From 81393647cbf2814234ea337b6133befccb73dc1b Mon Sep 17 00:00:00 2001 From: Laura A DeCicco Date: Fri, 22 Nov 2024 10:36:14 -0600 Subject: [PATCH 1/6] pushing up for a release --- DISCLAIMER.md | 2 +- README.md | 26 ++++++++++++-------------- code.json | 24 +++++++++++------------- 3 files changed, 24 insertions(+), 28 deletions(-) diff --git a/DISCLAIMER.md b/DISCLAIMER.md index 188939f2..f9b54957 100644 --- a/DISCLAIMER.md +++ b/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 has been approved for release by the U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. 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. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use. \ No newline at end of file diff --git a/README.md b/README.md index 92d6d564..aeb99271 100644 --- a/README.md +++ b/README.md @@ -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, -#> . +#> Observations_. R package version 1.4.0. #> #> A BibTeX entry for LaTeX users is #> @@ -200,19 +198,19 @@ 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. +This software has been approved for release by the U.S. Geological +Survey (USGS). Although the software has been subjected to rigorous +review, the USGS reserves the right to update the software as needed +pursuant to further analysis and review. 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. Furthermore, the software is +released on condition that neither the USGS nor the U.S. Government +shall be held liable for any damages resulting from its authorized or +unauthorized use. diff --git a/code.json b/code.json index d5b3784d..b48df03b 100644 --- a/code.json +++ b/code.json @@ -2,33 +2,31 @@ { "name": "toxEval", "organization": "U.S. Geological Survey", - "description": "Data analysis package for estimating potential biological effects from concentrations determined from environmental samples.", - "version": "main", - "status": "Development", + "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/main/LICENSE.md" + "URL": "https://code.usgs.gov/water/toxEval/-/raw/1.4.0/LICENSE.md" } ] }, - "homepageURL": "https://code.usgs.gov/water/toxEval", - "downloadURL": "https://code.usgs.gov/water/toxEval/-/archive/main/toxEval-main.zip", - "disclaimerURL": "https://code.usgs.gov/water/toxEval/-/raw/main/DISCLAIMER.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": 500, + "laborHours": 100, "tags": [ "R", - "rstats", - "USGS", - "water" + "rstats" ], "languages": [ @@ -36,12 +34,12 @@ ], "contact": { - "name": "Laura De Cicco", + "name": "Laura DeCicco", "email": "ldecicco@usgs.gov" }, "date": { - "metadataLastUpdated": "2022-12-29" + "metadataLastUpdated": "2024-11-22" } } ] From bf01bfb88dd886909838ad9c569ecc479cda240c Mon Sep 17 00:00:00 2001 From: Laura A DeCicco Date: Fri, 22 Nov 2024 10:56:01 -0600 Subject: [PATCH 2/6] back to development --- DESCRIPTION | 2 +- DISCLAIMER.md | 2 +- README.md | 19 +++++++++---------- code.json | 45 +++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 56 insertions(+), 12 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0439b9b3..076c9626 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: toxEval Type: Package Title: Exploring Biological Relevance of Environmental Chemistry Observations -Version: 1.4.0 +Version: 1.4.0.9000 Authors@R: c(person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov", diff --git a/DISCLAIMER.md b/DISCLAIMER.md index f9b54957..80dacaad 100644 --- a/DISCLAIMER.md +++ b/DISCLAIMER.md @@ -1,4 +1,4 @@ Disclaimer ========== -This software has been approved for release by the U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. 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. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use. \ No newline at end of file +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. \ No newline at end of file diff --git a/README.md b/README.md index aeb99271..2eab8051 100644 --- a/README.md +++ b/README.md @@ -204,13 +204,12 @@ citation(package = "toxEval") # Disclaimer -This software has been approved for release by the U.S. Geological -Survey (USGS). Although the software has been subjected to rigorous -review, the USGS reserves the right to update the software as needed -pursuant to further analysis and review. 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. Furthermore, the software is -released on condition that neither the USGS nor the U.S. Government -shall be held liable for any damages resulting from its authorized or -unauthorized use. +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. diff --git a/code.json b/code.json index b48df03b..88e6adfa 100644 --- a/code.json +++ b/code.json @@ -1,4 +1,49 @@ [ + { + "name": "toxEval", + "organization": "U.S. Geological Survey", + "description": "Data analysis package for estimating potential biological effects from concentrations determined from environmental samples.", + "version": "main", + "status": "Development", + + "permissions": { + "usageType": "openSource", + "licenses": [ + { + "name": "Public Domain, CC0-1.0", + "URL": "https://code.usgs.gov/water/toxEval/-/raw/main/LICENSE.md" + } + ] + }, + + "homepageURL": "https://code.usgs.gov/water/toxEval", + "downloadURL": "https://code.usgs.gov/water/toxEval/-/archive/main/toxEval-main.zip", + "disclaimerURL": "https://code.usgs.gov/water/toxEval/-/raw/main/DISCLAIMER.md", + "repositoryURL": "https://code.usgs.gov/water/toxEval.git", + "vcs": "git", + + "laborHours": 500, + + "tags": [ + "R", + "rstats", + "USGS", + "water" + ], + + "languages": [ + "R" + ], + + "contact": { + "name": "Laura De Cicco", + "email": "ldecicco@usgs.gov" + }, + + "date": { + "metadataLastUpdated": "2024-11-22" + } + }, { "name": "toxEval", "organization": "U.S. Geological Survey", From a546047794b9511b5ac5908d0981d23f60d568a1 Mon Sep 17 00:00:00 2001 From: Laura A DeCicco Date: Fri, 22 Nov 2024 14:29:09 -0600 Subject: [PATCH 3/6] Fix links --- .Rbuildignore | 1 + DESCRIPTION | 2 +- README.Rmd | 13 +++++-------- README.md | 22 +++++----------------- man/ToxCast_ACC.Rd | 2 +- vignettes/update_data.Rmd | 2 +- 6 files changed, 14 insertions(+), 28 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 5be24097..6d7564fa 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -98,4 +98,5 @@ vignettes/sites.png vignettes/thres.png ^docker$ ^review$ +vignettes/update_data.Rmd diff --git a/DESCRIPTION b/DESCRIPTION index 076c9626..0439b9b3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: toxEval Type: Package Title: Exploring Biological Relevance of Environmental Chemistry Observations -Version: 1.4.0.9000 +Version: 1.4.0 Authors@R: c(person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov", diff --git a/README.Rmd b/README.Rmd index 8a1fab90..4e93b7e8 100644 --- a/README.Rmd +++ b/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} -``` diff --git a/README.md b/README.md index 2eab8051..6cf98a6d 100644 --- a/README.md +++ b/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. @@ -201,15 +201,3 @@ citation(package = "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. diff --git a/man/ToxCast_ACC.Rd b/man/ToxCast_ACC.Rd index d5fa4841..bca411f3 100644 --- a/man/ToxCast_ACC.Rd +++ b/man/ToxCast_ACC.Rd @@ -20,7 +20,7 @@ head(ToxCast_ACC) } \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. } \keyword{datasets} diff --git a/vignettes/update_data.Rmd b/vignettes/update_data.Rmd index 51d71667..5b4aff6c 100644 --- a/vignettes/update_data.Rmd +++ b/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: - + To create a list of chemicals to input to the dashboard: From 36f7e84db07b530ced4d8d6008a86538e215162d Mon Sep 17 00:00:00 2001 From: Laura A DeCicco Date: Fri, 22 Nov 2024 14:31:22 -0600 Subject: [PATCH 4/6] Updated links --- R/toxEval.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/toxEval.R b/R/toxEval.R index b2ec0f5d..49031c2e 100644 --- a/R/toxEval.R +++ b/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} From f1fbddb31e7a285b4712795ff6a80b4a3c4bbad5 Mon Sep 17 00:00:00 2001 From: Laura A DeCicco Date: Fri, 22 Nov 2024 14:53:37 -0600 Subject: [PATCH 5/6] another link --- vignettes/PrepareData.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/PrepareData.Rmd b/vignettes/PrepareData.Rmd index 7a46f129..24346af4 100644 --- a/vignettes/PrepareData.Rmd +++ b/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). From 93ead3f0540b5fccbacb78c1f84c1743d999012c Mon Sep 17 00:00:00 2001 From: Laura A DeCicco Date: Fri, 22 Nov 2024 15:02:18 -0600 Subject: [PATCH 6/6] just in case --- .Rbuildignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.Rbuildignore b/.Rbuildignore index 6d7564fa..cfb31a5e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -99,4 +99,6 @@ vignettes/thres.png ^docker$ ^review$ vignettes/update_data.Rmd +vignettes/update_data.html +vignettes/update_data.R