Merge pull request #293 from ldecicco-USGS/master

Updating help docs

README.Rmd

@@ -23,7 +23,7 @@ knitr::opts_chunk$set(
 [![Coverage Status](https://coveralls.io/repos/github/USGS-R/toxEval/badge.svg?branch=master)](https://coveralls.io/github/USGS-R/toxEval?branch=master)
 [![status](https://img.shields.io/badge/USGS-Research-blue.svg)](https://owi.usgs.gov/R/packages.html#research)
 
-The `toxEval` R-package includes a set of functions to analyze, visualize, and organize measured concentration data as it relates to ToxCast data (default) or other user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. 
+The `toxEval` R-package includes a set of functions to analyze, visualize, and organize measured concentration data as it relates to [https://www.epa.gov/chemical-research/toxicity-forecasting](ToxCast data) (default) or other user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. 
 
 The functions within this package allow great flexibly for exploring the potential biological affects of measured chemicals. Also included in the package is a browser-based application made from the `Shiny` R-package (the app). The app is based on functions within the R-package and includes many convenient analyses and visualization options for users to choose. Use of the functions within the R-package allows for additional flexibility within the functions beyond what the app offers and provides options for the user to interact more directly with the data. The overview in this document focuses on the R-package. 
 
@@ -107,7 +107,7 @@ We want to encourage a warm, welcoming, and safe environment for contributing to
 
 ### Package Support
 
-The Water and Environmental Health  Mission Areas of the USGS, as well as the Great Lakes Restoration Initiative (GLRI) has supported the development of the `toxEval` R-package. Further maintenance is expected to be stable through September 2018. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the `toxEval` development team.
+The Water and Environmental Health  Mission Areas of the USGS, as well as the Great Lakes Restoration Initiative (GLRI) has supported the development of the `toxEval` R-package. Further maintenance is expected to be stable through September 2019. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the `toxEval` development team.
 
 [![USGS](http://usgs-r.github.io/images/usgs.png)](https://www.usgs.gov/)
 

README.md

@@ -3,7 +3,7 @@ toxEval <img src="man/figures/logo.png" alt="toxEval" height="150px" align="righ
 
 [![travis](https://travis-ci.org/USGS-R/toxEval.svg?branch=master)](https://travis-ci.org/USGS-R/toxEval) [![Build status](https://ci.appveyor.com/api/projects/status/i2hr35abwxx85vgs?svg=true)](https://ci.appveyor.com/project/ldecicco-USGS/toxEval) [![Coverage Status](https://coveralls.io/repos/github/USGS-R/toxEval/badge.svg?branch=master)](https://coveralls.io/github/USGS-R/toxEval?branch=master) [![status](https://img.shields.io/badge/USGS-Research-blue.svg)](https://owi.usgs.gov/R/packages.html#research)
 
-The `toxEval` R-package includes a set of functions to analyze, visualize, and organize measured concentration data as it relates to ToxCast data (default) or other user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays.
+The `toxEval` R-package includes a set of functions to analyze, visualize, and organize measured concentration data as it relates to [https://www.epa.gov/chemical-research/toxicity-forecasting](ToxCast%20data) (default) or other user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays.
 
 The functions within this package allow great flexibly for exploring the potential biological affects of measured chemicals. Also included in the package is a browser-based application made from the `Shiny` R-package (the app). The app is based on functions within the R-package and includes many convenient analyses and visualization options for users to choose. Use of the functions within the R-package allows for additional flexibility within the functions beyond what the app offers and provides options for the user to interact more directly with the data. The overview in this document focuses on the R-package.
 
@@ -131,7 +131,7 @@ We want to encourage a warm, welcoming, and safe environment for contributing to
 
 ### Package Support
 
-The Water and Environmental Health Mission Areas of the USGS, as well as the Great Lakes Restoration Initiative (GLRI) has supported the development of the `toxEval` R-package. Further maintenance is expected to be stable through September 2018. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the `toxEval` development team.
+The Water and Environmental Health Mission Areas of the USGS, as well as the Great Lakes Restoration Initiative (GLRI) has supported the development of the `toxEval` R-package. Further maintenance is expected to be stable through September 2019. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the `toxEval` development team.
 
 [![USGS](http://usgs-r.github.io/images/usgs.png)](https://www.usgs.gov/)
 
@@ -204,16 +204,17 @@ citation(package = "toxEval")
 #> 
 #> To cite toxEval in publications, please use:
 #> 
-#>   De Cicco, L.A., Corsi, S.R, 2018, toxEval: Evaluation of
-#>   measured concentration data using the ToxCast high-throughput
-#>   screening database or a user-defined set of concentration
-#>   benchmarks. R package version 1.0.0.,
-#>   https://code.usgs.gov/water/toxEval, doi:10.5066/P906UQ5I
+#>   De Cicco, L.A., Corsi, S.R., Villeneuve D.L, Blackwell, and B.R,
+#>   Ankley, G.T., 2018, toxEval: Evaluation of measured
+#>   concentration data using the ToxCast high-throughput screening
+#>   database or a user-defined set of concentration benchmarks. R
+#>   package version 1.0.0., https://code.usgs.gov/water/toxEval,
+#>   doi:10.5066/P906UQ5I
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     author = {Laura A. {De Cicco} and Steven R. Corsi},
+#>     author = {Laura A. {De Cicco} and Steven R. Corsi and Daniel L. Villeneuve and Brett R. Blackwell and Gerald T. Ankley},
 #>     title = {toxEval: Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks.},
 #>     publisher = {U.S. Geological Survey},
 #>     version = {1.0.0},