First CRAN release.
gce_tidy(effects = TRUE) covariate-effects
table. gce_tidy() has an effects
argument. With effects = TRUE it returns a comparison table
that, for each covariate, juxtaposes the hazard ratio for the primary
event, the competing event, the total (composite) event, and the
relative hazard ratio (the omega+ ratio) from the GCE model, each with a
confidence interval. The individual/total columns are estimated on the
model’s own scale — cause- specific Cox for gcecox(),
Fine-Gray subdistribution for gcefg() — so the reader can
see whether a covariate acts on the event of interest, the competing
event, both, or their balance. gcecox() and
gcefg() retain the model design matrix on the fitted object
($design) to support this.gcecif() cumulative-incidence-ratio GCE
model. A third GCE estimator alongside gcecox()
and gcefg(), on the cumulative-incidence scale: covariate
effects on the ratio of cumulative incidences rho(t) = F1(t)/F2(t) at a
landmark time t — the odds that a subject’s realized event
by time t is the event of interest, a cumulative-incidence-scale
analogue of omega+. Uses jackknife pseudo-observation regression of the
Aalen-Johansen estimator with a robust variance;
method = "logit" (default) fits the bounded share via a
logit-link GEE, method = "logratio" fits log(F1/F2) via an
identity-link GEE. Returns a gcemod object, so it works
with gce_tidy(), gce_scaling(), and
gce_riskscore() like the other fits. The full
methodological development is described in a companion manuscript (in
preparation).gcecox(),
gcefg(), and lunnmcneil() report omega+ ratios
per natural covariate unit by default; standardize = TRUE
reports them per 1 SD instead (a reparameterization, so p-values and the
omnibus test are identical). The GCE risk score is always the
normalized, mean-centered linear predictor, so the average patient has
risk score 0 and cutpoints / plots / calibration are unaffected by the
reporting choice.gce_scaling() and
gce_riskscore(). gce_scaling()
returns each covariate’s mean, SD, and per-SD omega+ ratio.
gce_riskscore(fit, newdata) scores new subjects with the
stored means/SDs and coefficients, returning the risk score and
omegaplus_rel = the subject’s omega+ relative to the
average subject in the fitting data (with absolute omega+/omega for
cause-specific models). $scaling, $center,
$scale, $coef_raw, and $coef_std
are stored on the fitted object.criterion = "cif" (joint Gray
statistic across both events) is available as an alternative.gce_cutpoints()$test reports the Lunn-McNeil test that the
ratio of cause-specific (or subdistribution) hazards differs between
groups, with the univariable omega+ ratio estimate and CI – the GCE test
that separate per-event Gray/log-rank tests miss. The per-event Gray
tests are also returned ($individual_gray) so the
difference is visible, along with a selection-adjusted permutation
p-value ($p.perm, via nperm > 0).gce_alligator()).
Draws the cumulative incidence of the event of interest and the
competing event on a single panel, with risk groups distinguished by
color and event types by line type (event of interest solid, competing
event dashed). By default it forms 2 groups at the optimal omega+
cutpoint (method = "optimal", log-scale;
criterion selectable) and annotates the cutpoint value and
group sizes. The x-axis is truncated at the readout time t
with 1-unit ticks; the y-axis auto-caps at the smallest of 25/50/75/100%
covering the peak incidence, with 5%/10% ticks (override with
ymax), so low-incidence plots are not compressed; and
numbers at risk are shown in an aligned panel below the plot (via
patchwork). Groups of 2-3 are labeled Low/High or
Low/Intermediate/High by default.hn,
prostate). Two competing-risks example datasets
show opposite GCE regimes: hn (head and neck, n = 1000) is
recurrence-dominant (omega+ > 1), while prostate (n =
1000) is competing-death-dominant (omega+ < 1). Both code
status as 0 = censored, 1 = event of interest, 2 =
competing, with time in years and sequential subject IDs.
They are provided for illustration only and do not represent real
patients. Categorical covariates (stage, site, Gleason, performance
status) are factors. All examples and the vignette use these
datasets.Refocused the package on modeling omega+ (event of interest vs. competing event).
$omega) for comparing model-predicted
with observed values.gce_tidy() no longer takes which (omega+
only). gce_cutpoints() now targets omega+ separation rather
than a log-rank split.lunnmcneil()
gains type = "finegray": a stacked, risk-set-weighted
(survival::finegray) model giving omega+ CIs and p-values
on the subdistribution scale from one joint model, replacing the
bootstrap in gcefg().gce_cutpoints(method = "optimal") finds cutpoints
maximizing the between-group omega+ separation (greedy maximum
between-group sum of squares).gce_alligator() — cumulative incidence of the event of
interest and the competing event within risk groups, with Gray’s
test.gce_calibration() — predicted vs. observed omega+ (or
omega) by rank group, user-specified number of groups.First release. gcemod is a successor to
gcerisk.
gceriskVariance for the omega ratio. Where
gcerisk estimates the variance of
log(omega ratio) by sampling independent normal deviates
for the cause-specific and all-cause coefficients and taking the
variance of their difference, gcemod uses a case-resampling
(nonparametric) bootstrap that refits the models on resampled subjects.
(This omega-ratio regression was removed in 0.2.0.)
Hypothesis testing added (Lunn-McNeil). The
omega-plus ratio (event of interest vs. competing event) is estimated
from a single stacked/augmented Cox model in the style of Lunn &
McNeil (1995). The event-type interaction coefficient is exactly
log(omega+ ratio) and carries a model-based (robust)
standard error, a per-covariate Wald test, and an omnibus multivariate
Wald test of no differential covariate effect across event types.
Because omega is a monotone transform of omega-plus
(omega = omega+/(1 + omega+)), this test applies to
both.
Cumulative hazard at time t.
gcerisk estimates cumulative hazards by regressing
-log(S(t)) on time with lm() and
extrapolating, which forces a linear cumulative hazard.
gcemod reads the Nelson-Aalen cumulative hazard
(cause-specific model) or the subdistribution cumulative hazard derived
from the Fine-Gray CIF (-log(1 - F(t))) directly at the
requested time via step functions.
Edge cases. Formula construction now uses
reformulate() instead of manual string pasting, which
failed for a single covariate (the 1:(p-1) loop). NA
handling (complete-case with a warning), single-covariate models, and
non-convergent bootstrap replicates (skipped with a warning) are
handled.
lunnmcneil() exposes the stacked-model estimator and
tests directly.gce_cutpoints() derives risk-stratification groups from
a GCE risk score (quantile groups, or an optimal two-group split by
log-rank scan).gce_performance() reports the cause-specific
concordance (C-index) and a grouped calibration table for the event of
interest.print(), summary(), and
gce_tidy() methods for compact, report-ready output.