This is a major release: the partial linear single index model family
gains three new fitting functions with automatic smoothness selection,
and several correctness bugs in the original fitting/plotting functions
are fixed. plsi.lr.auto() is now the recommended starting
point for continuous outcomes; plsi.lr.v2() remains
available for manual control over the link function’s degrees of freedom
(e.g. for simulation studies or when the right basis complexity is
already known).
plsi.lr.auto(): fits the partial linear single
index model for a continuous outcome with automatic smoothness selection
via mgcv::gam() (REML), removing the need to hand-tune
spline.num/degrees of freedom. Only an upper-bound basis
dimension k is required.plsi.logistic.auto(): binary-outcome (logistic)
analog of plsi.lr.auto(), using a binomial()
family GAM with the same automatic smoothness selection.plsi.log.auto(): count-outcome analog of
plsi.lr.auto(), supporting Poisson and negative binomial
(family = "nb", the default, recommended for real
overdispersed count data) families with a log link.*.auto() fitting functions report Wald-based
standard errors, confidence intervals, and effect-size summaries (odds
ratios for plsi.logistic.auto(), rate ratios for
plsi.log.auto()) for both the single-index coefficients and
the confounder coefficients.type
argument ("linear", "logistic",
"log") matching the fitting function used:
si.fun.plot(), si.coef.plot(),
e.main.plot(), e.interaction.plot(),
interquartile.quartile.plot(),
mixture.overall.plot().plsi.lr.v1() is superseded by
plsi.lr.v2(), which fixes all bugs listed below and adds a
seed argument for reproducibility. Existing code using
plsi.lr.v1() should switch to plsi.lr.v2() or,
preferably, plsi.lr.auto().t(beta_est) inside
cbind()) that produced incorrect matrix dimensions and
crashed the function whenever more than one exposure variable was used.
This was present in plsi.lr.v1() and is fixed in its
replacement, plsi.lr.v2().initial.random.num = 0 producing an invalid index
sequence in plsi.lr.v2() (the *.auto()
functions instead validate this input directly and raise an informative
error).as.numeric() coercion on
logLik() output in plsi.lr.v2().plsi.lr.v2()’s returned list element
names (intial.table -> initial.table,
all.intial.results ->
all.initial.results).e.interaction.plot() conditioning on the wrong
exposure’s quantiles in its second panel (a copy-paste bug meant both
panels were secretly conditioning on the same exposure’s quantiles
instead of each on the other’s).e.main.plot()
(out_value was referenced but never computed).ciTools::add_ci() calls across the
plotting functions with direct predict.gam(se.fit = TRUE)
calls, since ciTools does not support
mgcv::gam model objects (this previously caused errors such
as object 'AGE.c' not found when predicting from a
single-index value alone).plsi.lr.v2()’s si.fun output using
ciTools’s default pred column name instead of
fit, which caused si.fun.plot(type = "linear")
to fail on plsi.lr.v2() output despite being documented to
support it. si.fun now consistently uses
fit/lwr/upr across
plsi.lr.v2() and all three *.auto()
functions.plsi.logistic.auto()/plsi.log.auto()
collapsing to near-zero (~1e-16) due to residualizing against the full
model’s own fitted values rather than the actual observed outcome; the
confounder-free prediction model is now fit against real observed data
via a fixed offset, preserving genuine sampling variability.NaN when the numerically-differentiated information
matrix is not positive definite at the selected optimum;
negative/near-zero eigenvalues are now floored before inversion,
yielding conservative (rather than missing) standard errors, with a
warning noting when this occurs.@importFrom declarations (mgcv
functions were incorrectly listed under
@importFrom stats).\describe{}/\item{}{}) with
underscore-containing identifiers inside roxygen2’s markdown-mode
processing; @return documentation now uses markdown-native
syntax.stats, graphics, and
utils to Imports in DESCRIPTION.
These base packages are used extensively via :: throughout
the fitting and plotting functions but were previously undeclared, which
would have surfaced as an R CMD check NOTE/WARNING on the
next CRAN submission.plsi.lr.v2(), plsi.lr.auto(),
plsi.logistic.auto(), plsi.log.auto(), and all
six plotting functions.
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