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Changelog

Source: NEWS.md

HealthMarkers 0.1.2

CRAN release: 2026-05-19

New features

  • hm_normalize() — post-computation normalisation helper (new function). Apply z-score, rank-based inverse-normal transform (Rankit), min-max, or robust median/MAD scaling to any marker output data frame. Use cols to target specific columns and skip_cols to protect covariates (e.g. age, BMI) from being rescaled. This covers domain functions whose internal normalize argument currently has no effect (glycemic_markers(), lipid_markers(), renal_markers(), etc.). See ?hm_normalize.

  • Multi-biobank column inference (major). The internal synonym dictionary (.hm_default_col_patterns_exact()) now recognises column-naming conventions from 15+ major cohort studies and biobanks for all primary analytes:

    • UK Biobank — _0_0 / _1_0 field naming (e.g. glucose_0_0, creatinine_0_0, vitamin_d_0_0); standing_height, 25OHD.
    • NHANES — LBXS, LBDS, BPX, URX prefix variables (e.g. LBXGLU, LBXSCH, BPXSY1, URXUMA).
    • Danish national registers / EHR (LABKA/OPEN) — NPU codes (NPU01994 for creatinine, NPU01567 for cholesterol, NPU03609 for haemoglobin, etc.) and Danish clinical labels (kreatinin, kolesterol, blodsukker, leukocytter, trombocytter, d_vitamin).
    • HUNT Study and Tromsø Study (Norway) — Norwegian-language terms (blodsukkerfasting, systolisk_blodtrykk, triglyserider, karbamid, kjonn, midjeomkrets).
    • SCAPIS / TwinGene (Sweden) — Swedish-language terms (glukos, urinsyra, leukocyter, trombocyter, kön, längd, vikt).
    • FinnGen / THL Biobank (Finland) — Finnish-language terms (glukoosi, kolesteroli, kreatiniini, hemoglobiini, sukupuoli, virtsahappo, leukosyytit, ferritiini, D_vitamiini).
    • Estonian Biobank (EstBB) — Estonian terms (glukoos, kolesterool, kreatiniin, hemoglobiin, naatrium, kaalium, vanus, sugu).
    • LifeLines Cohort / Rotterdam Study (Netherlands) — Dutch terms (nuchtere_glucose, totaal_cholesterol, urinezuur, ureum, leukocyten, hemoglobine, vitamine_D, tailleomtrek).
    • Generation Scotland (GS:SFHS) — SBP_mean, DBP_mean, genetic_sex, ethnic_group.
    • All of Us / OMOP CDM — LOINC codes in LOINC_XXXX_X format for all major analytes (e.g. LOINC_2345_7 for fasting glucose, LOINC_2160_0 for creatinine, LOINC_718_7 for haemoglobin).
    • NAKO / KORA (Germany) — German-language terms (Cholesterin, Triglyzeride, Harnsäure, Harnstoff, Leukozyten, Thrombozyten).

  • Added hm_col_report() — an interactive column-mapping diagnostic. Call hm_col_report(your_data) before running any computation to see a formatted table of which internal keys were matched to columns in your data and how (exact synonym, case-insensitive, substring, or fuzzy), plus a ready-to-paste col_map template for any unmatched keys.
    The function uses a five-layer matching pipeline and returns the matched mappings invisibly so the result can be passed directly as col_map to any HealthMarkers function.

  • Auto-derivation of computed inputs. .hm_global_precompute() now automatically derives 18+ secondary columns before marker computation begins, so functions that require (e.g.) eGFR, UACR, WHR, LDL_c, or waist no longer fail silently when only the raw inputs are present. Affected keys include eGFR (from creatinine/age/sex via CKD-EPI), WHR (from waist and hip), UACR (from u_albumin / u_creatinine), LDL_c (Friedewald from TC/HDL_c/TG), MAP, PP, BMI (from height/weight), and more.

  • Expanded the internal synonym dictionary (R/utils_infer-cols.R) for all variable groups, additionally incorporating:

    • Inter99 / ADDITION real phenotype dataset labels
    • Common literature spellings (TryG, TAG, TRIG, triacylglycerol; SGPT/GPT/ALAT; hsCRP/hs_CRP)
    • Longitudinal follow-up suffixes (_0, _1, _3, _5)
    • NMR metabolomics (urine) panel, ECG markers, lifestyle covariates, and cytokine multiplex proteins.

Bug fixes

  • adiposity_sds(): fixed fn_name lookup bug that caused incorrect error messages when validation failed on non-standard column names.

Internal

HealthMarkers 0.1.1

New features

  • Added liver_fat_markers() for hepatic steatosis and fibrosis index calculation.
  • Added nfl_marker() for plasma neurofilament light chain (NfL) z-score computation.
  • Added impute_missing() for within-row imputation of missing biomarker values.

Bug fixes and improvements

  • pulmo_markers(): fixed column-inference logic for spirometry z-score inputs.
  • All marker functions: standardised verbose progress messages to emit at the "debug" level when verbose = FALSE, so that getOption("healthmarkers.verbose") controls visibility consistently across every function.
  • Computing-phase messages are now unconditionally emitted at "debug" level (independent of the per-call verbose argument) in bone_markers(), ckd_stage(), and corrected_calcium().
  • all_health_markers(): column inference is now keyed to the requested groups, falls back to regex-based infer_cols() when exact matches fail, and reports per-group status (including missing optional packages) in verbose summaries.
  • Cardiovascular risk wrappers: cvd_risk_qrisk3() now prefers the correctly named ethnicity column (typo tolerated for backward compatibility), and optional dependency errors now report the missing package name consistently.
  • Shared validation: lipid marker helpers now route through hm_validate_inputs() so duplicate/empty mappings are caught uniformly.

Internal

  • Package gains a _pkgdown.yml that lists all 46 vignettes in the articles index for the pkgdown site.