Updated MPM output in coef.BayesSurvive()

DESCRIPTION

@@ -1,8 +1,9 @@
 Package: BayesSurvive
 Title: Bayesian Survival Models for High-Dimensional Data
-Version: 0.0.3
-Date: 2024-06-05
+Version: 0.0.4
+Date: 2024-07-10
 Authors@R: c(person("Zhi", "Zhao", role=c("aut","cre"), email = "[email protected]"),
+             person("Waldir", "Leoncio", role=c("aut")),
              person("Katrin", "Madjar", role=c("aut")),
              person("Tobias", "Østmo Hermansen", role=c("aut")),
              person("Manuela", "Zucknick", role=c("ctb")),
@@ -15,19 +16,17 @@ VignetteBuilder: knitr
 Depends: R (>= 4.0)
 Encoding: UTF-8
 RoxygenNote: 7.3.1
-LinkingTo: Rcpp, RcppArmadillo (>= 0.9.000)
+LinkingTo: Rcpp, RcppArmadillo, testthat
 Imports: Rcpp, ggplot2, GGally, mvtnorm, survival, riskRegression,
         utils, stats
-Suggests: 
-    knitr,
-    testthat (>= 3.0.0)
+Suggests: knitr, testthat
 LazyData: true
 NeedsCompilation: yes
-Packaged: 2024-06-05 07:00:29 UTC; zhiz
+Packaged: 2024-07-10 08:34:27 UTC; zhiz
 Author: Zhi Zhao [aut, cre],
+  Waldir Leoncio [aut],
   Katrin Madjar [aut],
   Tobias Østmo Hermansen [aut],
   Manuela Zucknick [ctb],
   Jörg Rahnenführer [ctb]
 Maintainer: Zhi Zhao <[email protected]>
-Config/testthat/edition: 3

NEWS.md

@@ -1,3 +1,8 @@
+# BayesSurvive 0.0.4
+
+* Add units tests
+* Rename the output of MPM coefficients in function `coef.BayesSurvive()`
+
 # BayesSurvive 0.0.3
 
 * Add IPA in function `predict.BayesSurvive()`

R/BayesSurvive-package.R

@@ -8,3 +8,13 @@
 #' @useDynLib BayesSurvive, .registration = TRUE
 ## usethis namespace: end
 NULL
+
+## nocov start
+
+.onLoad <- function(libname, pkgname) {
+  # CRAN OMP THREAD LIMIT
+  Sys.setenv("OMP_THREAD_LIMIT" = 1)
+
+}
+
+## nocov end

R/coef.BayesSurvive.R

@@ -119,11 +119,10 @@ coef.BayesSurvive <- function(object, MPM = FALSE, type = "mean", CI = 95,
     }
     tbl <- data.frame(
       term = x_names,
-      beta_MPM = object$output$beta.margin,
-      gamma = object$output$gamma.margin
+      estimate = object$output$beta.margin
     )
-    tbl$estimate <- (object$output$gamma.margin >= 0.5) *
-      object$output$beta.margin / object$output$gamma.margin
+    tbl$estimate <- tbl$estimate / object$output$gamma.margin * 
+      (object$output$gamma.margin >= 0.5)
     tbl$estimate[is.na(tbl$estimate)] <- 0
   }
 

R/func_MCMC.R

@@ -155,10 +155,8 @@ func_MCMC <- function(survObj, hyperpar, initial,
   # MCMC sampling
 
   # Initializes the progress bar
-  if (verbose) {
-    cat("  Running MCMC iterations ...\n")
-    pb <- txtProgressBar(min = 0, max = nIter, style = 3, width = 50, char = "=")
-  }
+  if (verbose) cat("  Running MCMC iterations ...\n")
+  pb <- txtProgressBar(min = 0, max = nIter, style = 3, width = 50, char = "=")
 
   for (M in 1:nIter) {
     # if (method %in% c("CoxBVSSL", "Sub-struct") ||
@@ -285,9 +283,9 @@ func_MCMC <- function(survObj, hyperpar, initial,
     # }
 
     # Sets the progress bar to the current state
-    if (verbose) setTxtProgressBar(pb, M)
+    setTxtProgressBar(pb, M)
   } # the end of MCMC sampling
-  if (verbose) close(pb) # Close the connection of progress bar
+  close(pb) # Close the connection of progress bar
 
   if (S == 1 && MRF_G) {
     mcmcOutcome$gamma.margin <- mcmcOutcome$gamma.margin / (nIter - burnin)