Package: HealthMarkers 0.1.3

HealthMarkers: Clinical and Metabolic Biomarker Calculation Toolkit

Computes specialist biomarker indices and risk scores for metabolic, cardiovascular, renal, hepatic, inflammatory, frailty, and psychiatric health assessment. Includes fasting and OGTT insulin sensitivity/resistance indices, ASCVD/QRISK3/KFRE risk equations, liver and kidney markers, frailty and comorbidity indices, biofluid marker panels, and utilities for column mapping, normalization, imputation, and combined marker dispatch.

Authors:Sufyan Suleman [aut, cre]

HealthMarkers_0.1.3.tar.gz
HealthMarkers_0.1.3.zip(r-4.7)HealthMarkers_0.1.3.zip(r-4.6)HealthMarkers_0.1.3.zip(r-4.5)
HealthMarkers_0.1.3.tgz(r-4.6-any)HealthMarkers_0.1.3.tgz(r-4.5-any)
HealthMarkers_0.1.3.tar.gz(r-4.7-any)HealthMarkers_0.1.3.tar.gz(r-4.6-any)
HealthMarkers_0.1.3.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://sufyansuleman.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:

4.84 score 60 scripts 224 downloads 77 exports 17 dependencies

Last updated from:bc792e2391. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK190
source / vignettesOK237
linux-release-x86_64OK189
macos-release-arm64OK124
macos-oldrel-arm64OK119
windows-develOK304
windows-releaseOK164
windows-oldrelOK181
wasm-releaseOK139

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