From 4066f12912ccaebb16ca081d36eff77e929e26c1 Mon Sep 17 00:00:00 2001
From: Marc Suchard <msuchard@ucla.edu>
Date: Thu, 30 Jun 2022 16:21:20 -0700
Subject: [PATCH] change use of class() to inherits() for R 4.2 language; bump
 version

---
 DESCRIPTION        |  2 +-
 NEWS.md            |  4 +++-
 R/DataManagement.R |  6 +++---
 R/ModelFit.R       |  6 +++---
 cran-comments.md   | 10 ++++++----
 5 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5427b294..f9555bf2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Cyclops
 Type: Package
 Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
-Version: 3.1.2.9999
+Version: 3.2.0
 Authors@R: c(
     person("Marc A.", "Suchard", email = "msuchard@ucla.edu", role = c("aut","cre")),
     person("Martijn J.", "Schuemie", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index f78990b3..ee655c35 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,9 +1,11 @@
-Cyclops v3.1.3
+Cyclops v3.2.0
 
 Changes:
 
 1. fixed likelihood profiling when non-convex due to numerical instability
 2. fixed parsing of 64-bit covariate IDs
+3. fix BLR convergence criterion when there are 0 (survival) events
+3. add Jeffrey's prior for single regression coefficient
 
 Cyclops v3.1.2
 ==============
diff --git a/R/DataManagement.R b/R/DataManagement.R
index 77db9eda..c5b212e5 100644
--- a/R/DataManagement.R
+++ b/R/DataManagement.R
@@ -280,15 +280,15 @@ createCyclopsData <- function(formula, sparseFormula, indicatorFormula, modelTyp
             }
             time <- time[sortOrder]
             dx <- dx[sortOrder, ]
-            if (class(dx) == "numeric") {
+            if (inherits(dx,"numeric")) {
                 dx = as(dx,"dgeMatrix")
             }
             sx <- sx[sortOrder, ]
-            if (class(sx) == "numeric") {
+            if (inherits(sx, "numeric")) {
                 sx = Matrix(sx, ncol = 1, sparse = TRUE)
             }
             ix <- ix[sortOrder, ]
-            if (class(ix) == "numeric") {
+            if (inherits(ix, "numeric")) {
                 ix = Matrix(ix, ncol = 1, sparse = TRUE)
             }
         }
diff --git a/R/ModelFit.R b/R/ModelFit.R
index 62d393d2..ae71ec9d 100644
--- a/R/ModelFit.R
+++ b/R/ModelFit.R
@@ -355,7 +355,7 @@ fitCyclopsModel <- function(cyclopsData,
 
 .checkData <- function(x) {
     # Check conditions
-    if (missing(x) || is.null(x$cyclopsDataPtr) || class(x$cyclopsDataPtr) != "externalptr") {
+    if (missing(x) || is.null(x$cyclopsDataPtr) || !inherits(x$cyclopsDataPtr, "externalptr")) {
         stop("Improperly constructed cyclopsData object")
     }
     if (.isRcppPtrNull(x$cyclopsDataPtr)) {
@@ -366,7 +366,7 @@ fitCyclopsModel <- function(cyclopsData,
 .checkInterface <- function(x, computeDevice = "native", forceNewObject = FALSE, testOnly = FALSE) {
     if (forceNewObject
         || is.null(x$cyclopsInterfacePtr)
-        || class(x$cyclopsInterfacePtr) != "externalptr"
+        || !inherits(x$cyclopsInterfacePtr, "externalptr")
         || .isRcppPtrNull(x$cyclopsInterfacePtr)
         || .cyclopsGetComputeDevice(x$cyclopsInterfacePtr) != computeDevice
     ) {
@@ -434,7 +434,7 @@ coef.cyclopsFit <- function(object, rescale = FALSE, ignoreConvergence = FALSE,
 #'
 #' @export
 getHyperParameter <- function(object) {
-    if (class(object) == "cyclopsFit") {
+    if (inherits(object, "cyclopsFit")) {
         object$variance
     } else {
         NULL
diff --git a/cran-comments.md b/cran-comments.md
index 3e4bfe41..953a3c98 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,10 +1,12 @@
-## Initial submission of minor patch update to package
+## Initial submission of major patch update to package
 
-* optimized likelihood profiling when objective function is concave; no
-  changes to package dependencies or package API
+* fixed likelihood profiling when objective function is non-concave due
+  to floating-point truncation 
+* fixed parsing of 64-bit integer covariate IDs
+* added Jeffrey's prior for single regression coefficient
 
 ## Test environments
-* local OS X install, R 4.0.4
+* local OS X install, R 4.1
 * ubuntu 20.04 (via gh-actions: devel and release)
 * win-builder (devel and release)