From 57f0b610ef11de8fafb63a929301aa98cde05cc3 Mon Sep 17 00:00:00 2001
From: schuemie <schuemie@ohdsi.org>
Date: Tue, 16 Jul 2024 16:28:53 +0200
Subject: [PATCH] Renaming maxRetry to maxResets. Fixes #75

---
 DESCRIPTION                           |  2 +-
 NEWS.md                               |  2 +-
 R/ModelFit.R                          |  7 ++++---
 man/cyclops.Rd                        | 30 +++++++++++++++++++++++++++
 man/getCyclopsProfileLogLikelihood.Rd |  5 +++--
 5 files changed, 39 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1fca0135..cc0d6734 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -52,6 +52,6 @@ Suggests:
     microbenchmark,
     cmprsk
 NeedsCompilation: yes
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
diff --git a/NEWS.md b/NEWS.md
index bcae97c3..819da7fb 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,7 @@
 develop
 ==============
 
-1. make `maxRety` a function parameter
+1. make `maxResets` a function parameter
 
 Cyclops v3.4.1
 ==============
diff --git a/R/ModelFit.R b/R/ModelFit.R
index 5ad842d5..a7da0db0 100644
--- a/R/ModelFit.R
+++ b/R/ModelFit.R
@@ -902,7 +902,8 @@ confint.cyclopsFit <- function(object, parm, level = 0.95, #control,
 #' @param bounds    Pair of values to bound adaptive profiling
 #' @param tolerance Absolute tolerance allowed for adaptive profiling
 #' @param initialGridSize Initial grid size for adaptive profiling
-#' @param maxRetry  Maximum number of attempts to profile likelihood
+#' @param maxResets Maximum allowed number of recomputing the likelihood when coefficient drift is
+#'                  detected.
 #' @param includePenalty    Logical: Include regularized covariate penalty in profile
 #'
 #' @return
@@ -916,7 +917,7 @@ getCyclopsProfileLogLikelihood <- function(object,
                                            bounds = NULL,
                                            tolerance = 1E-3,
                                            initialGridSize = 10,
-                                           maxRetry = 10,
+                                           maxResets = 10,
                                            includePenalty = TRUE) {
 
     if (!xor(is.null(x), is.null(bounds))) {
@@ -965,7 +966,7 @@ getCyclopsProfileLogLikelihood <- function(object,
             deltaY <- profile$value[2:nrow(profile)] - profile$value[1:(nrow(profile) - 1)]
             slopes <- deltaY / deltaX
 
-            if (resetsPerformed < maxRetry && !all(slopes[2:length(slopes)] < slopes[1:(length(slopes)-1)])) {
+            if (resetsPerformed < maxResets && !all(slopes[2:length(slopes)] < slopes[1:(length(slopes)-1)])) {
                 warning("Coefficient drift detected. Resetting Cyclops object and recomputing all likelihood values computed so far.")
                 grid <- profile$point
                 profile <- tibble()
diff --git a/man/cyclops.Rd b/man/cyclops.Rd
index 91673aa5..2936c6f2 100644
--- a/man/cyclops.Rd
+++ b/man/cyclops.Rd
@@ -11,3 +11,33 @@ found in large-scale observational healthcare data.  Implementations focus
 on computational optimization and fine-scale parallelization to yield
 efficient inference in massive datasets.
 }
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/ohdsi/cyclops}
+  \item Report bugs at \url{https://github.com/ohdsi/cyclops/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Marc A. Suchard \email{msuchard@ucla.edu}
+
+Authors:
+\itemize{
+  \item Martijn J. Schuemie
+  \item Trevor R. Shaddox
+  \item Yuxi Tian
+  \item Jianxiao Yang
+  \item Eric Kawaguchi
+}
+
+Other contributors:
+\itemize{
+  \item Sushil Mittal [contributor]
+  \item Observational Health Data Sciences and Informatics [copyright holder]
+  \item Marcus Geelnard (provided the TinyThread library) [copyright holder, contributor]
+  \item Rutgers University (provided the HParSearch routine) [copyright holder, contributor]
+  \item R Development Core Team (provided the ZeroIn routine) [copyright holder, contributor]
+}
+
+}
diff --git a/man/getCyclopsProfileLogLikelihood.Rd b/man/getCyclopsProfileLogLikelihood.Rd
index f5b8e15b..e8ab4056 100644
--- a/man/getCyclopsProfileLogLikelihood.Rd
+++ b/man/getCyclopsProfileLogLikelihood.Rd
@@ -11,7 +11,7 @@ getCyclopsProfileLogLikelihood(
   bounds = NULL,
   tolerance = 0.001,
   initialGridSize = 10,
-  maxRetry = 10,
+  maxResets = 10,
   includePenalty = TRUE
 )
 }
@@ -29,7 +29,8 @@ either a vector of numbers of covariateId names}
 
 \item{initialGridSize}{Initial grid size for adaptive profiling}
 
-\item{maxRetry}{Maximum number of attempts to profile likelihood}
+\item{maxResets}{Maximum allowed number of recomputing the likelihood when coefficient drift is
+detected.}
 
 \item{includePenalty}{Logical: Include regularized covariate penalty in profile}
 }