From 7dfc1c6359dde72efeaa83bf8d37a13445ca6ebd Mon Sep 17 00:00:00 2001 From: klau506 Date: Mon, 25 Mar 2024 09:51:39 +0100 Subject: [PATCH] Improve documentation --- LICENSE | 24 ------------------- README.md | 12 +++++----- docs/index.html | 11 +++++---- docs/pkgdown.yml | 2 +- .../rsconnect/shinyapps.io/bc3lc/rfasstui.dcf | 2 +- inst/rfasstui/ui.R | 16 ++++++++----- 6 files changed, 25 insertions(+), 42 deletions(-) delete mode 100644 LICENSE diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 254fb53..0000000 --- a/LICENSE +++ /dev/null @@ -1,24 +0,0 @@ -BSD 2-Clause License - -Copyright (c) 2024, BC3 Low Carbon department - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -2. Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md index 4425523..06965ad 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ # rfasstUI -A web-based interactive scenario builder and visualization application for the rfasst air pollution model +A web-based interactive scenario builder and visualization application for the [rfasst](https://github.com/bc3LC/rfasst)^1 air pollution model, an R version of the air quality reduced-form model [TM5-FASST](https://acp.copernicus.org/articles/18/16173/2018/)^2. ## Using `rfasstui` @@ -50,9 +50,9 @@ collaborate! For more information about contributing, please contact Clàudia Rodés-Bachs at claudia.rodes@bc3research.org or Jon Sampedro at jon.sampedro@bc3research.org -## Learn More About Rfasst -Read more about the Rfasst air pollution model here: [`rfasst` Documentation](https://bc3lc.github.io/rfasst/). `Rfasst` has been published in the following: +## Learn More About rfasst +Read more about the rfasst air pollution model here: [`rfasst` Documentation](https://bc3lc.github.io/rfasst/), detailed in [Sampedro et al. 2022](https://doi.org/10.21105/joss.03820). It is an R version of the TM5-FASST model, detailed in [Van Dingenen et al. 2018](https://doi.org/10.5194/acp-18-16173-2018) -``` -Sampedro et al., (2022). rfasst: An R tool to estimate air pollution impacts on health and agriculture. Journal of Open Source Software, 7(69), 3820, https://doi.org/10.21105/joss.03820 -``` +- Sampedro et al., (2022). "rfasst: An R tool to estimate air pollution impacts on health and agriculture." Journal of Open Source Software, 7(69), 3820, https://doi.org/10.21105/joss.03820 + +- Van Dingenen, Rita, et al., (2018). "TM5-FASST: a global atmospheric source–receptor model for rapid impact analysis of emission changes on air quality and short-lived climate pollutants." Atmospheric Chemistry and Physics 18.21: 16173-16211. diff --git a/docs/index.html b/docs/index.html index b9c7d32..8968775 100644 --- a/docs/index.html +++ b/docs/index.html @@ -77,7 +77,7 @@

rfasstUI

-

A web-based interactive scenario builder and visualization application for the rfasst air pollution model

+

A web-based interactive scenario builder and visualization application for the rfasst^1 air pollution model, an R version of the air quality reduced-form model TM5-FASST^2.

Using rfasstui @@ -124,10 +124,13 @@

Contributing to rfasstui

For more information about contributing, please contact Clàudia Rodés-Bachs at or Jon Sampedro at

-

Learn More About Rfasst +

Learn More About rfasst

-

Read more about the Rfasst air pollution model here: rfasst Documentation. Rfasst has been published in the following:

-
Sampedro et al., (2022). rfasst: An R tool to estimate air pollution impacts on health and agriculture. Journal of Open Source Software, 7(69), 3820, https://doi.org/10.21105/joss.03820
+

Read more about the rfasst air pollution model here: rfasst Documentation, detailed in Sampedro et al. 2022. It is an R version of the TM5-FASST model, detailed in Van Dingenen et al. 2018

+
    +

  • Sampedro et al., (2022). “rfasst: An R tool to estimate air pollution impacts on health and agriculture.” Journal of Open Source Software, 7(69), 3820, https://doi.org/10.21105/joss.03820

    • +

  • Van Dingenen, Rita, et al., (2018). “TM5-FASST: a global atmospheric source–receptor model for rapid impact analysis of emission changes on air quality and short-lived climate pollutants.” Atmospheric Chemistry and Physics 18.21: 16173-16211.

    • +
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4ecfcc8..14ee3c5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: tutorial: tutorial.html -last_built: 2024-03-20T20:03Z +last_built: 2024-03-25T08:00Z urls: reference: https://bc3lc.github.io/gcamreport/reference article: https://bc3lc.github.io/gcamreport/articles diff --git a/inst/rfasstui/rsconnect/shinyapps.io/bc3lc/rfasstui.dcf b/inst/rfasstui/rsconnect/shinyapps.io/bc3lc/rfasstui.dcf index 3865532..7eac0fd 100644 --- a/inst/rfasstui/rsconnect/shinyapps.io/bc3lc/rfasstui.dcf +++ b/inst/rfasstui/rsconnect/shinyapps.io/bc3lc/rfasstui.dcf @@ -5,6 +5,6 @@ account: bc3lc server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 11517388 -bundleId: 8399473 +bundleId: 8399616 url: https://bc3lc.shinyapps.io/rfasstui/ version: 1 diff --git a/inst/rfasstui/ui.R b/inst/rfasstui/ui.R index 63bdb22..7aec0b7 100644 --- a/inst/rfasstui/ui.R +++ b/inst/rfasstui/ui.R @@ -44,7 +44,9 @@ fluidPage(theme = shinythemes::shinytheme("readable"), agricultural damages, and economic losses attributable to air pollution using scenario outputs from the Global Change Analysis Model (GCAM).", style = "float:left"), p("This interactive version is built upon previous work including the development of the initial ", - a("rfasst R Package", href="https://github.com/bc3LC/rfasst/", target="blank"), "."), + a("rfasst R Package", href="https://github.com/bc3LC/rfasst/", target="blank"), + ", which replicates the calculations of the air quality reduced-form model ", + a("TM5-FASST", href="https://doi.org/10.5194/acp-18-16173-2018", target="blank")), style = "float: left" )), column(4, div( @@ -293,12 +295,14 @@ fluidPage(theme = shinythemes::shinytheme("readable"), h5("Documentation/Downloads"), tags$hr(class="hrNav"), p("The primary link to the rfasst model documentation is the ", - a("online manual", href="https://jgcri.github.io/rfasst/index.html", target="blank"), + a("online manual", href="https://bc3lc.github.io/rfasst/index.html", target="blank"), ", which is included in the vignettes/manual directory. The code is also documented with ", a("Doxygen-style", href="http://doxygen.org", target="blank"), " comments."), p("A formal model description paper via ", - a("Sampedro et al. 2022", href="https://joss.theoj.org/papers/10.21105/joss.03820", target="blank")), + a("Sampedro et al. 2022", href="https://joss.theoj.org/papers/10.21105/joss.03820", target="blank"), + " and ", + a("Van Dingenen et al. 2018.", href="https://doi.org/10.5194/acp-18-16173-2018", target="blank")), tags$ul( tags$li( h5(tags$a("rfasst User Interface package download/source link ", href="https://github.com/bc3LC/rfasstui", target="blank"))), @@ -306,9 +310,9 @@ fluidPage(theme = shinythemes::shinytheme("readable"), h5(tags$a("rfasst R package download/source link", href="https://github.com/bc3LC/rfasst", target="blank"))), tags$li( h5(tags$a("Code and data for rfasst", href="https://zenodo.org/records/7417835", target="blank"), - tags$img(src="https://zenodo.org/badge/DOI/10.5281/zenodo.344924589.svg", class="zenodo", alt="DOI") - ) - ) + tags$img(src="https://zenodo.org/badge/DOI/10.5281/zenodo.344924589.svg", class="zenodo", alt="DOI"))), + tags$li( + h5(tags$a("Theorical description of TM5-FASST", href="https://doi.org/10.5194/acp-18-16173-2018", target="blank"))) ), br(), h5("Tools and software that work with rfasst"),