From 6803c2c5bee581cab432cbc9f1eae047dfbb3098 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 29 Jan 2024 10:04:39 -0600
Subject: [PATCH] Getting rid of CRAN notes

---
 DESCRIPTION                |  2 +-
 NEWS                       |  2 +-
 R/clean_endPoint_info.R    |  4 ++--
 R/endpoint_hits.R          |  1 -
 R/toxEval.R                |  5 ++---
 man/clean_endPoint_info.Rd |  4 ++--
 man/createLink.Rd          |  2 --
 man/toxEval-package.Rd     | 10 +++++++++-
 8 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 25932951..6fd94979 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -60,4 +60,4 @@ BugReports: https://github.com/DOI-USGS/toxEval/issues
 VignetteBuilder: knitr
 BuildVignettes: true
 LazyLoad: yes
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NEWS b/NEWS
index 3d4510af..f54fd8ed 100644
--- a/NEWS
+++ b/NEWS
@@ -1,7 +1,7 @@
 toxEval 1.3.1
 ===========
 * Made "Chemical" a required column in the Chemical tab. Now all plot names will key off that column instead of the names listed in tox_chemicals.
-*
+* Updated documentation to remove some notes.
 
 toxEval 1.3.0
 ===========
diff --git a/R/clean_endPoint_info.R b/R/clean_endPoint_info.R
index 4e80194e..dfff07e9 100644
--- a/R/clean_endPoint_info.R
+++ b/R/clean_endPoint_info.R
@@ -1,8 +1,8 @@
 #' clean_endPoint_info
 #'
 #' Define a subset of the ToxCast database for relevance to toxEval analyses.
-#' Subsetting is done based upon methods defined by
-#' \doi{10.1021/acs.est.7b01613}{Blackwell et al., 2017}.
+#' Subsetting is done based upon methods defined by Blackwell et al., 2017 (
+#' \doi{10.1021/acs.est.7b01613}).
 #' Specifically, this function removes endPoints that are ATG sources with
 #' signal loss, and NVS with signal gain (basically: some assay/signal combinations
 #' are removed because they target non-specific endpoints). Also, this function adds additional
diff --git a/R/endpoint_hits.R b/R/endpoint_hits.R
index efc6237a..cb476dcc 100644
--- a/R/endpoint_hits.R
+++ b/R/endpoint_hits.R
@@ -224,7 +224,6 @@ endpoint_hits <- function(chemical_summary,
 #'
 #' Create links
 #' @param cas character
-#' @param hits character
 #' @export
 #' @keywords internal
 createLink <- function(cas) {
diff --git a/R/toxEval.R b/R/toxEval.R
index 313f0911..80d85b68 100644
--- a/R/toxEval.R
+++ b/R/toxEval.R
@@ -39,12 +39,11 @@ dbVersion <- function() {
 #' LazyLoad: \tab yes\cr
 #' }
 #'
-#'
 #' @name toxEval-package
 #' @docType package
 #' @author Laura De Cicco \email{ldecicco@@usgs.gov}. Steven Corsi
-#' @keywords ToxCast
-NULL
+#' @keywords internal 
+"_PACKAGE"
 
 #' ACC values included with toxEval.
 #'
diff --git a/man/clean_endPoint_info.Rd b/man/clean_endPoint_info.Rd
index 7fe2e001..eacdf7a6 100644
--- a/man/clean_endPoint_info.Rd
+++ b/man/clean_endPoint_info.Rd
@@ -17,8 +17,8 @@ are revised to look more appealing in graphs and tables.
 }
 \description{
 Define a subset of the ToxCast database for relevance to toxEval analyses.
-Subsetting is done based upon methods defined by
-\doi{10.1021/acs.est.7b01613}{Blackwell et al., 2017}.
+Subsetting is done based upon methods defined by Blackwell et al., 2017 (
+\doi{10.1021/acs.est.7b01613}).
 Specifically, this function removes endPoints that are ATG sources with
 signal loss, and NVS with signal gain (basically: some assay/signal combinations
 are removed because they target non-specific endpoints). Also, this function adds additional
diff --git a/man/createLink.Rd b/man/createLink.Rd
index 26d8b84b..21a3c828 100644
--- a/man/createLink.Rd
+++ b/man/createLink.Rd
@@ -8,8 +8,6 @@ createLink(cas)
 }
 \arguments{
 \item{cas}{character}
-
-\item{hits}{character}
 }
 \description{
 Create links
diff --git a/man/toxEval-package.Rd b/man/toxEval-package.Rd
index 80ab1f83..5c11989c 100644
--- a/man/toxEval-package.Rd
+++ b/man/toxEval-package.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/toxEval.R
 \docType{package}
 \name{toxEval-package}
+\alias{toxEval}
 \alias{toxEval-package}
 \title{Analyze ToxCast data in relation to measured concentrations.}
 \description{
@@ -28,8 +29,15 @@ official USGS copyright policy at
 https://www.usgs.gov/visual-id/credit_usgs.html#copyright\cr
 LazyLoad: \tab yes\cr
 }
+}
+\seealso{
+Useful links:
+\itemize{
+  \item Report bugs at \url{https://github.com/DOI-USGS/toxEval/issues}
+}
+
 }
 \author{
 Laura De Cicco \email{ldecicco@usgs.gov}. Steven Corsi
 }
-\keyword{ToxCast}
+\keyword{internal}