liver', diabetes -> 'diabetes', diab_comp -> 'diab_comp', hemiplegia -> 'hemiplegia', renal -> 'renal', cancer -> 'cancer', leukemia -> 'leukemia', lymphoma -> 'lymphoma', sev_liver -> 'sev_liver', metastatic_cancer -> 'metastatic_cancer', hiv -> 'hiv'
charlson_index(): results: charlson_index 1/1
charlson_index(): preparing inputs
charlson_index(): results: charlson_index 1/1
charlson_index(): preparing inputs
charlson_index(): column map: mi -> 'mi', chf -> 'chf', pvd -> 'pvd', stroke -> 'stroke', dementia -> 'dementia', copd -> 'copd', rheum -> 'rheum', ulcer -> 'ulcer', mild_liver -> 'mild_liver', diabetes -> 'diabetes', diab_comp -> 'diab_comp', hemiplegia -> 'hemiplegia', renal -> 'renal', cancer -> 'cancer', leukemia -> 'leukemia', lymphoma -> 'lymphoma', sev_liver -> 'sev_liver', metastatic_cancer -> 'metastatic_cancer', hiv -> 'hiv'
ckd_stage(): completed
ckd_stage(): results: CKD_stage 2/2, Albuminuria_stage 2/2, KDIGO_risk 2/2
ckd_stage(): completed
ckd_stage(): results: CKD_stage 2/2, Albuminuria_stage 2/2, KDIGO_risk 2/2
ckd_stage(): column map: eGFR -> 'eGFR', UACR -> 'UACR'
ckd_stage(): completed
corrected_calcium(): column map: calcium -> 'Ca', albumin -> 'Alb'
corrected_calcium(): completed 1 rows.
corrected_calcium(): results: corrected_calcium 1/1
corrected_calcium(): preparing inputs
corrected_calcium(): completed 1 rows.
corrected_calcium(): results: corrected_calcium 1/1
corrected_calcium(): preparing inputs
corrected_calcium(): column map: calcium -> 'Ca', albumin -> 'Alb'
corrected_calcium(): completed 1 rows.

This unofficial R package was based on open-sourced free original QRISK3-2017 algorithm

You may find the source code and the official disclaimer of the original open-sourced

QRISK3-2017 algorithm (published by ClinRisk Ltd.) from below path by runing following in R

sourcePath <- system.file("extdata/QRISK3_2017_src.txt", package = "QRISK3")

print(sourcePath)

The risk score calculated from this R package can only be used for research purpose.

You may want to visit official QRISK3 website for more information

https://qrisk.org/

This unofficial R package was based on open-sourced free original QRISK3-2017 algorithm

You may find the source code and the official disclaimer of the original open-sourced

QRISK3-2017 algorithm (published by ClinRisk Ltd.) from below path by runing following in R

sourcePath <- system.file("extdata/QRISK3_2017_src.txt", package = "QRISK3")

print(sourcePath)

The risk score calculated from this R package can only be used for research purpose.

You may want to visit official QRISK3 website for more information

https://qrisk.org/
cvd_marker_aip(): column map: TG -> 'TG', HDL_c -> 'HDL_c'
cvd_marker_aip(): results: AIP 1/1
cvd_marker_aip(): preparing inputs
cvd_marker_aip(): results: AIP 1/1
cvd_marker_aip(): preparing inputs
cvd_marker_aip(): column map: TG -> 'TG', HDL_c -> 'HDL_c'
cvd_marker_ldl_particle_number(): column map: ApoB -> 'ApoB'
cvd_marker_ldl_particle_number(): results: LDL_PN 1/1
cvd_marker_ldl_particle_number(): preparing inputs
cvd_marker_ldl_particle_number(): results: LDL_PN 1/1
cvd_marker_ldl_particle_number(): preparing inputs
cvd_marker_ldl_particle_number(): column map: ApoB -> 'ApoB'

This unofficial R package was based on open-sourced free original QRISK3-2017 algorithm

You may find the source code and the official disclaimer of the original open-sourced

QRISK3-2017 algorithm (published by ClinRisk Ltd.) from below path by runing following in R

sourcePath <- system.file("extdata/QRISK3_2017_src.txt", package = "QRISK3")

print(sourcePath)

The risk score calculated from this R package can only be used for research purpose.

You may want to visit official QRISK3 website for more information

https://qrisk.org/
fasting_is(): column map: G0 -> 'G0', I0 -> 'I0'
fasting_is(): results: Fasting_inv 1/1, Raynaud 1/1, HOMA_IR_inv 1/1, FIRI 1/1, QUICKI 1/1, Belfiore_basal 1/1, Ig_ratio_basal 1/1, Isi_basal 1/1, Bennett 1/1, HOMA_IR_rev_inv 1/1
fasting_is(): preparing inputs
fasting_is(): results: Fasting_inv 1/1, Raynaud 1/1, HOMA_IR_inv 1/1, FIRI 1/1, QUICKI 1/1, Belfiore_basal 1/1, Ig_ratio_basal 1/1, Isi_basal 1/1, Bennett 1/1, HOMA_IR_rev_inv 1/1
fasting_is(): preparing inputs
fasting_is(): column map: G0 -> 'G0', I0 -> 'I0'
[1] "Please use lower # of bins. Current # is 5"
frailty_index(): column map: d1, d2
frailty_index(): results: di range [0.500, 0.500] (2 rows, 2 deficits)
frailty_index(): preparing inputs (2 rows, 2 deficits)
frailty_index(): results: di range [0.500, 0.500] (2 rows, 2 deficits)
frax_score(): column map: age -> 'Age', sex -> 'Sex'
frax_score(): results: frax_major_percent 1/1, frax_hip_percent 1/1, frax_sex_norm 1/1, frax_age_used 1/1, frax_bmd_tscore 0/1
frax_score(): preparing inputs
frax_score(): results: frax_major_percent 1/1, frax_hip_percent 1/1, frax_sex_norm 1/1, frax_age_used 1/1, frax_bmd_tscore 0/1
frax_score(): preparing inputs
frax_score(): column map: age -> 'Age', sex -> 'Sex'
glycemic_markers(): column map: HDL_c -> 'HDL_c', TG -> 'TG', BMI -> 'BMI'
glycemic_markers(): optional markers not computed (columns absent): glucose, HbA1c, C_peptide, G0, I0, leptin, adiponectin
glycemic_markers(): results: SPISE 1/1, METS_IR 0/1, prediabetes 0/1, diabetes 0/1, HOMA_CP 0/1, LAR 0/1, ASI 0/1, TyG_index 0/1
glycemic_markers(): preparing inputs
glycemic_markers(): optional markers not computed (columns absent): glucose, HbA1c, C_peptide, G0, I0, leptin, adiponectin
glycemic_markers(): results: SPISE 1/1, METS_IR 0/1, prediabetes 0/1, diabetes 0/1, HOMA_CP 0/1, LAR 0/1, ASI 0/1, TyG_index 0/1
glycemic_markers(): preparing inputs
glycemic_markers(): column map: HDL_c -> 'HDL_c', TG -> 'TG', BMI -> 'BMI'
glycemic_markers(): optional markers not computed (columns absent): glucose, HbA1c, C_peptide, G0, I0, leptin, adiponectin

This unofficial R package was based on open-sourced free original QRISK3-2017 algorithm

You may find the source code and the official disclaimer of the original open-sourced

QRISK3-2017 algorithm (published by ClinRisk Ltd.) from below path by runing following in R

sourcePath <- system.file("extdata/QRISK3_2017_src.txt", package = "QRISK3")

print(sourcePath)

The risk score calculated from this R package can only be used for research purpose.

You may want to visit official QRISK3 website for more information

https://qrisk.org/
all_health_markers(): preparing inputs
Column mapping summary: TC->TC (user), HDL_c->HDL_c (user), TG->TG (user), LDL_c->LDL_c (user), BMI->BMI (user)
health_markers(): calling lipid
lipid_markers(): preparing inputs
lipid_markers(): column map: TC -> 'TC', HDL_c -> 'HDL_c', TG -> 'TG'
lipid_markers(): results: non_HDL_c 1/1, remnant_c 1/1, ratio_TC_HDL 1/1, ratio_TG_HDL 1/1, ratio_LDL_HDL 1/1, ApoB_ApoA1 0/1
all_health_markers(): summary - computed: lipid
all_health_markers(): preparing inputs
health_markers(): calling lipid
lipid_markers(): preparing inputs
lipid_markers(): column map: TC -> 'TC', HDL_c -> 'HDL_c', TG -> 'TG'
lipid_markers(): results: non_HDL_c 1/1, remnant_c 1/1, ratio_TC_HDL 1/1, ratio_TG_HDL 1/1, ratio_LDL_HDL 1/1, ApoB_ApoA1 0/1
all_health_markers(): summary - computed: lipid
all_health_markers(): preparing inputs
Column mapping summary: TC->TC (user), HDL_c->HDL_c (user), TG->TG (user), LDL_c->LDL_c (user), BMI->BMI (user)
health_markers(): calling lipid
lipid_markers(): preparing inputs
lipid_markers(): column map: TC -> 'TC', HDL_c -> 'HDL_c', TG -> 'TG'
lipid_markers(): results: non_HDL_c 1/1, remnant_c 1/1, ratio_TC_HDL 1/1, ratio_TG_HDL 1/1, ratio_LDL_HDL 1/1, ApoB_ApoA1 0/1
hormone_markers(): column map: total_testosterone -> 'total_testosterone', SHBG -> 'SHBG', LH -> 'LH', FSH -> 'FSH', estradiol -> 'estradiol', progesterone -> 'progesterone', free_T3 -> 'free_T3', free_T4 -> 'free_T4', TSH -> 'TSH', aldosterone -> 'aldosterone', renin -> 'renin', insulin -> 'insulin', glucagon -> 'glucagon', GH -> 'GH', IGF1 -> 'IGF1', prolactin -> 'prolactin', cortisol_0 -> 'cortisol_0', cortisol_30 -> 'cortisol_30'
hormone_markers(): results: FAI 1/1, LH_FSH 1/1, E2_P 1/1, E2_T 1/1, T3_T4 1/1, TSH_fT4 1/1, ARR 1/1, Ins_Glu 1/1, GH_IGF1 1/1, PRL_T 1/1, CAR_slope 1/1
hormone_markers(): preparing inputs
hormone_markers(): results: FAI 1/1, LH_FSH 1/1, E2_P 1/1, E2_T 1/1, T3_T4 1/1, TSH_fT4 1/1, ARR 1/1, Ins_Glu 1/1, GH_IGF1 1/1, PRL_T 1/1, CAR_slope 1/1
hormone_markers(): preparing inputs
hormone_markers(): column map: total_testosterone -> 'total_testosterone', SHBG -> 'SHBG', LH -> 'LH', FSH -> 'FSH', estradiol -> 'estradiol', progesterone -> 'progesterone', free_T3 -> 'free_T3', free_T4 -> 'free_T4', TSH -> 'TSH', aldosterone -> 'aldosterone', renin -> 'renin', insulin -> 'insulin', glucagon -> 'glucagon', GH -> 'GH', IGF1 -> 'IGF1', prolactin -> 'prolactin', cortisol_0 -> 'cortisol_0', cortisol_30 -> 'cortisol_30'
impute_missing(): results: imputed 3 values across 2 columns [x=1, y=2]
impute_missing(): preparing inputs (3 rows, 2 column(s), method='mean')
impute_mice(): results: imputed 2 values across 2 columns.
impute_mice(): preparing inputs (3 rows, 2 columns)
impute_missforest(): results: fallback mean imputation; imputed 2 values across 2 columns.
impute_missforest(): preparing inputs (3 rows, 2 columns)
iAge(): column map: CRP -> 'CRP', IL6 -> 'IL6', TNFa -> 'TNFa'
iAge(): results: iAge 1/1
iAge(): preparing inputs
iAge(): results: iAge 1/1
iAge(): preparing inputs
iAge(): column map: CRP -> 'CRP', IL6 -> 'IL6', TNFa -> 'TNFa'
inflammatory_markers(): column map: neutrophils -> 'neutrophils', lymphocytes -> 'lymphocytes'
inflammatory_markers(): results: NLR 0/0, PLR 0/0, LMR 0/0, dNLR 0/0, SII 0/0, SIRI 0/0, AISI 0/0, CRP_category 0/0
inflammatory_markers(): preparing inputs
inflammatory_markers(): results: NLR 0/0, PLR 0/0, LMR 0/0, dNLR 0/0, SII 0/0, SIRI 0/0, AISI 0/0, CRP_category 0/0
inflammatory_markers(): preparing inputs
inflammatory_markers(): column map: neutrophils -> 'neutrophils', lymphocytes -> 'lymphocytes'
kidney_failure_risk(): column map: age -> 'age', sex -> 'sex', eGFR -> 'eGFR', UACR -> 'UACR'
kidney_failure_risk(): results: KFRE_2yr 1/1, KFRE_5yr 1/1
kidney_failure_risk(): preparing inputs
kidney_failure_risk(): results: KFRE_2yr 1/1, KFRE_5yr 1/1
kidney_failure_risk(): preparing inputs
kidney_failure_risk(): column map: age -> 'age', sex -> 'sex', eGFR -> 'eGFR', UACR -> 'UACR'
kyn_trp_ratio(): column map: kynurenine -> 'Kyn_nM', tryptophan -> 'Trp_uM'
kyn_trp_ratio(): results: kyn_trp_ratio 1/1
kyn_trp_ratio(): preparing inputs
kyn_trp_ratio(): results: kyn_trp_ratio 1/1
kyn_trp_ratio(): preparing inputs
kyn_trp_ratio(): column map: kynurenine -> 'Kyn_nM', tryptophan -> 'Trp_uM'
lipid_markers(): column map: TC -> 'TC', HDL_c -> 'HDL_c', TG -> 'TG'
lipid_markers(): results: non_HDL_c 1/1, remnant_c 1/1, ratio_TC_HDL 1/1, ratio_TG_HDL 1/1, ratio_LDL_HDL 1/1, ApoB_ApoA1 0/1
lipid_markers(): preparing inputs
lipid_markers(): results: non_HDL_c 1/1, remnant_c 1/1, ratio_TC_HDL 1/1, ratio_TG_HDL 1/1, ratio_LDL_HDL 1/1, ApoB_ApoA1 0/1
lipid_markers(): preparing inputs
lipid_markers(): column map: TC -> 'TC', HDL_c -> 'HDL_c', TG -> 'TG'
liver_fat_markers(): column map: ALT -> 'ALT', AST -> 'AST', BMI -> 'BMI'
liver_fat_markers(): results: HSI 1/1, NAFLD_LFS 0/1
liver_fat_markers(): preparing inputs
liver_fat_markers(): results: HSI 1/1, NAFLD_LFS 0/1
liver_fat_markers(): preparing inputs
liver_fat_markers(): column map: ALT -> 'ALT', AST -> 'AST', BMI -> 'BMI'
liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
liver_markers(): results: FLI 1/1, NFS 1/1, APRI 1/1, FIB4 1/1, BARD 1/1, ALBI 1/1, MELD_XI 1/1
liver_markers(): preparing inputs
liver_markers(): results: FLI 1/1, NFS 1/1, APRI 1/1, FIB4 1/1, BARD 1/1, ALBI 1/1, MELD_XI 1/1
liver_markers(): preparing inputs
liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
liver_markers(): preparing inputs
liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
liver_markers(): results: FLI 1/1, NFS 1/1, APRI 1/1, FIB4 1/1, BARD 1/1, ALBI 1/1, MELD_XI 1/1
liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
liver_markers(): results: FLI 1/1, NFS 1/1, APRI 1/1, FIB4 1/1, BARD 1/1, ALBI 1/1, MELD_XI 1/1
liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
liver_markers(): results: FLI 1/1, NFS 1/1, APRI 1/1, FIB4 1/1, BARD 1/1, ALBI 1/1, MELD_XI 1/1
liver_markers(): preparing inputs
liver_markers(): column map: BMI -> 'BMI', waist -> 'waist', TG -> 'TG', GGT -> 'GGT', age -> 'age', AST -> 'AST', ALT -> 'ALT', platelets -> 'platelets', albumin -> 'albumin', diabetes -> 'diabetes', bilirubin -> 'bilirubin', creatinine -> 'creatinine'
marker_summary(): summarizing numeric columns
marker_summary(): results: 1 variables; all-NA=0
metabolic_risk_features(): column map: chol_total -> 'chol_total', chol_ldl -> 'chol_ldl', chol_hdl -> 'chol_hdl', triglycerides -> 'triglycerides', age_year -> 'age_year', z_HOMA -> 'z_HOMA', glucose -> 'glucose', HbA1c -> 'HbA1c', bp_sys_z -> 'bp_sys_z', bp_dia_z -> 'bp_dia_z'
metabolic_risk_features(): results: dyslipidemia 1/1, insulin_resistance 1/1, hyperglycemia 1/1, hypertension 1/1
metabolic_risk_features(): preparing inputs
metabolic_risk_features(): results: dyslipidemia 1/1, insulin_resistance 1/1, hyperglycemia 1/1, hypertension 1/1
metabolic_risk_features(): preparing inputs
metabolic_risk_features(): column map: chol_total -> 'chol_total', chol_ldl -> 'chol_ldl', chol_hdl -> 'chol_hdl', triglycerides -> 'triglycerides', age_year -> 'age_year', z_HOMA -> 'z_HOMA', glucose -> 'glucose', HbA1c -> 'HbA1c', bp_sys_z -> 'bp_sys_z', bp_dia_z -> 'bp_dia_z'
metabolic_risk_features(): preparing inputs
metabolic_risk_features(): column map: chol_total -> 'chol_total', chol_ldl -> 'chol_ldl', chol_hdl -> 'chol_hdl', triglycerides -> 'triglycerides', age_year -> 'age_year', z_HOMA -> 'z_HOMA', glucose -> 'glucose', HbA1c -> 'HbA1c', bp_sys_z -> 'bp_sys_z', bp_dia_z -> 'bp_dia_z'
metabolic_risk_features(): results: dyslipidemia 1/1, insulin_resistance 1/1, hyperglycemia 1/1, hypertension 1/1
metss(): column map: waist -> 'waist', bp_sys -> 'bp_sys', bp_dia -> 'bp_dia', TG -> 'TG', HDL_c -> 'HDL_c', glucose -> 'glucose', sex -> 'sex', race -> 'race'
metss(): results: MetSSS 1/1
metss(): preparing inputs
metss(): results: MetSSS 1/1
metss(): preparing inputs
metss(): column map: waist -> 'waist', bp_sys -> 'bp_sys', bp_dia -> 'bp_dia', TG -> 'TG', HDL_c -> 'HDL_c', glucose -> 'glucose', sex -> 'sex', race -> 'race'
nfl_marker(): column map: nfl -> 'NfL'
nfl_marker(): results: nfl_value 2/2
nfl_marker(): preparing inputs
nfl_marker(): results: nfl_value 2/2
nfl_marker(): preparing inputs
nfl_marker(): column map: nfl -> 'NfL'
nutrient_markers(): column map: ferritin -> 'ferritin', transferrin_sat -> 'transferrin_sat'
nutrient_markers(): results: FerritinTS 1/1, AGR 0/1, Omega3Index 0/1, Mg_Cr_Ratio 0/1, GlycatedAlbuminPct 0/1, UA_Cr_Ratio 0/1, BUN_Cr_Ratio 0/1, Ca_x_Phosphate 0/1, AnionGap 0/1, Tyr_Phe_Ratio 0/1
nutrient_markers(): preparing inputs
nutrient_markers(): results: FerritinTS 1/1, AGR 0/1, Omega3Index 0/1, Mg_Cr_Ratio 0/1, GlycatedAlbuminPct 0/1, UA_Cr_Ratio 0/1, BUN_Cr_Ratio 0/1, Ca_x_Phosphate 0/1, AnionGap 0/1, Tyr_Phe_Ratio 0/1
nutrient_markers(): preparing inputs
nutrient_markers(): column map: ferritin -> 'ferritin', transferrin_sat -> 'transferrin_sat'
nutrient_markers(): preparing inputs
nutrient_markers(): column map: ferritin -> 'ferritin', transferrin_sat -> 'transferrin_sat'
nutrient_markers(): results: FerritinTS 1/1, AGR 0/1, Omega3Index 0/1, Mg_Cr_Ratio 0/1, GlycatedAlbuminPct 0/1, UA_Cr_Ratio 0/1, BUN_Cr_Ratio 0/1, Ca_x_Phosphate 0/1, AnionGap 0/1, Tyr_Phe_Ratio 0/1
obesity_indices(): column map: weight -> 'wt', height -> 'ht', waist -> 'waist', hip -> 'hip'
obesity_indices(): results: weight_kg 2/2, height_m 2/2, BMI 2/2, BMI_cat 2/2, WHR 2/2, waist_to_height_ratio 2/2, waist_to_BMI_ratio 2/2, weight_to_height_ratio 2/2, AVI 2/2, BAI 2/2, ABSI 2/2, BRI 2/2, CI 2/2
obesity_indices(): preparing inputs
obesity_indices(): results: weight_kg 2/2, height_m 2/2, BMI 2/2, BMI_cat 2/2, WHR 2/2, waist_to_height_ratio 2/2, waist_to_BMI_ratio 2/2, weight_to_height_ratio 2/2, AVI 2/2, BAI 2/2, ABSI 2/2, BRI 2/2, CI 2/2
obesity_indices(): preparing inputs
obesity_indices(): column map: weight -> 'wt', height -> 'ht', waist -> 'waist', hip -> 'hip'
ogtt_is(): column map: G0 -> 'G0', I0 -> 'I0', G30 -> 'G30', I30 -> 'I30', G120 -> 'G120', I120 -> 'I120', weight -> 'weight', bmi -> 'bmi', age -> 'age', sex -> 'sex'
ogtt_is(): results: Isi_120 1/1, Cederholm_index 1/1, Gutt_index 1/1, Avignon_Si0 1/1, Avignon_Si120 1/1, Avignon_Sim 1/1, Modified_stumvoll 1/1, Stumvoll_Demographics 1/1, Matsuda_AUC 1/1, Matsuda_ISI 1/1, BigttSi 1/1, Ifc_inv 1/1, HIRI_inv 1/1, Belfiore_isi_gly 1/1
ogtt_is(): preparing inputs
ogtt_is(): results: Isi_120 1/1, Cederholm_index 1/1, Gutt_index 1/1, Avignon_Si0 1/1, Avignon_Si120 1/1, Avignon_Sim 1/1, Modified_stumvoll 1/1, Stumvoll_Demographics 1/1, Matsuda_AUC 1/1, Matsuda_ISI 1/1, BigttSi 1/1, Ifc_inv 1/1, HIRI_inv 1/1, Belfiore_isi_gly 1/1
ogtt_is(): preparing inputs
ogtt_is(): column map: G0 -> 'G0', I0 -> 'I0', G30 -> 'G30', I30 -> 'I30', G120 -> 'G120', I120 -> 'I120', weight -> 'weight', bmi -> 'bmi', age -> 'age', sex -> 'sex'
oxidative_markers(): column map: GSH -> 'GSH', GSSG -> 'GSSG'
oxidative_markers(): results: GSH_GSSG_Ratio 2/2
oxidative_markers(): preparing inputs
oxidative_markers(): results: GSH_GSSG_Ratio 2/2
oxidative_markers(): preparing inputs
oxidative_markers(): column map: GSH -> 'GSH', GSSG -> 'GSSG'
psych_markers(): results: 1 rows, 2 new columns
psych_markers(): preparing inputs
phq9_score(): results: PHQ9_total 1/1, PHQ9_severity 1/1
phq9_score(): preparing inputs
psych_markers(): results: 1 rows, 2 new columns
psych_markers(): preparing inputs
pulmo_markers(): column map: age -> 'age', sex -> 'sex', height -> 'height', ethnicity -> 'ethnicity', fev1 -> 'fev1', fvc -> 'fvc'
pulmo_markers(): converting height from cm to m
pulmo_markers(): results: fev1_pred 1/1, fev1_z 1/1, fev1_pctpred 1/1, fev1_LLN 1/1, fvc_pred 1/1, fvc_z 1/1, fvc_pctpred 1/1, fvc_LLN 1/1, fev1_fvc_ratio 1/1, fev1_fvc_pred 1/1, fev1_fvc_z 0/1, fev1_fvc_pctpred 1/1, fev1_fvc_LLN 0/1
pulmo_markers(): preparing inputs [GLI]
pulmo_markers(): converting height from cm to m
pulmo_markers(): results: fev1_pred 1/1, fev1_z 1/1, fev1_pctpred 1/1, fev1_LLN 1/1, fvc_pred 1/1, fvc_z 1/1, fvc_pctpred 1/1, fvc_LLN 1/1, fev1_fvc_ratio 1/1, fev1_fvc_pred 1/1, fev1_fvc_z 0/1, fev1_fvc_pctpred 1/1, fev1_fvc_LLN 0/1
pulmo_markers(): preparing inputs [GLI]
pulmo_markers(): column map: age -> 'age', sex -> 'sex', height -> 'height', ethnicity -> 'ethnicity', fev1 -> 'fev1', fvc -> 'fvc'
pulmo_markers(): converting height from cm to m
renal_markers(): column map: creatinine -> 'Cr', age -> 'Age', sex -> 'Sex', race -> 'Race', BUN -> 'BUN'
renal_markers(): results: eGFR_cr 1/1, eGFR_cys 0/1, eGFR_combined 0/1, BUN_Cr_ratio 1/1, FE_Urea 0/1, NGAL 0/1, KIM1 0/1, NAG 0/1, Beta2Micro 0/1, IL18 0/1, L_FABP 0/1
renal_markers(): preparing inputs
renal_markers(): results: eGFR_cr 1/1, eGFR_cys 0/1, eGFR_combined 0/1, BUN_Cr_ratio 1/1, FE_Urea 0/1, NGAL 0/1, KIM1 0/1, NAG 0/1, Beta2Micro 0/1, IL18 0/1, L_FABP 0/1
renal_markers(): preparing inputs
renal_markers(): column map: creatinine -> 'Cr', age -> 'Age', sex -> 'Sex', race -> 'Race', BUN -> 'BUN'
saliva_markers(): column map: cort1 -> 'saliva_cort1', cort2 -> 'saliva_cort2', cort3 -> 'saliva_cort3', amylase -> 'saliva_amylase', glucose -> 'saliva_glucose'
saliva_markers(): results: log_cortisol_wake 1/1, CAR_AUC 1/1, log_amylase 1/1, saliva_glucose 1/1
saliva_markers(): preparing inputs
saliva_markers(): results: log_cortisol_wake 1/1, CAR_AUC 1/1, log_amylase 1/1, saliva_glucose 1/1
saliva_markers(): preparing inputs
saliva_markers(): column map: cort1 -> 'saliva_cort1', cort2 -> 'saliva_cort2', cort3 -> 'saliva_cort3', amylase -> 'saliva_amylase', glucose -> 'saliva_glucose'
sarc_f_score(): column map: strength -> 'Strength', walking -> 'Walking', chair -> 'Chair', stairs -> 'Stairs', falls -> 'Falls'
sarc_f_score(): results: sarc_f_score 1/1, sarc_f_high_risk 1/1
sarc_f_score(): preparing inputs
sarc_f_score(): results: sarc_f_score 1/1, sarc_f_high_risk 1/1
sarc_f_score(): preparing inputs
sarc_f_score(): column map: strength -> 'Strength', walking -> 'Walking', chair -> 'Chair', stairs -> 'Stairs', falls -> 'Falls'
spirometry_markers(): column map: fev1 -> 'FEV1', fvc -> 'FVC'
spirometry_markers(): results: ratio_pre 1/1, ratio_post 0/1, copd_flag_fixed 1/1, obstruction_lln 0/1, fev1_pp 0/1, fvc_pp 0/1, fev1_z 0/1, fvc_z 0/1, ratio_z 0/1, gold_grade 0/1, bdr_fev1 0/1, bdr_fvc 0/1
spirometry_markers(): preparing inputs
spirometry_markers(): results: ratio_pre 1/1, ratio_post 0/1, copd_flag_fixed 1/1, obstruction_lln 0/1, fev1_pp 0/1, fvc_pp 0/1, fev1_z 0/1, fvc_z 0/1, ratio_z 0/1, gold_grade 0/1, bdr_fev1 0/1, bdr_fvc 0/1
spirometry_markers(): preparing inputs
spirometry_markers(): column map: fev1 -> 'FEV1', fvc -> 'FVC'
sweat_markers(): column map: sweat_chloride -> 'sweat_chloride', sweat_Na -> 'sweat_Na', sweat_K -> 'sweat_K', sweat_lactate -> 'sweat_lactate', weight_before -> 'weight_before', weight_after -> 'weight_after', duration -> 'duration', body_surface_area -> 'body_surface_area'
sweat_markers(): results: sweat_chloride 1/1, Na_K_ratio 1/1, sweat_lactate 1/1, sweat_rate 1/1
sweat_markers(): preparing inputs
sweat_markers(): results: sweat_chloride 1/1, Na_K_ratio 1/1, sweat_lactate 1/1, sweat_rate 1/1
sweat_markers(): preparing inputs
sweat_markers(): column map: sweat_chloride -> 'sweat_chloride', sweat_Na -> 'sweat_Na', sweat_K -> 'sweat_K', sweat_lactate -> 'sweat_lactate', weight_before -> 'weight_before', weight_after -> 'weight_after', duration -> 'duration', body_surface_area -> 'body_surface_area'
tracer_dxa_is(): column map: I0 -> 'I0', rate_palmitate -> 'rate_palmitate', rate_glycerol -> 'rate_glycerol', fat_mass -> 'fat_mass', weight -> 'weight', HDL_c -> 'HDL_c', bmi -> 'bmi'
tracer_dxa_is(): adipose-only indices
tracer_dxa_is(): results: LIRI_inv 1/1, Lipo_inv 1/1, ATIRI_inv 1/1
tracer_dxa_is(): preparing inputs
tracer_dxa_is(): adipose-only indices
tracer_dxa_is(): results: LIRI_inv 1/1, Lipo_inv 1/1, ATIRI_inv 1/1
tracer_dxa_is(): preparing inputs
tracer_dxa_is(): column map: I0 -> 'I0', rate_palmitate -> 'rate_palmitate', rate_glycerol -> 'rate_glycerol', fat_mass -> 'fat_mass', weight -> 'weight', HDL_c -> 'HDL_c', bmi -> 'bmi'
tracer_dxa_is(): adipose-only indices
urine_markers(): column map: urine_albumin -> 'urine_albumin', urine_creatinine -> 'urine_creatinine'
urine_markers(): results: UACR 1/1, albuminuria_stage 1/1, microalbuminuria 1/1, UPCR 0/1, U_Na_K_ratio 0/1, NGAL_per_gCr 0/1, KIM1_per_gCr 0/1, NAG_per_gCr 0/1, Beta2Micro_per_gCr 0/1, A1Micro_per_gCr 0/1, IL18_per_gCr 0/1, L_FABP_per_gCr 0/1
urine_markers(): preparing inputs
urine_markers(): results: UACR 1/1, albuminuria_stage 1/1, microalbuminuria 1/1, UPCR 0/1, U_Na_K_ratio 0/1, NGAL_per_gCr 0/1, KIM1_per_gCr 0/1, NAG_per_gCr 0/1, Beta2Micro_per_gCr 0/1, A1Micro_per_gCr 0/1, IL18_per_gCr 0/1, L_FABP_per_gCr 0/1
urine_markers(): preparing inputs
urine_markers(): column map: urine_albumin -> 'urine_albumin', urine_creatinine -> 'urine_creatinine'
vitamin_d_status(): column map: vitamin_d -> 'VitD'
vitamin_d_status(): results: vitamin_d_status 2/2
vitamin_d_status(): preparing inputs
vitamin_d_status(): results: vitamin_d_status 2/2
vitamin_d_status(): preparing inputs
vitamin_d_status(): column map: vitamin_d -> 'VitD'
vitamin_markers(): column map: VitD -> 'VitD', VitD_ref_mean -> 'VitD_ref_mean', VitD_ref_sd -> 'VitD_ref_sd', B12 -> 'B12', Folate -> 'Folate', Ferritin -> 'Ferritin', TSat -> 'TSat', Cortisol -> 'Cortisol', DHEAS -> 'DHEAS', Testosterone -> 'Testosterone', Estradiol -> 'Estradiol', TSH -> 'TSH', free_T4 -> 'free_T4', Retinol -> 'Retinol', Retinol_ref_mean -> 'Retinol_ref_mean', Retinol_ref_sd -> 'Retinol_ref_sd', Tocopherol -> 'Tocopherol', Total_lipids -> 'Total_lipids', PIVKA_II -> 'PIVKA_II', VitC -> 'VitC', Homocysteine -> 'Homocysteine', MMA -> 'MMA', Magnesium -> 'Magnesium', Zinc -> 'Zinc', Copper -> 'Copper'
vitamin_markers(): results: VitD_Z 1/1, B12_Fol_Ratio 1/1, Ferr_TSat_R 1/1, Cort_DHEA_R 1/1, T_E2_Ratio 1/1, TSH_fT4_R 1/1, Retinol_Z 1/1, Toco_Lip_R 1/1, PIVKA_II 1/1, VitC 1/1, Homocysteine 1/1, MMA 1/1, Mg_Zn_R 1/1, Cu_Zn_R 1/1
vitamin_markers(): preparing inputs
vitamin_markers(): results: VitD_Z 1/1, B12_Fol_Ratio 1/1, Ferr_TSat_R 1/1, Cort_DHEA_R 1/1, T_E2_Ratio 1/1, TSH_fT4_R 1/1, Retinol_Z 1/1, Toco_Lip_R 1/1, PIVKA_II 1/1, VitC 1/1, Homocysteine 1/1, MMA 1/1, Mg_Zn_R 1/1, Cu_Zn_R 1/1
vitamin_markers(): preparing inputs
vitamin_markers(): column map: VitD -> 'VitD', VitD_ref_mean -> 'VitD_ref_mean', VitD_ref_sd -> 'VitD_ref_sd', B12 -> 'B12', Folate -> 'Folate', Ferritin -> 'Ferritin', TSat -> 'TSat', Cortisol -> 'Cortisol', DHEAS -> 'DHEAS', Testosterone -> 'Testosterone', Estradiol -> 'Estradiol', TSH -> 'TSH', free_T4 -> 'free_T4', Retinol -> 'Retinol', Retinol_ref_mean -> 'Retinol_ref_mean', Retinol_ref_sd -> 'Retinol_ref_sd', Tocopherol -> 'Tocopherol', Total_lipids -> 'Total_lipids', PIVKA_II -> 'PIVKA_II', VitC -> 'VitC', Homocysteine -> 'Homocysteine', MMA -> 'MMA', Magnesium -> 'Magnesium', Zinc -> 'Zinc', Copper -> 'Copper'
[ FAIL 0 | WARN 7 | SKIP 4 | PASS 1578 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• QRISK3 installed; skip missing-package path test (1):
  'test-health_markers.R:258:3'
• requireNamespace("PooledCohort", quietly = TRUE) is TRUE (1):
  'test-cvd_risk.R:191:3'
• requireNamespace("QRISK3", quietly = TRUE) is TRUE (1):
  'test-cvd_risk.R:219:3'
• requireNamespace("RiskScorescvd", quietly = TRUE) is TRUE (1):
  'test-cvd_risk.R:231:3'

[ FAIL 0 | WARN 7 | SKIP 4 | PASS 1578 ]
> 
> proc.time()
   user  system elapsed 
  28.18    3.59   31.96