2024-07-07 Wenjie Wang <wang@wwenjie.org> * Fixed CRAN warning: "warning: template-id not allowed for constructor in C++20". * Changed package version to 0.4-7. 2023-11-27 Wenjie Wang <wang@wwenjie.org> * Fixed CRAN warning: "GibbsSampler.h:91:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘Size’". * Changed package version to 0.4-6. 2023-08-19 Wenjie Wang <wang@wwenjie.org> * Fixed broken roxygen2 documentation. * Changed package version to 0.4-5. 2023-04-28 Wenjie Wang <wang@wwenjie.org> * Fixed CRAN warning: "a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]". * Changed package version to 0.4-4. 2022-02-15 Wenjie Wang <wang@wwenjie.org> * Fixed `coef` method for `splineCox` * Changed package version to 0.4-3. 2020-09-05 Wenjie Wang <wang@wwenjie.org> * Removed checks of examples to pass CRAN checks on Soloris. * Changed package version to 0.4-2. 2020-08-23 Wenjie Wang <wang@wwenjie.org> * Added function `bayesCoxMcmc` for extracting MCMC samples from a given `bayesCox` object. * Added default `out` in function `bayesCox` to a temporary directory. * Fixed default grid generation for some cases. * Removed argument `cache` from function `survCurve` and `survDiff`. * Removed package dependency reshape, plyr, and utils * Added package dependency data.table and splines2 * Changed package version to 0.4-1. 2019-08-27 Wenjie Wang <wenjie.2.wang@uconn.edu> * Fixed call of `<=` in function `tvTran`. * Changed package version to 0.3-7. 2017-11-14 Wenjie Wang <wenjie.2.wang@uconn.edu> * Added exact event times to the grid. * Fixed the dependency of the whole survival package by importing the survival package and exporting the function `survival::Surv`. * Changed package version to 0.3-6. 2017-01-08 Wenjie Wang <wenjie.2.wang@uconn.edu> * Added adjustment for endpoints of censoring intervals from `grid` specified in the function call of `bayesCox`. * Added compatibility of function `survCurve` to all available models from function `bayesCox`. * Changed package version to 0.3-5. 2016-12-24 Wenjie Wang <wenjie.2.wang@uconn.edu> * Added the generation of `grid` from the data provided, which allow `grid` to be unspecified in the function call of `bayesCox`. * Changed package version to 0.3-4. 2016-10-14 Wenjie Wang <wenjie.2.wang@uconn.edu> * Fixed compilation error in Solaris: "The function `exp` must have a prototype" by replacing `exp` with `std::exp`. * Fixed possibly invalid URL for tooth24.RData. * Changed CRAN URL into the canonical form. * Changed package version to 0.3-3. 2016-08-30 Wenjie Wang <wenjie.2.wang@uconn.edu> * Fixed warning on compilation flags in Makevars: "Non-portable flags in variable 'PKG_CXXFLAGS': -g" by removal of "-g" flag. * Fixed invalid URL for tooth24.RData. * Changed package version to 0.3-2. 2016-07-12 Wenjie Wang <wenjie.2.wang@uconn.edu> * Fixed compiling error from clang v3.9 due to including R headers inside extern "C" by commenting out the extern "C" in rng.h and GibbsSampler.h. * Fixed print function for `bayesCox` object. * Fixed invalid url for tooth dataset. * Added formula and xlevels to `bayesCox` object. * Added optional arguement to `coef.bayesCox`, `coef.tvTran`, and `coef.splineCox` to allow user to specify credible level by matching "..." argument with possible "level" argument. * Added function `survCuvre`, `survDiff`, and `plotSurv` to estimate and plot the survival function, cumulative hazard function, and their pair difference for Bayesian dynamic model with dynamic hazard from posterior sample. Specific examples are added to `bayesCox`. * Added Roxygen2 inline documentation for all exported function. * Added citation for package to /inst. * Removed redundant COPYRIGHT file bundled in source package. It is available online at <http://www.gnu.org/licenses/>. * Changed package version to 0.3-0. * Changed maintainer from Jun Yan to Wenjie Wang. 2014-05-01 Jun Yan <jun.yan@uconn.edu> * Changed the dependence on boost to package BH. 2014-04-10 Jun Yan <jun.yan@uconn.edu> * Fixed compiling error from clang in thg constructor LogDenPar: changed this->N to static_cast<int> (this->N_). * Fixed warnings from clang in arm.c by commenting out the display function. Added random number state control to u_random. 2014-03-04 Jun Yan <jun.yan@uconn.edu> * Fixed the problem that splineCox did not work with a single covariate by adding drop=FALSE in splineCox: DF <- cbind(id=1:N, mf[, 1][, 1:2], mf[, -1, drop=FALSE]) * Changed depends to import in DESCRIPTION and NAMESPACE. However, package survival is kept under "Depends"; otherwise, function Surv was not found in model.matrix. This may need to be fixed later. * Modified example codes to use mydata and myformula instead of data and formula. 2012-03-14 Jun Yan <jun.yan@uconn.edu> * Removed tiCox.h and tiCox.cpp. Functions there are covered by bayesCox. * Cleaned the style of the code under src with astyle -s2. 2012-03-10 Jun Yan <jun.yan@uconn.edu> * Added system dependence on the boost library, which allows removal of the boost headers files from the src directory. The configure.ac file was adapted from that in package RQuantLib; thank Dirk Eddelbuettel <edd@debian.org>. * Removed std:cout lines (Xiaojing Wang). * Replaced exit with return whenever possible. May need more fix later.