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"survival" outcome family.
set_ipd() accepts time-to-event data with right, left,
interval and delayed-entry censoring through a
survival::Surv() object or
time/status/entry_time columns,
and set_agd_surv() takes the comparator arm as
reconstructed pseudo-IPD plus its covariate moments.
outcome is not required for this family.distribution argument of mlumr(): proportional
hazards ("exponential", "weibull",
"gompertz"), accelerated failure time
("exponential-aft", "weibull-aft",
"lognormal", "loglogistic",
"gamma", "gengamma") and flexible hazards
("mspline", "pexp") with a random-walk
smoothing prior. make_knots() places spline knots;
knots accepts a custom set.aux_by = ".study"), each stratum with its own knots over
its own observed support, as multinma::nma() does.
aux_by = "none" shares one baseline across studies.prior_aux, prior_aux2
(second generalized-gamma auxiliary) and prior_smooth, with
default_prior_aux() and
default_prior_smooth().predict() on a survival fit returns
"survival", "hazard", "cumhaz",
"rmst", "median" and "loghr"
curves. times picks evaluation times (snapped to the fitted
grid, with a message when they move), pred_times sets the
grid, "median" carries p_not_reached, and RMST
rows carry their horizon.
conditional_effects() and
conditional_predict() give covariate-conditional
versions.marginal_effects() reports survival effects on
the natural scale: the hazard ratio (HR) for
proportional-hazards fits, the time ratio (TR) for
shared-shape AFT fits, the exponentiated contrast
(EXP_DELTA_ETA) otherwise, plus the RMST difference
(RMSTD) and ratio (RMSTR). Marginal hazard
ratios carry an at_time column because they are
time-varying and non-collapsible; predict(type = "loghr")
gives the whole curve.effect = "tr" on a
proportional-hazards fit, effect = "hr" on an AFT fit, and
either on a relaxed or study-specific-shape AFT fit.naive() returns the
unadjusted Cox log hazard ratio and refuses a partial likelihood with no
maximum or no convergence. stc() returns the RMST
difference by parametric G-computation with flexsurv, with
a bootstrap interval (n_boot, default 200) and an
rmst_horizon argument.survival_unit on calculate_loo(),
calculate_waic() and compare_models() chooses
what one held-out unit is for the reconstructed comparator:
"observation" (default, optimistic), "arm" or
"aggregate".summary() are labeled
by covariate name (beta[age], beta_index[age],
beta_comparator[age]); the stored variable
strings are unchanged.?mlumr.mlumr() refuses an M-spline basis column that no
subject was at risk under, judged over the merged
[entry, exit] intervals of each study, and refuses a shared
baseline (aux_by = "none") whose studies never overlap on a
spline column. See ?mlumr.predict(type = "rmst") and
predict(type = "median") warn when the prediction grid is
too coarse to trust and point at a finer n_rmst_grid or
pred_times.?set_agd_surv states that reconstruction
uncertainty is not propagated and which population the covariate moments
must describe under delayed entry.newdata argument on
marginal_effects() and predict() standardizes
effects and absolute predictions to an arbitrary target population by
Bayesian g-computation, for every family. Standardizing to the index
covariates reproduces population = "index" exactly.
Survival RMST effects and absolute predictions transport; the marginal
hazard ratio is reported for a target too, with its
at_time.marginal_effects() on a relaxed fit
queried for the index population prints a one-line note with the
marginal posterior variance change of beta_comparator per
covariate, descriptive only. Silence it with
options(mlumr.quiet_relaxed_index = TRUE).plot() methods for
marginal_effects() (forest), predict() (curves
with credible bands, or point-intervals for scalar types) and
conditional_effects() (effects by profile). Each forest
draws the null its measure implies, uses a log axis for ratio measures,
and reads its interval level from the result.geom_km() overlays the observed Kaplan-Meier
curves on a model survival plot, colored by treatment, honoring delayed
entry, one panel per population. It draws right-censored data only.plot_prior_posterior() overlays each named
parameter’s posterior on the prior the fit recorded for it.mlumr_forest() draws a forest from a plain
data frame, for mixed comparisons such as naive(),
stc() and both ML-UMR models on one axis; a single very
wide interval is clipped with an arrow instead of squeezing the
rest.marginal_effects(), predict()
and conditional_effects() return lightweight
data.frame subclasses so the methods dispatch; data frame
behavior is unchanged.check_identification() reports, before
fitting, whether the aggregate subgroup rows can identify
beta_comparator in model = "relaxed": the row
count against K + 1, and the balance, effective dimension
and spread of the centered subgroup-mean matrix, with a descriptive-only
label for nonlinear links.prior_beta_comparator argument to
mlumr() sets a separate prior on
beta_comparator, including a different family. Defaults to
prior_beta; ignored for model = "spfa";
reported by prior_summary() and swept by
prior_sensitivity().set_agd() row as evidence; it triggers on the rank of the
mean design under the identity link and on the number of distinct
integration grids otherwise.distr() honors arguments passed by position.
distr(qnorm, 10, 2) previously integrated a standard normal
without any message. Positional and abbreviated arguments are now
matched against the quantile function’s formals at construction, and an
argument matching nothing is an error.qgamma()/pgamma()/dgamma() and
qlogitnorm()/plogitnorm()/dlogitnorm()
accept mean and sd, so
distr(qgamma, mean = age_mean, sd = age_sd) works as
printed in a baseline table. Without those arguments they forward to
stats. See ?GammaDist and
?logitNormal.set_agd() no longer rejects a valid binary
covariate SD. The bound was the population SD
sqrt(p (1 - p)); it is now the finite-sample maximum with a
rounding allowance. See ?set_agd.set_agd() requires outcome_n
when normal aggregate data have more than one row, and the multi-row
comparator estimand for the normal family is the sample-size-weighted
mean of the strata rather than an inverse-variance average.
naive() and stc() use the same weights.set_ipd() warns about a rank-deficient or
nearly collinear covariate design and names the near-redundant
covariates. Autoscaling of a covariate with no usable empirical scale
falls back to the unscaled prior with a warning.add_integration() rejects
cor_adjust = "pearson" with non-Gaussian margins, warns
about a nonbinary discrete margin (count or ordered category) that the
copula correction does not cover, and warns when a supplied
distr() grossly contradicts the declared
set_agd() moments.check_integration() compares realized and
target correlations on the same method (Pearson or Spearman), reports
fidelity of each grid margin to the declared mean and SD, lists which
correlation pairs it could and could not measure
(correlation_pairs, with "partial" and
"review" verdicts), withholds the comparison under
cor_adjust = "none", and reports a comparison it could not
make as "unavailable" instead of "close".family = "normal" the default priors are
on the outcome’s scale. Under the identity link the intercepts and
coefficients are in the outcome’s units, and the residual SD is under
either link, so the fixed normal(0, 10) intercept and
half-normal(0, 2.5) residual-SD defaults were informative for an outcome
such as a 0 to 100 score or a blood pressure in mmHg. They pulled each
intercept toward zero, the comparator’s (resting on one aggregate mean)
the most, which moved the mean difference, and they understated the
residual SD, which narrowed the intervals. With sd(y) the
IPD outcome SD, the defaults are now normal(0, 10 * sd(y))
for the intercepts and normal(0, 2.5 * sd(y)) for the
coefficients (identity link), and a half-normal with scale
2.5 * sd(y) for the residual SD (either link);
autoscale = TRUE multiplies a coefficient’s scale by
sd(y) as well as dividing it by sd(x) under
the identity link. Priors written out in full are used as given.
prior_summary() prints the scales the model used, and
prior_sensitivity() sweeps a default or autoscaled
prior_beta in the same outcome-SD units. Refit
normal-family analyses that relied on the defaults or on
autoscale.prior_normal(autoscale = TRUE) rescales the prior
location as well as the scale, so a nonzero prior mean is on the
covariate’s own scale.prior_sensitivity() varies the prior and
nothing else: every model-defining setting is replayed from the fit and
... may not override it. Relaxed fits sweep the comparator
prior alongside the index one
(prior_beta_comparator_scales, reported in
scale_comparator), survival rows carry effect
and at_time, and a refit that cannot replay a sampler
argument the original fit used (such as thin or
init) warns and names it.prior_sensitivity() quantile columns are
named q2.5, q50, q97.5, matching
marginal_effects(), rather than q2 and
q98. Duplicate probs are refused.prior_sensitivity() no longer claims a
scale sweep proves the inference is data-driven; its interpretation text
points at check_identification().prior_summary() names constrained priors
correctly: a truncated normal or t with a nonzero location is not a
half-normal or half-t, and an exponential is not truncated at all.naive() and
stc()stc() no longer reports an index-population
contrast. That estimate assumed a constant link-scale effect, which
population adjustment exists to avoid. stc() returns the
comparator-population estimand only; use mlumr() when the
index population is the target.stc() under a log link
reports the log mean ratio in $estimate and the mean
difference in $md, $md_se,
$md_lower, $md_upper. Under the identity link
the two coincide.stc() refuses a binomial outcome model with
complete separation and, when detectseparation is
installed, tests exactly for quasi-complete separation; the result
records a separation status. A Poisson model with no events
is refused the same way. See ?stc.naive(), and the observed comparator proportion in a
binomial stc(), use exact Clopper-Pearson and Garwood
intervals instead of Wald intervals, which excluded the truth at zero
counts. Contrasts remain Wald.naive() combines several aggregate rows as strata;
the comparator standard error is that of the size-weighted mean of the
row proportions.naive() and stc() apply a continuity
correction only to an observed proportion of 0 or 1 instead of clamping
every proportion, which slightly changes the reported effect for arms
with no events or no non-events.mlumr() gains model-defining arguments ahead
of chains, iter and the other sampler
controls. Pass sampler settings by name.mlumr() centers covariates by default
(center = TRUE), which removes the intercept-versus-slope
collinearity that pushed the sampler into deep trajectories on raw-scale
covariates. Reported contrasts are unchanged;
prior_intercept then applies at the pooled covariate mean.
qr = TRUE offers a QR-rotated design instead.fit$summary$se_mean is
the Monte Carlo standard error of the posterior mean from
posterior::mcse_mean(). It was the posterior SD over the
square root of the bulk ESS, which is computed on rank-normalized draws
and misstates the error for skewed quantities such as a ratio.mlumr() refuses a normal fit whose outcome is
constant or reproduced exactly by its covariates, where the posterior
for the residual SD is improper, and warns when the design is
saturated.safe_logit() and
safe_divide() clamps are gone, so ratios with a near-zero
comparator are no longer understated and lor_* is finite
where it used to hit the clamp. A ratio beyond double precision is
Inf. See ?mlumr-numerical-evaluation.predict(type = "link") returns the marginal
link g(E[g^-1(eta)]) rather than the mean linear predictor
E[eta]; the two agree for the identity link only. This
differs from multinma on purpose, since every effect mlumr
reports is population-standardized.seed = NULL uses the documented default of
2026 with a warning instead of drawing an unrecorded seed from the
session RNG.verbose = FALSE silences the cmdstanr
sampler banner as well.control list is merged with the
backend’s instead of failing argument matching.checkmate on a temporary path.#include, the CmdStan version and its build flags; a
changed include no longer reuses a stale executable. Expect one
recompile after upgrading.check_diagnostics() and the fit summary no longer
drop an infinite Rhat before taking the maximum, report missing or
non-numeric diagnostics as unknown rather than as zero, and compute tail
ESS.predict(),
marginal_effects(), conditional_effects() and
conditional_predict() warn once per call when
NA or NaN draws were dropped from a
summary.conditional_predict() names quantile columns from
the requested probabilities, so non-round probs no longer
return NA.calculate_loo() refuses
moment_match = TRUE, which loo ignores for a
matrix.compare_models() with "loo" or
"waic" refuses fits whose stored outcomes differ.
loo_compare() pairs the pointwise scores by position, so
the same data fitted in another row order gave a wrong
se_diff. The calculate_loo() and
calculate_waic() results carry the outcomes as
loo’s yhash, so
loo::loo_compare() warns on the same mismatch.compare_models() printout no longer
presents se_diff > 2 as a decision rule.psoriasis_ipd/psoriasis_agd (binary),
shoulder_ipd/shoulder_agd (continuous),
caries_ipd/caries_agd (count) and
ndmm_ipd/ndmm_agd/ndmm_agd_covs
(survival). Provenance and known quirks are on each help page;
data-raw/prepare_multinma_subsets.R rebuilds them.introduction, data-preparation,
binary-outcomes, continuous-outcomes,
count-outcomes, survival-outcomes,
subgroup-identification,
fitting-and-diagnostics, choosing-a-method),
precompiled through R.rsp so no Stan model runs at check
time.?set_agd states what an aggregate Poisson
row assumes about exposure, and the shoulder and
caries help pages describe their reference comparison as an
estimate rather than a known truth.vignette("count-outcomes") explains why its SPFA
rate ratio is the same in both populations and at every covariate
profile (a directly transportable effect), and the README states that
the marginal hazard ratio varies over time even when both studies share
one baseline shape.splines2 and survival added to Imports;
ggplot2 moved from Suggests to Imports
(>= 3.4.0).flexsurv, detectseparation,
ggsurvfit and R.rsp added to Suggests.copula is no longer imported: the Gaussian-copula
integration points are built from the Cholesky factor in base R.Additional_repositories is pinned to
https://mc-stan.org/r-packages so that rstan
and StanHeaders resolve from one source. cmdstanr itself
comes from https://stan-dev.r-universe.dev;
mlumr_engine("cmdstanr") offers to install it from
there.Initial CRAN release.
mlumr_engine() or the engine argument.set_ipd(), set_agd(),
combine_data() and add_integration() (Sobol
quasi-Monte Carlo points with a Gaussian copula), mirroring the
multinma interface.prior_normal(),
prior_student_t(), prior_cauchy() and
prior_exponential(), per-coefficient priors,
autoscale, prior_summary() and
prior_sensitivity().predict(), marginal_effects(),
conditional_effects() and
conditional_predict().calculate_dic(), calculate_loo(),
calculate_waic() and compare_models().check_diagnostics() and
check_integration().stc() (parametric G-computation)
and naive().These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.