getting CRAN ready

.Rbuildignore

@@ -98,4 +98,7 @@ vignettes/sites.png
 vignettes/thres.png
 ^docker$
 ^review$
+vignettes/update_data.Rmd
+vignettes/update_data.html
+vignettes/update_data.R
 

DISCLAIMER.md

@@ -1,4 +1,4 @@
 Disclaimer
 ==========
 
-This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.
+This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

R/toxEval.R

@@ -52,7 +52,7 @@ dbVersion <- function() {
 #' \url{https://www.frontiersin.org/articles/10.3389/ftox.2023.1275980/full}.
 #'
 #' @references U.S. EPA. 2023. ToxCast & Tox21 Summary Files. 
-#' Retrieved from \url{https://www.epa.gov/chemical-research/toxicity-forecaster-toxcasttm-data}
+#' Retrieved from \url{https://www.epa.gov/comptox-tools/exploring-toxcast-data}
 #' on September 2023. 
 #'
 #' @source \url{https://www.epa.gov/comptox-tools/exploring-toxcast-data}

README.Rmd

@@ -108,10 +108,10 @@ There are 4 vignettes to help introduce and navigate the `toxEval` package:
 
 |Name|R command|Description |
 |----------|------------|-----------------------------------------|
-|[Introduction](https://rconnect.usgs.gov/toxEval_docs/articles/Introduction.html) | `vignette("Introduction", package="toxEval")`|Introduction to the toxEval |
-|[Basic Workflow](https://rconnect.usgs.gov/toxEval_docs/articles/basicWorkflow.html) | `vignette("basicWorkflow", package="toxEval")`|Quickstart guide to get overview of available functions |
-|[Prepare Data](https://rconnect.usgs.gov/toxEval_docs/articles/PrepareData.html) | `vignette("PrepareData", package="toxEval")`|Guide to preparing your data for toxEval analysis|
-|[Shiny App Guide](https://rconnect.usgs.gov/toxEval_docs/articles/shinyApp.html) | `vignette("shinyApp", package="toxEval")`|Guide to the toxEval shiny application|
+|[Introduction](https://doi-usgs.github.io/toxEval/articles/Introduction.html) | `vignette("Introduction", package="toxEval")`|Introduction to the toxEval |
+|[Basic Workflow](https://doi-usgs.github.io/toxEval/articles/basicWorkflow.html) | `vignette("basicWorkflow", package="toxEval")`|Quickstart guide to get overview of available functions |
+|[Prepare Data](https://doi-usgs.github.io/toxEval/articles/PrepareData.html) | `vignette("PrepareData", package="toxEval")`|Guide to preparing your data for toxEval analysis|
+|[Shiny App Guide](https://doi-usgs.github.io/toxEval/articles/shinyApp.html) | `vignette("shinyApp", package="toxEval")`|Guide to the toxEval shiny application|
 
 ### Reporting bugs
 
@@ -125,7 +125,7 @@ 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 2024. 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 2025. 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.
 
 
 ### Sunset date 
@@ -154,6 +154,3 @@ citation(package = "toxEval")
 ```
 
 
-
-```{r disclaimer, child="DISCLAIMER.md", eval=TRUE}
-```

README.md

@@ -137,10 +137,10 @@ package:
 
 | Name | R command | Description |
 |------------|--------------|----------------------------------------------|
-| [Introduction](https://rconnect.usgs.gov/toxEval_docs/articles/Introduction.html) | `vignette("Introduction", package="toxEval")` | Introduction to the toxEval |
-| [Basic Workflow](https://rconnect.usgs.gov/toxEval_docs/articles/basicWorkflow.html) | `vignette("basicWorkflow", package="toxEval")` | Quickstart guide to get overview of available functions |
-| [Prepare Data](https://rconnect.usgs.gov/toxEval_docs/articles/PrepareData.html) | `vignette("PrepareData", package="toxEval")` | Guide to preparing your data for toxEval analysis |
-| [Shiny App Guide](https://rconnect.usgs.gov/toxEval_docs/articles/shinyApp.html) | `vignette("shinyApp", package="toxEval")` | Guide to the toxEval shiny application |
+| [Introduction](https://doi-usgs.github.io/toxEval/articles/Introduction.html) | `vignette("Introduction", package="toxEval")` | Introduction to the toxEval |
+| [Basic Workflow](https://doi-usgs.github.io/toxEval/articles/basicWorkflow.html) | `vignette("basicWorkflow", package="toxEval")` | Quickstart guide to get overview of available functions |
+| [Prepare Data](https://doi-usgs.github.io/toxEval/articles/PrepareData.html) | `vignette("PrepareData", package="toxEval")` | Guide to preparing your data for toxEval analysis |
+| [Shiny App Guide](https://doi-usgs.github.io/toxEval/articles/shinyApp.html) | `vignette("shinyApp", package="toxEval")` | Guide to the toxEval shiny application |
 
 ### Reporting bugs
 
@@ -159,7 +159,7 @@ more information.
 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 2024. Resources are available primarily
+to be stable through September 2025. 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.
@@ -189,9 +189,7 @@ citation(package = "toxEval")
 #> 
 #>   DeCicco L, Corsi S, Villeneuve D, Blackwell B, Ankley G (2024).
 #>   _toxEval: Exploring Biological Relevance of Environmental Chemistry
-#>   Observations_. R package version 1.4.0, commit
-#>   a37e823cef5c31903dad50537e1a517953ef505a,
-#>   <https://code.usgs.gov/water/toxEval>.
+#>   Observations_. R package version 1.4.0.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
@@ -200,19 +198,6 @@ citation(package = "toxEval")
 #> Observations},
 #>     author = {Laura DeCicco and Steven Corsi and Daniel Villeneuve and Brett Blackwell and Gerald Ankley},
 #>     year = {2024},
-#>     note = {R package version 1.4.0, commit a37e823cef5c31903dad50537e1a517953ef505a},
-#>     url = {https://code.usgs.gov/water/toxEval},
+#>     note = {R package version 1.4.0},
 #>   }
 ```
-
-# Disclaimer
-
-This software is preliminary or provisional and is subject to revision.
-It is being provided to meet the need for timely best science. The
-software has not received final approval by the U.S. Geological Survey
-(USGS). No warranty, expressed or implied, is made by the USGS or the
-U.S. Government as to the functionality of the software and related
-material nor shall the fact of release constitute any such warranty. The
-software is provided on the condition that neither the USGS nor the U.S.
-Government shall be held liable for any damages resulting from the
-authorized or unauthorized use of the software.

code.json

@@ -1,5 +1,5 @@
 [
-  {
+    {
     "name": "toxEval",
     "organization": "U.S. Geological Survey",
     "description": "Data analysis package for estimating potential biological effects from concentrations determined from environmental samples.",
@@ -41,7 +41,50 @@
     },
 
     "date": {
-      "metadataLastUpdated": "2022-12-29"
+      "metadataLastUpdated": "2024-11-22"
+    }
+  },
+  {
+    "name": "toxEval",
+    "organization": "U.S. Geological Survey",
+    "description": "Description of package.",
+    "version": "1.4.0",
+    "status": "Production",
+
+    "permissions": {
+      "usageType": "openSource",
+      "licenses": [
+        {
+          "name": "Public Domain, CC0-1.0",
+          "URL": "https://code.usgs.gov/water/toxEval/-/raw/1.4.0/LICENSE.md"
+        }
+      ]
+    },
+
+    "homepageURL": "https://code.usgs.gov/water/toxEval/-/tags/1.4.0",
+    "downloadURL": "https://code.usgs.gov/water/toxEval/-/archive/1.4.0/toxEval-1.4.0.zip",
+    "disclaimerURL": "https://code.usgs.gov/water/toxEval/-/raw/1.4.0/DISCLAIMER.md",
+    "repositoryURL": "https://code.usgs.gov/water/toxEval.git",
+    "vcs": "git",
+
+    "laborHours": 100,
+
+    "tags": [
+      "R",
+      "rstats"
+    ],
+
+    "languages": [
+      "R"
+    ],
+
+    "contact": {
+      "name": "Laura DeCicco",
+      "email": "[email protected]"
+    },
+
+    "date": {
+      "metadataLastUpdated": "2024-11-22"
     }
   }
 ]

vignettes/PrepareData.Rmd

@@ -136,7 +136,7 @@ Note: Additional columns may be useful to organize the data. These additional co
 
 ## Benchmarks
 
-The user may provide a set of concentration benchmarks to be used in place of the ToxCast database. For example, there may be a need to perform similar `toxEval` analysis using EPA aquatic life benchmarks to compare measured concentrations against established toxicity thresholds. The "Benchmarks" sheet is used for this purpose. For more information, see [here](https://rconnect.usgs.gov/toxEval_docs/articles/benchmarks.html).
+The user may provide a set of concentration benchmarks to be used in place of the ToxCast database. For example, there may be a need to perform similar `toxEval` analysis using EPA aquatic life benchmarks to compare measured concentrations against established toxicity thresholds. The "Benchmarks" sheet is used for this purpose. For more information, see [here](https://doi-usgs.github.io/toxEval/articles/benchmarks.html).
 
 The "Benchmarks" sheet is optional, but if used, five columns are required: "CAS", "Chemical", "endPoint", "Value", and "groupCol". They can be in any order, but the first row of the sheet should be the header (column names).
 

vignettes/update_data.Rmd

@@ -152,7 +152,7 @@ tox_chemicals41 <- mc5_raw |>
 
 We need molecular weights to convert the ACC values to concentrations. We can either join previous versions of the toxEval package, and/or get new values from the CompTox Dashboard via the batch search:
 
-<https://comptox.epa.gov/dashboard/batch-search\>
+<https://comptox.epa.gov/dashboard/batch-search/>
 
 To create a list of chemicals to input to the dashboard: