R: Clinical and Metabolic Biomarker Calculation Toolkit

# Clinical and Metabolic Biomarker Calculation Toolkit

## Documentation for package ‘HealthMarkers’ version 0.1.4

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

adiposity_sds | Calculate standardized scores (SDS) for adiposity measures
adiposity_sds_strat | Compute sex-stratified standardized scores (SDS) for adiposity measures
adipo_is | Adipose insulin sensitivity indices (QUICKI, VAI, LAP, TyG, TG/HDL, Belfiore)
allostatic_load | Allostatic Load Index
all_health_markers | Compute all available HealthMarkers categories
all_insulin_indices | Compute insulin sensitivity/resistance panels (fasting, OGTT, adipose, tracer/DXA)
alm_bmi_index | Appendicular Lean Mass to BMI Index
asrs_score | Adult ADHD Self-Report Scale scoring
atherogenic_indices | Compute atherogenic indices
bis_score | Barratt Impulsiveness Scale (key-driven)
bode_index | BODE Index (BMI, Obstruction, Dyspnea, Exercise capacity)
bone_markers | Compute Bone Health & Body-Composition Markers (HM-CS v3)
calc_sds | Calculate Standard Deviation Scores (SDS; z-scores) for health markers
charlson_index | Charlson Comorbidity Index (CCI)
ckd_stage | CKD staging (GFR and albuminuria) and KDIGO risk
cognitive_score | Cognitive composite (z-mean or PCA1)
corrected_calcium | Albumin-Corrected Calcium
cvd_marker_aip | Atherogenic Index of Plasma (AIP)
cvd_marker_ldl_particle_number | LDL Particle Number Estimate (via ApoB)
cvd_risk | Compute cardiovascular risk or marker by selected model
cvd_risk_ascvd | ASCVD risk (ACC/AHA Pooled Cohort Equations)
cvd_risk_qrisk3 | QRISK3 10-year risk (UK QRISK3-2017)
cvd_risk_scorescvd | RiskScorescvd calculator
cvd_risk_stroke | Stroke 10-year risk
fasting_is | Calculate fasting-based insulin sensitivity indices
frailty_index | Compute Frailty (Deficit) Index using di::di with QA and verbose summaries
frax_score | FRAX 10-Year Fracture Risk Score (simplified placeholder)
gad7_score | GAD-7 scoring
ghq12_score | GHQ-12 scoring (Likert or binary)
glycemic_markers | Calculate glycemic-, C-peptide-, and additional metabolic markers
health_summary | Summarize selected numeric marker columns
hm_col_report | Diagnose and report column name mapping for your data
hm_normalize | Normalise marker columns in a data frame
hormone_markers | Compute a suite of hormone ratio markers with QA and verbose summaries
iAge | Compute a simplified Inflammatory Age Index (iAge) with QA and verbose summaries
impute_mice | Impute missing values via Multiple Imputation (mice)
impute_missforest | Impute missing values via random forest (missForest)
impute_missing | Impute missing values in a data.frame or tibble (simple, column-wise)
inflammatory_markers | Compute inflammatory indices (classic, eosinophil, or both)
isi_score | Insomnia Severity Index (ISI) scoring
k10_score | K10 scoring
k6_score | K6 scoring
kidney_failure_risk | Kidney Failure Risk Equation (KFRE, 2- and 5-year risk)
kyn_trp_ratio | Kynurenine/Tryptophan Ratio (KTR)
lipid_markers | Calculate lipid-panel markers, Visceral Adiposity Index (VAI), Lipid Accumulation Product (LAP), and TyG-BMI index
liver_fat_markers | Liver fat surrogates: HSI and NAFLD Liver Fat Score
liver_markers | Compute liver-related indices (FLI, NFS, APRI, FIB-4, BARD, ALBI, MELD-XI) with validation and diagnostics
marker_summary | Summarize marker outputs
mdq_score | Mood Disorder Questionnaire scoring
metabolic_markers | Aggregate selected metabolic marker groups
metabolic_risk_features | Calculate metabolic risk feature flags (pediatric-friendly thresholds)
metss | Metabolic Syndrome Severity Score (MetSSS)
nfl_marker | Neurofilament Light Chain (NfL) Biomarker
normalize_vec | Normalize a numeric vector
nutrient_markers | Compute a Suite of Nutrient-Based Health Markers
obesity_indices | Compute anthropometric obesity & adiposity indices
ogtt_is | Calculate OGTT-based insulin sensitivity indices
oxidative_markers | Oxidative stress markers
phq9_score | PHQ-9 / PHQ-8 scoring
plot_frailty_age | Plot FI vs age (convenience wrapper)
psych_dx_flags | Psychiatric diagnosis flags aggregator
psych_markers | Psychometric markers dispatcher
psych_med_flags | Psychiatric medication flags aggregator
pulmo_markers | Calculate pulmonary function markers (FEV1/FVC, z-scores, percent predicted, LLN, etc.)
renal_markers | Calculate a Suite of Renal Function, Injury, and Excretion Markers
saliva_markers | Calculate saliva-based stress & glycemic markers
sarc_f_score | SARC-F Sarcopenia Screening Score
spirometry_markers | Spirometry markers: FEV1/FVC, LLN-based obstruction, GOLD grade, bronchodilator response
spq_score | Schizotypal Personality Questionnaire (key-driven)
sweat_markers | Calculate sweat-based ionic & metabolic markers
tracer_dxa_is | Compute tracer/DXA-based insulin sensitivity indices
urine_markers | Calculate urine-only renal and tubular markers (research-ready)
validate_inputs | Validate required inputs for a calling function
vitamin_d_status | Vitamin D Status Category
vitamin_markers | Compute composite vitamin and endocrine marker ratios and z-scores
who5_score | WHO-5 scoring