wnpmle 0.1.3
- The censoring-corrected sandwich variance
(
se = "sandwich_adj", the default) now follows the formula
in Bellach and Kosorok (2026, Appendix B.3) exactly. Two coding issues
in the correction term were fixed: the correction is now subtracted from
the subject-wise scores (which are on the negative log-likelihood
scale), and two internal matrices are now filled in the right order. In
the settings checked, the effect on the standard errors was in the
fourth decimal place or smaller.
- Subject-wise scores and the censoring correction are now computed
with TMB (new templates in
inst/tmb/), which makes
se = "sandwich" and se = "sandwich_adj" much
faster for larger data sets.
- Compiled TMB templates are now kept between R sessions (in
tools::R_user_dir("wnpmle", "cache")), so they are compiled
only once per installed version instead of once per session. A different
folder can be set with options(wnpmle.cache_dir = ...) or
the environment variable WNPMLE_CACHE_DIR, e.g. to share
one compiled copy between cluster jobs.
- The meat of the sandwich is computed with
crossprod(),
which uses much less memory.
- New example data
readmission_prep(): hospital
readmissions of 403 colorectal cancer patients with death as terminal
event (Gonzalez et al., 2005; copy of the readmission data
from frailtypack). The vignette now uses these data as its main example,
including model selection with plot_loglik(). The bladder
quick start now compares the Ghosh-Lin fit with the estimates reported
by Ghosh and Lin (2002).
predict() now handles factor covariates (same coding as
in the fit), and uses the correct limit log(1 + x) for the
Box-Cox model at rho = 0.summary() now returns an object that is printed once
(before, printing the result of summary() showed the
coefficients twice).plot_loglik(): wider default PDF (width,
height arguments), titles no longer overlap, and the points
rho = 1 and r = 1 are labelled.- Documentation:
"sandwich_adj" is listed as the default
for se; references now cite the arXiv preprint of Bellach
and Kosorok (2026) with its DOI, and DOIs were added to all references
where available.
wnpmle 0.1.2