Package: HealthMarkers 0.1.2

Sufyan Suleman

HealthMarkers: Toolkit for Clinical, Metabolic, and Cardiovascular Biomarker Calculations

Computes over 50 specialist health marker functions covering insulin sensitivity and resistance indices (fasting, oral glucose tolerance test, adipose-tissue, tracer, and dual-energy X-ray absorptiometry (DXA)-based), glycaemic and lipid markers, atherogenic and metabolic syndrome scores, liver steatosis and fibrosis scores, and cardiovascular risk algorithms (Framingham Heart Study equations, atherosclerotic cardiovascular disease (ASCVD) Pooled Cohort Equations, the QRISK3 cardiac risk score, and Systematic Coronary Risk Evaluation 2 (SCORE2) including the Older Persons variant (SCORE2-OP)). Also implements renal function (estimated glomerular filtration rate (eGFR), Kidney Failure Risk Equation (KFRE), chronic kidney disease (CKD) staging), pulmonary function (spirometry z-scores, Body-mass index, airflow Obstruction, Dyspnea, and Exercise capacity index (BODE)), inflammatory markers and the inflammatory age clock (iAge), hormonal panels, body composition and anthropometric z-scores, bone turnover markers and fracture risk (Fracture Risk Assessment Tool (FRAX)), frailty and comorbidity indices (Rockwood, Charlson), psychiatric rating scales, and biomarker panels from alternative biofluids (urine, saliva, sweat). Missing value imputation helpers, pre or post computation normalization and a unified all_health_markers() dispatcher that returns all requested marker groups as a single wide tibble are included.

Authors:Sufyan Suleman [aut, cre]

HealthMarkers_0.1.2.tar.gz
HealthMarkers_0.1.2.tar.gz(r-4.7-any)HealthMarkers_0.1.2.tar.gz(r-4.6-any)
HealthMarkers_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
HealthMarkers/json (API)
NEWS

# Install 'HealthMarkers' in R:
install.packages('HealthMarkers', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sufyansuleman/healthmarkers/issues

Pkgdown/docs site:https://sufyansuleman.github.io

On CRAN:

Conda:

2.48 score 60 scripts 77 exports 17 dependencies

Last updated from:67bfc5ed8c. Checks:2 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR184
source / vignettesOK245
linux-release-x86_64ERROR180
wasm-releaseOK136

Exports:adipo_isadiposity_sdsadiposity_sds_stratall_health_markersall_insulin_indicesallostatic_loadalm_bmi_indexasrs_scoreatherogenic_indicesbis_scorebode_indexbone_markerscalc_sdscharlson_indexckd_stagecognitive_scorecorrected_calciumcvd_marker_aipcvd_marker_ldl_particle_numbercvd_riskcvd_risk_ascvdcvd_risk_qrisk3cvd_risk_scorescvdcvd_risk_strokefasting_isfrailty_indexfrax_scoregad7_scoreghq12_scoreglycemic_markershealth_summaryhm_col_reporthm_normalizehormone_markersiAgeimpute_miceimpute_missforestimpute_missinginfer_colsinflammatory_markersisi_scorek10_scorek6_scorekidney_failure_riskkyn_trp_ratiolipid_markersliver_fat_markersliver_markersmarker_summarymdq_scoremetabolic_markersmetabolic_risk_featuresmetssnfl_markernormalize_vecnutrient_markersobesity_indicesogtt_isoxidative_markersphq9_scoreplot_frailty_agepsych_dx_flagspsych_markerspsych_med_flagspulmo_markersrenal_markerssaliva_markerssarc_f_scorespirometry_markersspq_scoresweat_markerstracer_dxa_isurine_markersvalidate_inputsvitamin_d_statusvitamin_markerswho5_score

Dependencies:clidplyrgenericsgluelifecyclemagrittrpillarpkgconfigR6rbibutilsRdpackrlangtibbletidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Adipose insulin sensitivity indices (QUICKI, VAI, LAP, TyG, TG/HDL, Belfiore)adipo_is
Calculate standardized scores (SDS) for adiposity measuresadiposity_sds
Compute sex-stratified standardized scores (SDS) for adiposity measuresadiposity_sds_strat
Compute all available HealthMarkers categoriesall_health_markers
Compute insulin sensitivity/resistance panels (fasting, OGTT, adipose, tracer/DXA)all_insulin_indices
Allostatic Load Indexallostatic_load
Appendicular Lean Mass to BMI Indexalm_bmi_index
Adult ADHD Self-Report Scale scoringasrs_score
Compute atherogenic indicesatherogenic_indices
Barratt Impulsiveness Scale (key-driven)bis_score
BODE Index (BMI, Obstruction, Dyspnea, Exercise capacity)bode_index
Compute Bone Health & Body-Composition Markers (HM-CS v3)bone_markers
Calculate Standard Deviation Scores (SDS; z-scores) for health markerscalc_sds
Charlson Comorbidity Index (CCI)charlson_index
CKD staging (GFR and albuminuria) and KDIGO riskckd_stage
Cognitive composite (z-mean or PCA1)cognitive_score
Albumin-Corrected Calciumcorrected_calcium
Atherogenic Index of Plasma (AIP)cvd_marker_aip
LDL Particle Number Estimate (via ApoB)cvd_marker_ldl_particle_number
Compute cardiovascular risk or marker by selected modelcvd_risk
ASCVD risk (ACC/AHA Pooled Cohort Equations)cvd_risk_ascvd
QRISK3 10-year risk (UK QRISK3-2017)cvd_risk_qrisk3
RiskScorescvd calculatorcvd_risk_scorescvd
Stroke 10-year riskcvd_risk_stroke
Calculate fasting-based insulin sensitivity indicesfasting_is
Compute Frailty (Deficit) Index using di::di with QA and verbose summariesfrailty_index
FRAX 10-Year Fracture Risk Score (simplified placeholder)frax_score
GAD-7 scoringgad7_score
GHQ-12 scoring (Likert or binary)ghq12_score
Calculate glycemic-, C-peptide-, and additional metabolic markersglycemic_markers
Summarize selected numeric marker columnshealth_summary
Diagnose and report column name mapping for your datahm_col_report
Normalise marker columns in a data framehm_normalize
Compute a suite of hormone ratio markers with QA and verbose summarieshormone_markers
Compute a simplified Inflammatory Age Index (iAge) with QA and verbose summariesiAge
Impute missing values via Multiple Imputation (mice)impute_mice
Impute missing values via random forest (missForest)impute_missforest
Impute missing values in a data.frame or tibble (simple, column-wise)impute_missing
Compute inflammatory indices (classic, eosinophil, or both)inflammatory_markers
Insomnia Severity Index (ISI) scoringisi_score
K10 scoringk10_score
K6 scoringk6_score
Kidney Failure Risk Equation (KFRE, 2- and 5-year risk)kidney_failure_risk
Kynurenine/Tryptophan Ratio (KTR)kyn_trp_ratio
Calculate lipid-panel markers, Visceral Adiposity Index (VAI), Lipid Accumulation Product (LAP), and TyG-BMI indexlipid_markers
Liver fat surrogates: HSI and NAFLD Liver Fat Scoreliver_fat_markers
Compute liver-related indices (FLI, NFS, APRI, FIB-4, BARD, ALBI, MELD-XI) with validation and diagnosticsliver_markers
Summarize marker outputsmarker_summary
Mood Disorder Questionnaire scoringmdq_score
Aggregate selected metabolic marker groupsmetabolic_markers
Calculate metabolic risk feature flags (pediatric-friendly thresholds)metabolic_risk_features
Metabolic Syndrome Severity Score (MetSSS)metss
Neurofilament Light Chain (NfL) Biomarkernfl_marker
Normalize a numeric vectornormalize_vec
Compute a Suite of Nutrient-Based Health Markersnutrient_markers
Compute anthropometric obesity & adiposity indicesobesity_indices
Calculate OGTT-based insulin sensitivity indicesogtt_is
Oxidative stress markersoxidative_markers
PHQ-9 / PHQ-8 scoringphq9_score
Plot FI vs age (convenience wrapper)plot_frailty_age
Psychiatric diagnosis flags aggregatorpsych_dx_flags
Psychometric markers dispatcherpsych_markers
Psychiatric medication flags aggregatorpsych_med_flags
Calculate pulmonary function markers (FEV1/FVC, z-scores, percent predicted, LLN, etc.)pulmo_markers
Calculate a Suite of Renal Function, Injury, and Excretion Markersrenal_markers
Calculate saliva-based stress & glycemic markerssaliva_markers
SARC-F Sarcopenia Screening Scoresarc_f_score
Spirometry markers: FEV1/FVC, LLN-based obstruction, GOLD grade, bronchodilator responsespirometry_markers
Schizotypal Personality Questionnaire (key-driven)spq_score
Calculate sweat-based ionic & metabolic markerssweat_markers
Compute tracer/DXA-based insulin sensitivity indicestracer_dxa_is
Calculate urine-only renal and tubular markers (research-ready)urine_markers
Validate required inputs for a calling functionvalidate_inputs
Vitamin D Status Categoryvitamin_d_status
Compute composite vitamin and endocrine marker ratios and z-scoresvitamin_markers
WHO-5 scoringwho5_score