version 2.0.6

cran · Mar 22, 2024 · c0f78f8 · c0f78f8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: psbcSpeedUp
 Title: Penalized Semiparametric Bayesian Cox Models
-Version: 2.0.5
-Date: 2023-12-08
+Version: 2.0.6
+Date: 2024-03-21
 URL: https://github.com/ocbe-uio/psbcSpeedUp
 BugReports: https://github.com/ocbe-uio/psbcSpeedUp/issues
 Authors@R: c(person("Zhi", "Zhao", role=c("aut","cre"), email = "zhi.zhao@medisin.uio.no"), 
@@ -23,11 +23,11 @@ Imports: Rcpp, xml2, ggplot2, GGally, MASS, survival, riskRegression,
 Suggests: knitr
 LazyData: true
 NeedsCompilation: yes
-Packaged: 2023-12-08 13:29:37 UTC; zhiz
+Packaged: 2024-03-21 17:28:53 UTC; zhiz
 Author: Zhi Zhao [aut, cre],
   Manuela Zucknick [aut],
   Maral Saadati [aut],
   Axel Benner [aut]
 Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
 Repository: CRAN
-Date/Publication: 2023-12-08 14:00:02 UTC
+Date/Publication: 2024-03-21 18:00:02 UTC
diff --git a/MD5 b/MD5
@@ -1,12 +1,12 @@
-2100e91bb0b3d40e8dab72338c31364e *DESCRIPTION
+2b9e3c3c821628b9812138e3d364e7e9 *DESCRIPTION
 528177306a09bb4b73a2d277e4774f41 *NAMESPACE
-589656534e41b8049f499f8588b24cb7 *NEWS.md
+9bfa0eb7cc347e4c7ad8b6ed6da29531 *NEWS.md
 7ae1823500df61c6e97cd9c55c9887ee *R/RcppExports.R
 e72d4c8e2051f1c3b28f183877177cfa *R/coef.psbcSpeedUp.R
 c0dd2e03b926a0d3c5ee44898121cfbe *R/exampleData.R
 705a0e2e69bd51f57ba3946767b27d3e *R/plot.psbcSpeedUp.R
 2d4e430e28f76e8f8ecf4e559f4e27ba *R/plotBrier.R
-ad667492d82cfeb09de126ff0ef00df9 *R/predict.psbcSpeedUp.R
+a54afc778da9a74f4d758e25df637651 *R/predict.psbcSpeedUp.R
 0f897c98dfb5e258207f57b477748efc *R/psbcSpeedUp.R
 bb43106f8e2b174e93d6b5be3258e87c *README.md
 f5f1417afaaf64682000372990355e1c *build/vignette.rds
@@ -17,14 +17,14 @@ f91c2ee39ced0e6e91f98b81e9344f11 *data/datalist
 7b548c9bd6a373f888b1abd5f788be24 *data/exampleData.rda
 8f9e9b60cc3d91d8587aac05992e1578 *inst/doc/BayesCox.R
 c9b3cf22cbf9c151eff3cd5138214bb3 *inst/doc/BayesCox.Rmd
-c1714fc32357cecdc7b9a25dbd310495 *inst/doc/BayesCox.html
+54c12c2fe73d4521e7daf9861e19cd27 *inst/doc/BayesCox.html
 c71ddfcaa90c21b64cbff740de7f58e1 *man/coef.psbcSpeedUp.Rd
 ceb1aaadfdec68603d5cc77d5f796051 *man/exampleData.Rd
 198b70412d51b344f358c6bdf480f5c7 *man/figures/README_plot_beta.png
 9d60f8c028133fa5c6a3cd284e1e00ed *man/figures/README_plot_brier.png
 335479598736f774954c56b098dfc737 *man/plot.psbcSpeedUp.Rd
 09fec13c66ae23170a78f21c5cf5b2e9 *man/plotBrier.Rd
-26494214e06876cf942b75ecfde81728 *man/predict.psbcSpeedUp.Rd
+3cc3f823166fb8254c9967ccb8da935f *man/predict.psbcSpeedUp.Rd
 7dc417e48efb39b297c96a458967937f *man/psbcSpeedUp.Rd
 2a825488988b01ee93aea8f884fc9070 *src/Makevars.in
 83488be6b1f2f015234720a0a25ff076 *src/Makevars.win
@@ -34,7 +34,7 @@ a4d019b89b1606ffd530751c1e640f63 *src/drive.h
 99fa8dc58ea0ffc37d1e6e5e2e51d378 *src/global.cpp
 05ad67a54a213f89504a68cc7a253f86 *src/global.h
 cc174f5cdd978352648cec44c0919628 *src/init.c
-b3fe30bb06c10bed689613b6c0d7c82c *src/psbc.cpp
+82590cb2ba3d45f9528598a05d5336bf *src/psbc.cpp
 ca15a2e754117b535063fb35585ad1ca *src/psbc.h
 63fb7f837f5ead3567c138071d25469d *src/pugiconfig.h
 2a482565cd695663ed7426f6302af0ae *src/pugixml.cpp

diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,11 @@
 * add R functions for feature (stability) selection
 * extend C++ source code for implementing other shrinkage and group priors
 
+# psbcSpeedUp 2.0.6
+
+* Fixed a bug in function `updateBH_cpp()`
+* Other minor changes
+
 # psbcSpeedUp 2.0.5
 
 * Added R functions for survival predictions, e.g. time-dependent Brier scores, integrated Brier score

diff --git a/R/predict.psbcSpeedUp.R b/R/predict.psbcSpeedUp.R
@@ -19,8 +19,8 @@
 #' @param times time points at which to evaluate the risks. If \code{NULL}
 #' (default), the event/censoring times are used. If \code{type="brier"}, the
 #' largest one of the \code{times} is used
-#' @param type option to chose for predicting survival probabilities
-#' (\code{type="probability"}) and brier scores (\code{type="brier"})
+#' @param type option to chose for predicting survival probabilities (one of
+#' \code{c('hazard','cumhazard','survival')}) or brier scores (\code{type="brier"})
 #' @param method option to use the posterior mean (\code{"mean"}) of coefficients
 #' for prediction or Bayesian model averaging (\code{"BMA"}) for prediction
 #' @param \dots not used

diff --git a/inst/doc/BayesCox.html b/inst/doc/BayesCox.html
@@ -49,7 +49,7 @@
 </style>
 <style type="text/css" data-origin="pandoc">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }

diff --git a/man/predict.psbcSpeedUp.Rd b/man/predict.psbcSpeedUp.Rd
diff --git a/src/psbc.cpp b/src/psbc.cpp
@@ -88,7 +88,7 @@ arma::vec PSBC::updateBH_cpp(arma::mat &ind_r_d_, arma::vec hPriorSh_, arma::vec
     for( unsigned int i=0; i<J_; ++i )
      //h_rate(i) += arma::accu( ind_r_d_.col(i) % arma::exp( xbeta_ ) );
         h_rate(i) += arma::dot( ind_r_d_.col(i), xbeta_ );*/
-    arma::vec h_rate = c0_ + sumMatProdVec(ind_r_d_, exp_xbeta);
+    arma::vec h_rate = c0_ + sumMatProdVec(ind_r_d_, arma::exp( xbeta_ ));
 
     // arma::vec shape = hPriorSh_ + d_;
     arma::vec h_ = arma::zeros<arma::vec>(J_);