EPLSIM 1.0.0

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).

New features

• New 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.
• New plsi.logistic.auto(): binary-outcome (logistic) analog of plsi.lr.auto(), using a binomial() family GAM with the same automatic smoothness selection.
• New 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.
• All three *.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.
• New/updated plotting functions, all supporting a 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().

Deprecated / removed

• plsi.lr.v1() is superseded by plsi.lr.v2(), which fixes all bugs listed below and adds a seed argument for reproducibility.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().

Bug fixes

• Fixed a transposition bug (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().
• Fixed 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).
• Fixed missing as.numeric() coercion on logLik() output in plsi.lr.v2().
• Fixed two typos in plsi.lr.v2()’s returned list element names (intial.table -> initial.table, all.intial.results -> all.initial.results).
• Fixed 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).
• Fixed an undefined-variable bug in e.main.plot() (out_value was referenced but never computed).
• Replaced all 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).
• Fixed 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.
• Fixed standard errors for the single-index coefficients in 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.
• Standard errors for the single-index coefficients no longer silently return 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.

Documentation

• Corrected @importFrom declarations (mgcv functions were incorrectly listed under @importFrom stats).
• Fixed Rd generation corruption caused by mixing raw Rd markup (\describe{}/\item{}{}) with underscore-containing identifiers inside roxygen2’s markdown-mode processing; @return documentation now uses markdown-native syntax.

Internal

• Added 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.
• Expanded the test suite with dedicated test files for plsi.lr.v2(), plsi.lr.auto(), plsi.logistic.auto(), plsi.log.auto(), and all six plotting functions.