
\name{NEWS}
\title{NEWS file for the tram package}

\section{Changes in Version 1.4-4 (2026-07-10)}{
  \itemize{
    \item{More robust handling of variable names in \code{perm_test.mmlt}.}
    \item{Update \code{structure} calls.}
  }
}

\section{Changes in Version 1.4-3 (2026-06-05)}{
  \itemize{
    \item{Update \code{inst} subdir.}
  }
}

\section{Changes in Version 1.4-2 (2026-05-06)}{
  \itemize{
    \item{New \code{perm_test.mmlt}.}
    \item{Update demo reference output.}
  }
}

\section{Changes in Version 1.4-1 (2026-03-06)}{
  \itemize{
    \item{Update to \pkg{mlt} 1.7-4.}
    \item{Update reference output.}
  }
}


\section{Changes in Version 1.4-0 (2026-02-25)}{
  \itemize{
    \item{All references in \code{inst/REFERENCES.bib}.}
  }
}

\section{Changes in Version 1.3-2 (2025-12-15)}{
  \itemize{
    \item{Update \code{Mmlt} simulation code.}
  }
}


\section{Changes in Version 1.3-1 (2025-12-02)}{
  \itemize{
    \item{Update \code{survtram} vignette.}
    \item{Update \code{mtram} vignette.}
  }
}


\section{Changes in Version 1.3-0 (2025-11-18)}{
  \itemize{
    \item{Adapt to \pkg{mlt} 1.7-0 changes.}
    \item{Avoid tedious data-driven determination of the support of polynomials in
          Bernstein form by applying a pre-transformation inspired by 
          nonparametric estimates of the unconditional response
          distribution. Parameters of the transformation polynomial
          in Bernstein form are now estimated from input data which
          is symmetric on the support defined by the range of the response
          observations. This, specifying \code{support}, \code{prob}, or
          \code{log_first} in calls to models should be no longer necessary.
          The old behaviour is still available.}
    \item{Improve computations defining the support of polynomials in
          Bernstein form (especially for interval-censored data using
          the fast Turnbull estimator from package \code{icenReg}).}
    \item{Bring back reference output.}
    \item{Explain \code{na.action = na.pass} behaviour in \code{tram} manual page.}
  }
}

\section{Changes in Version 1.2-4 (2025-09-23)}{
  \itemize{
    \item{\code{summary.tram} now works for univariate models.}
    \item{New \code{survtram} vignette.}
    \item{Ship without reference output allowing a more
          substantial \pkg{mlt} update soon.} 
  }
}

\section{Changes in Version 1.2-3 (2025-06-17)}{
  \itemize{
    \item{Update to \pkg{mlt} 1.6-6.}
    \item{New vignette instroducing nonparanormal marginal adjusted
          inference (\code{NAMI}) as an application of \code{Mmlt}.}
  }
}


\section{Changes in Version 1.2-2 (2025-05-09)}{
  \itemize{
    \item{Update \code{survtram} demo.}
    \item{Avoid partial argument matches.}
    \item{\code{rep} to \code{rep_len}.}
  }
}

\section{Changes in Version 1.2-1 (2025-02-25)}{
  \itemize{
    \item{Make \code{model.matrix} more flexible for \code{tram} objects.}
    \item{New doubly robust score test added as \code{robust_score_test}.}
    \item{Add \code{fit} argument to \code{Compris}.}
    \item{Fix broken bib file.}
    \item{Don't refit instable mixed models for toe nail data in vignette.}
  }
}


\section{Changes in Version 1.2-0 (2024-11-18)}{
  \itemize{
    \item{Adding scores for discrete \code{mtram} models.}
    \item{Update \code{mtram} to internal interface changes.}
    \item{Use \code{mltoptim} also in \code{mtram}.}
    \item{Ship proper \code{mtram} vignette (so far only the rendered output
          was supplied).}
    \item{Make sure demos are in shape (again).}
  }
}

\section{Changes in Version 1.1-2 (2024-10-02)}{
  \itemize{
    \item{Gradient check failed on Fedora noLD.}
  }
}

\section{Changes in Version 1.1-1 (2024-09-27)}{
  \itemize{
    \item{Gradient check failed on MacOS.}
  }
}

\section{Changes in Version 1.1-0 (2024-09-24)}{
  \itemize{
    \item{\code{mmlt} moved to \pkg{mlt} 1.6-0.}
    \item{New \code{Mmlt} allowing arbitrary mixes of continuous
          and discrete data, including exact and censored observations
          for the same variable; implementing three (potentially) convex
          approximations; allowing for non-informative missings encoded as
          \code{-Inf, Inf}.}
    \item{\code{Compris} now also uses the parametric likelihood for
          the competing risk case.}
    \item{Allow density predictions for all continuous variables (regardless
          of censoring in training data).}
  }
}

\section{Changes in Version 1.0-5 (2024-08-17)}{
  \itemize{
    \item{Add example for \code{Compris}.}
    \item{Correct \code{simulate.mmlt}.}
    \item{Change to \code{R\_Calloc} and friends.}
  }
}


\section{Changes in Version 1.0-4 (2024-05-13)}{
  \itemize{
    \item{Allow larger then needed \code{args$w} argument in \code{mmlt}.}
    \item{Fix bug in \code{predict.mmlt}.}
  }
}

\section{Changes in Version 1.0-3 (2024-04-15)}{
  \itemize{
    \item{Add sequential fits to \code{mmlt}.}
    \item{Add \code{fixed = TRUE/FALSE} argument to \code{coef.mmlt}
          such that the whole parameter vector can be retrieved.}
    \item{Handle constraints for fixed parameters in \code{mmlt} correctly (as \code{mlt}
          always did).}
    \item{\code{tram} and \code{Polr} allow binary responses (and return
          results identical to \code{glm} with appropriate \code{family}).}
  }
}

\section{Changes in Version 1.0-2 (2024-01-30)}{
  \itemize{
    \item{New \code{demo("survtram")} and \code{demo("hcc")}.}
    \item{\code{predict} methods for \code{tram} and \code{stram} 
          now offer the same \code{type} argument as 
          \code{mlt::predict.ctm} offers.}
  }
}

\section{Changes in Version 1.0-1 (2023-12-18)}{
  \itemize{
    \item{Allow shift-scale transformation models in \code{mmlt}.}
    \item{Add nonparametric log-likelihood to \code{Compris}.}
  }
}

\section{Changes in Version 1.0-0 (2023-08-25)}{
  \itemize{
    \item{Improved, simplified, and generalised implementation of \code{mmlt}.}
    \item{\code{Coxph}, \code{Colr}, and \code{BoxCox} allow unbiased
          estimation of time-to-event distributions under dependent
          censoring.}
    \item{All \code{tram} models can be equipped with frailty terms.}
    \item{Fix some minor issues.}
  }
}

\section{Changes in Version 0.8-2 (2023-03-28)}{
  \itemize{
    \item{Update demo \code{stram}.}
  }
}

\section{Changes in Version 0.8-1 (2023-03-09)}{
  \itemize{
    \item{Add \code{simulate.mmlt}.}
    \item{\code{Survreg} didn't work with constraints, reported by Lucas Kook.}
    \item{\code{mtram} didn't deal properly with interval censoring in all cases.}
    \item{Enable stratification for shift-scale transformation models (still experimental).}
    \item{Fix S3 argument issues.}
    \item{Try to detect negative SEs.}
  }
}

\section{Changes in Version 0.8-0 (2022-11-02)}{
  \itemize{
    \item{Stabilise and generalise \code{mmlt}: Alternative link functions, 
          separate lower triangular matrix storage and computations from
          \code{mmlt}.}
    \item{\code{coef(<mmlt>, type = "Sigma")} and \code{coef(<mmlt>, type = "Corr")}
          were incorrect for more than three dimensions.}
    \item{Improved numerical stability in \code{mtram}.}
  }
}

\section{Changes in Version 0.7-2 (2022-08-05)}{
  \itemize{
    \item{New location-scale functionality, see \code{demo("stram")}.}
    \item{New Laplace link function.}
    \item{New cauchit link function.}
  }
}


\section{Changes in Version 0.7-1 (2022-05-18)}{
  \itemize{
    \item{Minor bug fixed for shift-scale transformation models (still experimental).}
    \item{\code{bread.tram} added for \code{sandwich} to work.}
    \item{Update \code{mtram} vignette; move code to demo.}
  }
}


\section{Changes in Version 0.7-0 (2022-04-01)}{
  \itemize{
    \item{Add shift-scale transformation models (experimental).}
    \item{Add methods for probabilistic indices and overlap coefficients + friends.}
    \item{Export \code{Gradient} and \code{Hessian} methods.}
    \item{Simplify \code{score_test} and \code{profile}: Use \code{fixed}
          instead of \code{offset}.}
    \item{Models with standardisation now available in \code{mtram} for exact
          continuous outcomes and link functions other than probit.}
  }
}

\section{Changes in Version 0.6-4 (2022-01-14)}{
  \itemize{
    \item{Remove arguments ignored by \code{mlt}.}
    \item{Move mtram vignette code to demo as it took too long 
          on Windows for CRAN.}
  }
}

\section{Changes in Version 0.6-3 (2022-01-04)}{
  \itemize{
    \item{Deal with stratum - covariate interactions,
          overparameterised coefficients are constraint to zero.}
  }
}

\section{Changes in Version 0.6-2 (2021-10-19)}{
  \itemize{
    \item{Make sure to use the Schur complement when computing
          variances in for linear transformation models in 
          \code{score_test} and \code{perm_test}.}
    \item{Fix LaTeX problems.}
  }
}

\section{Changes in Version 0.6-1 (2021-09-16)}{
  \itemize{
    \item{Add \code{dofit} argument to \code{mmlt}.}
    \item{Robustify \code{vcov} for \code{mmlt} objects.}
    \item{Add experimental \code{score_test} and \code{perm_test} methods
          for \code{glm}.}
  }
}


\section{Changes in Version 0.6-0 (2021-03-08)}{
  \itemize{
    \item{Add \code{simulate} method.}
    \item{Enable nonparametric likelihood estimation by \code{Polr}.}
    \item{New argument \code{sparse_nlevels} to \code{tram}, requesting
          a model \code{Matrix} for ordered factors with at least
          \code{sparse_nlevels} levels.}
  }
}


\section{Changes in Version 0.5-2 (2020-10-23)}{
  \itemize{
    \item{Add experimental \code{score_test} and \code{perm_test} for
          \code{survival::coxph}.}
    \item{Update simulation code.}
  }
}


\section{Changes in Version 0.5-1 (2020-09-03)}{
  \itemize{
    \item{Robustify computation of score intervals.}
    \item{Add Spearman correlation to \code{mmlt} example.}
  }
}

\section{Changes in Version 0.5-0 (2020-08-27)}{
  \itemize{
    \item{\code{Lehmann()} parameter is now labelled as proportional reverse time hazard ratio.}
    \item{Add \code{mmlt} for multivariate conditional transformation models
          (continuous responses only for now).}
    \item{Reproducibility material for <arxiv:1906.03151> added to package.}
  }
}


\section{Changes in Version 0.4-0 (2020-05-11)}{
  \itemize{
    \item{Force support to start at time zero and constrain cumulative
          hazard to zero for time zero in \code{Aareg}.}
  }
}


\section{Changes in Version 0.4-0 (2020-05-11)}{
  \itemize{
    \item{Add \code{Aareg} for Aalen additive hazard models.}
  }
}


\section{Changes in Version 0.3-3 (2020-01-16)}{
  \itemize{
    \item{\code{score_test} generic and method added for computing 
          score tests and corresponding confidence intervals.}
    \item{\code{perm_test} generic and method added for computing 
          permutation score tests.}
    \item{\code{PI} converts log-odds ratios to probabilistic indices and 
          vice versa.}
  }
}


\section{Changes in Version 0.3-2 (2020-01-08)}{
  \itemize{
    \item{\code{profile} method added for computing 
          profile likelihood confidence intervals.}
    \item{Allow additional linear inequality constraints for regression
          coefficients.}
  }
}

\section{Changes in Version 0.3-1 (2019-11-05)}{
  \subsection{Bugfixes}{
    \itemize{
      \item{Fix problem in C header file.}
      \item{Fix problems with responses of class \code{R}, spotted by Balint Tamasi.}
    }
  }
}

\section{Changes in Version 0.3-2 (2019-12-02)}{
  \itemize{
    \item{Add new demo.}
  }
  \subsection{Bugfixes}{
    \itemize{
      \item{Deal with \code{model_only} in \code{Survreg}, spotted by Balint Tamasi.}
    }
  }
}


\section{Changes in Version 0.3-0 (2019-10-09)}{
  \subsection{Bugfixes}{
    \itemize{
      \item{\code{y | s1:s2 ~ x} lead to rank-deficit models, the intercept is
            now removed.}
      \item{Not really a bug, but time-consuming examples were removed
            (or replaced by static output) in package vignettes to make
            CRAN happy.}
      \item{\code{as.mlt} returned an object of class \code{mlt} but not
            \code{mlt_fit}.}
    }
  }
  \subsection{New Features}{
    \itemize{
      \item{New marginally interpretable models for clustered data
            in \code{mtram}, see \code{mtram} vignette. This is still
            experimental and very rough, so please be careful.}
      \item{Compute \code{vcov.tram} via Schur complement when possible.}
  }
  }
}

\section{Changes in Version 0.2-6 (2019-06-20)}{
  \itemize{
    \item{Add regression test for count data and \code{log_first = TRUE}.}
  }
}


\section{Changes in Version 0.2-5 (2019-02-25)}{
  \itemize{
    \item{\code{tram} objects are now in line with \code{multcomp::glht},
          allowing post-hoc multiple comparisons.}
  }
}

\section{Changes in Version 0.2-4 (2019-01-22)}{
  \itemize{
    \item{\code{log_first = TRUE} is now accepted by \code{tram} and all 
          model functions calling \code{tram}. This is still experimental.}
    \item{Silence regression tests on Windows.}
  }
}


\section{Changes in Version 0.2-3 (2018-09-17)}{
  \itemize{
    \item{New \code{extrapolate = TRUE} option for all models constraints
          the second derivate of the Bernstein transformation function to be
          zero at \code{support}. This helps to get rid of possible
          discontinuous densities at \code{support}.}
    \item{Add \code{Lehmann} for fitting shift transformation models those
          linear predictor can be interpreted as log-Lehmann-alternative.}
    \item{Add \code{method = "loglog"} to \code{Polr}.}
    \item{New \code{update} method.}
  }
}

\section{Changes in Version 0.2-2 (2018-06-22)}{
  \itemize{
    \item{Use default \code{bounds = c(0, Inf)} for \code{Surv} objects (for example
          in \code{Coxph}.}
    \item{Update to \pkg{mlt} 1.0-2.}
  }
}


\section{Changes in Version 0.2-1 (2018-04-20)}{
  \itemize{
    \item{Likelihood ratio tests with fixed parameters gave an error.}
    \item{Remove strata from linear predictor (experimental).}
    \item{Try to implement a better guess for the \code{add} argument
          later defining the axes corresponding to the response
          in plots.}
    \item{All models accept \code{add} and \code{bounds} arguments.}
  }
}

\section{Changes in Version 0.2-0 (2018-02-25)}{
  \itemize{
    \item{\pkg{tram} first published on CRAN.}
  }
}
