This release follows a systematic, script-by-script audit of every marker-calculation function in the package, checking each formula and its unit handling against the original publication. The supporting/utility scripts were also confirmed to apply no hidden unit conversions (column inference maps names only; the global pre-computation helper keeps variables in their canonical units). The fixes below correct genuine formula/unit bugs; the great majority of functions were verified correct and unchanged.
fasting_is() —
HOMA_IR_inv. HOMA-IR (Matthews et al. 1985) is
defined with glucose in mmol/L (divisor 22.5). The previous code applied
the mg/dL conversion (*18) while keeping the 22.5 divisor,
yielding values 18x too large. Now uses raw mmol/L glucose.
HOMA_IR_rev_inv (mg/dL convention, /405)
already produced the correct value and is unchanged; the two columns are
now equal, as intended.
fasting_is() — FIRI.
The Fasting Insulin Resistance Index (Duncan et al. 1995) is defined
with glucose in mmol/L (divisor 25). Now uses raw mmol/L glucose instead
of the mg/dL-converted value (previously 18x too large).
fasting_is() — QUICKI.
Now uses log10 (as defined by Katz et al.
ogtt_is() —
Cederholm_index. Cederholm & Wibell (1990) is
defined with glucose in mmol/L; the formula’s *180 term is
itself the mmol/L->mg conversion. The previous code pre-converted
glucose to mg/dL (*18), causing a double conversion and a
non-linear distortion of the index. Now uses raw mmol/L glucose.
Gutt_index (defined in mg/dL, no *180 term) is
unchanged and correct.
glycemic_markers() — SPISE and
METS_IR. Both indices are defined for inputs in
mg/dL (SPISE: Paulmichl 2016; METS-IR: Bello-Gaytan
2018) and carry validated cut-offs in those units. The previous code fed
raw mmol/L values, giving systematically wrong (non-constant) results.
Now converts HDL-c (*38.67), TG (*88.57) and
glucose (*18) to mg/dL internally. TyG_index
was already correct.
liver_fat_markers() —
NAFLD_LFS. The NAFLD Liver Fat Score (Kotronen et
al. 2009) codes type-2 diabetes as yes = 2 / no = 0, so
the diabetic contribution is 0.45 * 2 = 0.90. The previous
code used a 0/1 indicator, giving half the intended contribution for
people with diabetes. Fixed.
renal_markers() —
eGFR_combined. The combined creatinine–cystatin C
CKD-EPI equation (Inker et al. 2012) uses its own creatinine
alpha (-0.207 male / -0.248 female) and its own female
(x0.969) and Black (x1.08) multipliers. The
previous code reused the creatinine-only alpha (-0.411 /
-0.329) and incorrect multipliers (1.008,
1.145). All three corrected. eGFR_cr (2009)
and eGFR_cys (2012) were already correct.
ckd_stage() —
KDIGO_risk. Two cells of the KDIGO 2012 risk
heatmap were mis-mapped: G1/G2 + A3 now returns High
(was “Moderate”), and G3a + A3 now returns Very High
(was “High”). GFR and albuminuria stage cut-offs were already
correct.
kidney_failure_risk() — KFRE. The
4-variable Kidney Failure Risk Equation (Tangri et al. 2011) was
reimplemented correctly. The previous linear predictor used
log-transformed age and eGFR (the equation uses age/10 and
eGFR/5 linearly), the wrong sign on age, no covariate
centring, an incorrect sex coefficient, and baseline-survival constants
matching no published calibration. Now uses the non-North-American
calibration:
PI = -0.2201*(age/10 - 7.036) + 0.2467*(male - 0.5642) - 0.5567*(eGFR/5 - 7.222) + 0.4510*(ln(ACR_mmol) - 5.137),
S0(2y) = 0.9832, S0(5y) = 0.9365. UACR
continues to be supplied in mg/g and is converted internally to mg/mmol
(/8.84).
obesity_indices() —
BRI. The Body Roundness Index (Thomas et al. 2013)
eccentricity ratio is WC / (pi * height); the previous code
used WC / (2*pi * height) (half the correct value), which
produced near-zero or negative BRI for normal adults. Fixed.
atherogenic_indices() and
cvd_marker_aip() — AIP units. The Atherogenic
Index of Plasma log10(TG/HDL) is not scale-invariant (TG
and HDL-c convert to mg/dL with different factors), and its published
risk strata assume mmol/L. Documentation and the
atherogenic_indices() example were corrected to mmol/L,
with an explicit note that mg/dL inputs shift AIP by about +0.36.
Formulas are unchanged.obesity_indices() — dplyr deprecation.
Replaced the unit-normalization dplyr::case_when() calls
with scalar conversion factors. weight_unit and
height_unit are scalar arguments, so the previous size-1
LHS / vector RHS pattern triggered a deprecation warning under dplyr
>= 1.2.0. Behaviour is unchanged.Version to 0.1.4.CRAN / Fedora
r-devel-linux-x86_64-fedora-gcc ERROR fix.
test-frailty_index.R test 1 (“frailty_index errors without
di installed”) failed on Fedora because the di namespace is
already resident in memory for the whole test session, so
requireNamespace("di") always returns TRUE
regardless of withr::with_libpaths() or mocking
base::requireNamespace. Fixed by mocking
.need_pkg_di() directly in the HealthMarkers
namespace via
testthat::local_mocked_bindings(.package = "HealthMarkers").
This is reliable on all platforms regardless of whether di
is installed or loaded.
Metadata — Bumped Version to 0.1.3
and updated CRAN-SUBMISSION and
cran-comments.md to reflect the resubmission.
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:
_0_0 / _1_0
field naming (e.g. glucose_0_0,
creatinine_0_0, vitamin_d_0_0);
standing_height, 25OHD.LBXGLU, LBXSCH, BPXSY1,
URXUMA).NPU01994 for creatinine, NPU01567 for
cholesterol, NPU03609 for haemoglobin, etc.) and Danish
clinical labels (kreatinin, kolesterol,
blodsukker, leukocytter,
trombocytter, d_vitamin).blodsukkerfasting,
systolisk_blodtrykk, triglyserider,
karbamid, kjonn,
midjeomkrets).glukos, urinsyra, leukocyter,
trombocyter, kön, längd,
vikt).glukoosi, kolesteroli,
kreatiniini, hemoglobiini,
sukupuoli, virtsahappo,
leukosyytit, ferritiini,
D_vitamiini).glukoos, kolesterool,
kreatiniin, hemoglobiin,
naatrium, kaalium, vanus,
sugu).nuchtere_glucose,
totaal_cholesterol, urinezuur,
ureum, leukocyten, hemoglobine,
vitamine_D, tailleomtrek).SBP_mean, DBP_mean, genetic_sex,
ethnic_group.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).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:
TryG, TAG,
TRIG, triacylglycerol;
SGPT/GPT/ALAT;
hsCRP/hs_CRP)_0, _1,
_3, _5)adiposity_sds(): fixed fn_name lookup bug
that caused incorrect error messages when validation failed on
non-standard column names.hm_col_report() to hm_fmt_col_map() to avoid a
name collision with the new exported function.liver_fat_markers() for hepatic steatosis and
fibrosis index calculation.nfl_marker() for plasma neurofilament light chain
(NfL) z-score computation.impute_missing() for within-row imputation of
missing biomarker values.pulmo_markers(): fixed column-inference logic for
spirometry z-score inputs.verbose = FALSE, so that
getOption("healthmarkers.verbose") controls visibility
consistently across every function.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.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.hm_validate_inputs() so duplicate/empty mappings are caught
uniformly._pkgdown.yml that lists all 46
vignettes in the articles index for the pkgdown site.
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