Changelog • hazrd

hazrd 0.2.1

New features

phs_km_curve(): new intervals parameter accepts a list of c(lo, hi) percentile pairs, enabling overlapping KM strata (e.g. top 5%, top 20%, bottom 20%). Default produces four bands: 0.95-1, 0.80-1, 0.30-0.70, and 0-0.20. The legacy breaks parameter is retained for backward compatibility.

Bug fixes

phs_km_curve(): fixed malformed man/phs_km_curve.Rd caused by percent signs in roxygen @param text corrupting the \arguments{} block and producing R CMD check warnings.

Documentation

Vignette updated with overlapping intervals examples and breaks legacy usage.
README installation section updated to use devtools::install_github(); dev-branch instructions added (@dev).
NEWS.md corrected: function name phs_km -> phs_km_curve, stale preset list removed, phs_cox_curve entry added.

hazrd 0.2.0

New functions

phs_metrics() — single entry point for all discrimination metrics (HR, C-index, OR, HR_SD). Returns a tidy tibble with one row per metric. Supports built-in bootstrapping via boot::boot() with "percentile", "bca", and "normal" CI methods.
phs_km_curve() — Kaplan-Meier curves stratified by PHS percentile group. Returns a ggplot object by default (output = "plot") or a tidy data frame (output = "data"). Accepts an intervals list for overlapping strata (e.g. 95–100 %, 80–100 %) or a breaks vector for exclusive bins. Supports a ref_data argument for train/validation percentile workflows.
phs_cox_curve() — Cox model-based survival curves at specified PHS percentiles. Fits a Cox PH model with phs as the sole predictor and returns smooth predicted curves at user-supplied percentile values. Supports ref_data for train/validation workflows.

Deprecated functions

The following functions are deprecated as of 0.2.0 and will be removed in 0.3.0. They continue to work and emit a deprecation warning pointing to the replacement call.

get_hr() → use phs_metrics(data, metrics = "HR")
get_or() → use phs_metrics(data, metrics = "OR", or_age = ...)
get_cindex() → use phs_metrics(data, metrics = "C_index")
get_hrsd() → use phs_metrics(data, metrics = "HR_SD")
km_curve() → use phs_km_curve()

Removed functions

create_lookup_table() — superseded by the upcoming phs_abs_risk().
cum_inc() — out of scope for the package API.
get_phs_age() — internal helper; will be re-exposed via phs_abs_risk().

Bug fixes

phs_metrics() with metrics = "OR": or_age values outside the observed KM time range now return NA with an informative warning instead of propagating silent NA or infinite odds (#or-edge-case).
phs_metrics() with metrics = "HR_SD" and bootstrap = TRUE: HR_SD is now correctly included in the bootstrap statistic vector so that conf_low, conf_high, and se are populated.

hazrd 0.1.0

Initial release.