diff --git a/DESCRIPTION b/DESCRIPTION index 2593295..6fd9497 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 3d4510a..f54fd8e 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 4e80194..dfff07e 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 efc6237..cb476dc 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 313f091..80d85b6 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 7fe2e00..eacdf7a 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 26d8b84..21a3c82 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 80ab1f8..5c11989 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}